5ftj Citations

2.3 Å resolution cryo-EM structure of human p97 and mechanism of allosteric inhibition.

Abstract

p97 is a hexameric AAA+ adenosine triphosphatase (ATPase) that is an attractive target for cancer drug development. We report cryo-electron microscopy (cryo-EM) structures for adenosine diphosphate (ADP)-bound, full-length, hexameric wild-type p97 in the presence and absence of an allosteric inhibitor at resolutions of 2.3 and 2.4 angstroms, respectively. We also report cryo-EM structures (at resolutions of ~3.3, 3.2, and 3.3 angstroms, respectively) for three distinct, coexisting functional states of p97 with occupancies of zero, one, or two molecules of adenosine 5'-O-(3-thiotriphosphate) (ATPγS) per protomer. A large corkscrew-like change in molecular architecture, coupled with upward displacement of the N-terminal domain, is observed only when ATPγS is bound to both the D1 and D2 domains of the protomer. These cryo-EM structures establish the sequence of nucleotide-driven structural changes in p97 at atomic resolution. They also enable elucidation of the binding mode of an allosteric small-molecule inhibitor to p97 and illustrate how inhibitor binding at the interface between the D1 and D2 domains prevents propagation of the conformational changes necessary for p97 function.

Reviews - 5ftj mentioned but not cited (7)

  1. Structure and function of the AAA+ ATPase p97/Cdc48p. Xia D, Tang WK, Ye Y. Gene 583 64-77 (2016)
  2. The AAA+ ATPase p97, a cellular multitool. Stach L, Freemont PS. Biochem J 474 2953-2976 (2017)
  3. Targeted protein degradation as a powerful research tool in basic biology and drug target discovery. Wu T, Yoon H, Xiong Y, Dixon-Clarke SE, Nowak RP, Fischer ES. Nat Struct Mol Biol 27 605-614 (2020)
  4. Resolution advances in cryo-EM enable application to drug discovery. Subramaniam S, Earl LA, Falconieri V, Milne JL, Egelman EH. Curr Opin Struct Biol 41 194-202 (2016)
  5. AAA ATPases as therapeutic targets: Structure, functions, and small-molecule inhibitors. Zhang G, Li S, Cheng KW, Chou TF. Eur J Med Chem 219 113446 (2021)
  6. Structural Mapping of Missense Mutations in the Pex1/Pex6 Complex. Schieferdecker A, Wendler P. Int J Mol Sci 20 E3756 (2019)
  7. Molecular Mechanisms Driving and Regulating the AAA+ ATPase VCP/p97, an Important Therapeutic Target for Treating Cancer, Neurological and Infectious Diseases. Valimehr S, Sethi A, Shukla M, Bhattacharyya S, Kazemi M, Rouiller I. Biomolecules 13 737 (2023)

Articles - 5ftj mentioned but not cited (14)

  1. 2.3 Å resolution cryo-EM structure of human p97 and mechanism of allosteric inhibition. Banerjee S, Bartesaghi A, Merk A, Rao P, Bulfer SL, Yan Y, Green N, Mroczkowski B, Neitz RJ, Wipf P, Falconieri V, Deshaies RJ, Milne JL, Huryn D, Arkin M, Subramaniam S. Science 351 871-875 (2016)
  2. Folding and Misfolding of Human Membrane Proteins in Health and Disease: From Single Molecules to Cellular Proteostasis. Marinko JT, Huang H, Penn WD, Capra JA, Schlebach JP, Sanders CR. Chem Rev 119 5537-5606 (2019)
  3. A Multi-model Approach to Assessing Local and Global Cryo-EM Map Quality. Herzik MA, Fraser JS, Lander GC. Structure 27 344-358.e3 (2019)
  4. High-Resolution Cryo-EM Maps and Models: A Crystallographer's Perspective. Wlodawer A, Li M, Dauter Z. Structure 25 1589-1597.e1 (2017)
  5. Allosteric p97 Inhibitors Can Overcome Resistance to ATP-Competitive p97 Inhibitors for Potential Anticancer Therapy. Wang F, Li S, Gan T, Stott GM, Flint A, Chou TF. ChemMedChem 15 685-694 (2020)
  6. A structure- and chemical genomics-based approach for repositioning of drugs against VCP/p97 ATPase. Segura-Cabrera A, Tripathi R, Zhang X, Gui L, Chou TF, Komurov K. Sci Rep 7 44912 (2017)
  7. Cryo-EM structures of human p97 double hexamer capture potentiated ATPase-competent state. Gao H, Li F, Ji Z, Shi Z, Li Y, Yu H. Cell Discov 8 19 (2022)
  8. A threonine turnstile defines a dynamic amphiphilic binding motif in the AAA ATPase p97 allosteric binding site. Burnett JC, Lim C, Peyser BD, Samankumara LP, Kovaliov M, Colombo R, Bulfer SL, LaPorte MG, Hermone AR, McGrath CF, Arkin MR, Gussio R, Huryn DM, Wipf P. Org Biomol Chem 15 4096-4114 (2017)
  9. Crystal structure of the catalytic D2 domain of the AAA+ ATPase p97 reveals a putative helical split-washer-type mechanism for substrate unfolding. Stach L, Morgan RM, Makhlouf L, Douangamath A, von Delft F, Zhang X, Freemont PS. FEBS Lett 594 933-943 (2020)
  10. A conserved inter-domain communication mechanism regulates the ATPase activity of the AAA-protein Drg1. Prattes M, Loibl M, Zisser G, Luschnig D, Kappel L, Rössler I, Grassegger M, Hromic A, Krieger E, Gruber K, Pertschy B, Bergler H. Sci Rep 7 44751 (2017)
  11. The p97/VCP adaptor UBXD1 drives AAA+ remodeling and ring opening through multi-domain tethered interactions. Braxton JR, Altobelli CR, Tucker MR, Tse E, Thwin AC, Arkin MR, Southworth DR. Nat Struct Mol Biol 30 2009-2019 (2023)
  12. research-article Cryo2StructData: A Large Labeled Cryo-EM Density Map Dataset for AI-based Modeling of Protein Structures. Giri N, Wang L, Cheng J. bioRxiv 2023.06.14.545024 (2024)
  13. Known allosteric proteins have central roles in genetic disease. Abrusán G, Ascher DB, Inouye M. PLoS Comput Biol 18 e1009806 (2022)
  14. research-article The p97/VCP adapter UBXD1 drives AAA+ remodeling and ring opening through multi-domain tethered interactions. Braxton JR, Altobelli CR, Tucker MR, Tse E, Thwin AC, Arkin MR, Southworth DR. bioRxiv 2023.05.15.540864 (2023)


Reviews citing this publication (50)

  1. Unravelling biological macromolecules with cryo-electron microscopy. Fernandez-Leiro R, Scheres SH. Nature 537 339-346 (2016)
  2. Mechanistic insights into ER-associated protein degradation. Wu X, Rapoport TA. Curr Opin Cell Biol 53 22-28 (2018)
  3. Cryo-EM in drug discovery: achievements, limitations and prospects. Renaud JP, Chari A, Ciferri C, Liu WT, Rémigy HW, Stark H, Wiesmann C. Nat Rev Drug Discov 17 471-492 (2018)
  4. The molecular principles governing the activity and functional diversity of AAA+ proteins. Puchades C, Sandate CR, Lander GC. Nat Rev Mol Cell Biol 21 43-58 (2020)
  5. A Mighty "Protein Extractor" of the Cell: Structure and Function of the p97/CDC48 ATPase. Ye Y, Tang WK, Zhang T, Xia D. Front Mol Biosci 4 39 (2017)
  6. The Interplay of Cofactor Interactions and Post-translational Modifications in the Regulation of the AAA+ ATPase p97. Hänzelmann P, Schindelin H. Front Mol Biosci 4 21 (2017)
  7. Toward an understanding of the Cdc48/p97 ATPase. Bodnar N, Rapoport T. F1000Res 6 1318 (2017)
  8. Mutations in the Human AAA+ Chaperone p97 and Related Diseases. Tang WK, Xia D. Front Mol Biosci 3 79 (2016)
  9. Ring of Change: CDC48/p97 Drives Protein Dynamics at Chromatin. Franz A, Ackermann L, Hoppe T. Front Genet 7 73 (2016)
  10. Cryo-EM: beyond the microscope. Earl LA, Falconieri V, Milne JL, Subramaniam S. Curr Opin Struct Biol 46 71-78 (2017)
  11. Targeting p97 to Disrupt Protein Homeostasis in Cancer. Vekaria PH, Home T, Weir S, Schoenen FJ, Rao R. Front Oncol 6 181 (2016)
  12. Proteasome Inhibitors: Harnessing Proteostasis to Combat Disease. Sherman DJ, Li J. Molecules 25 E671 (2020)
  13. Disposing of misfolded ER proteins: A troubled substrate's way out of the ER. Oikonomou C, Hendershot LM. Mol Cell Endocrinol 500 110630 (2020)
  14. The integrative role of cryo electron microscopy in molecular and cellular structural biology. Orlov I, Myasnikov AG, Andronov L, Natchiar SK, Khatter H, Beinsteiner B, Ménétret JF, Hazemann I, Mohideen K, Tazibt K, Tabaroni R, Kratzat H, Djabeur N, Bruxelles T, Raivoniaina F, Pompeo LD, Torchy M, Billas I, Urzhumtsev A, Klaholz BP. Biol Cell 109 81-93 (2017)
  15. Identifying and Visualizing Macromolecular Flexibility in Structural Biology. Palamini M, Canciani A, Forneris F. Front Mol Biosci 3 47 (2016)
  16. The ways and means of fragment-based drug design. Doak BC, Norton RS, Scanlon MJ. Pharmacol Ther 167 28-37 (2016)
  17. Cryo-EM for Small Molecules Discovery, Design, Understanding, and Application. Scapin G, Potter CS, Carragher B. Cell Chem Biol 25 1318-1325 (2018)
  18. Frontiers in Cryo Electron Microscopy of Complex Macromolecular Assemblies. Ognjenović J, Grisshammer R, Subramaniam S. Annu Rev Biomed Eng 21 395-415 (2019)
  19. Enzymatic complexes across scales. Kastritis PL, Gavin AC. Essays Biochem 62 501-514 (2018)
  20. Valosin-Containing Protein (VCP)/p97: A Prognostic Biomarker and Therapeutic Target in Cancer. Costantini S, Capone F, Polo A, Bagnara P, Budillon A, Budillon A. Int J Mol Sci 22 10177 (2021)
  21. Structural studies of RNA-protein complexes: A hybrid approach involving hydrodynamics, scattering, and computational methods. Patel TR, Chojnowski G, Astha, Koul A, McKenna SA, Bujnicki JM. Methods 118-119 146-162 (2017)
  22. AAA+ ATPases in Protein Degradation: Structures, Functions and Mechanisms. Zhang S, Mao Y. Biomolecules 10 E629 (2020)
  23. Modulating protein-protein interaction networks in protein homeostasis. Zhong M, Lee GM, Sijbesma E, Ottmann C, Arkin MR. Curr Opin Chem Biol 50 55-65 (2019)
  24. Computational methods for analyzing conformational variability of macromolecular complexes from cryo-electron microscopy images. Jonić S. Curr Opin Struct Biol 43 114-121 (2017)
  25. Structure and mechanism of the ESCRT pathway AAA+ ATPase Vps4. Han H, Hill CP. Biochem Soc Trans 47 37-45 (2019)
  26. Adapting Secretory Proteostasis and Function Through the Unfolded Protein Response. Wong MY, DiChiara AS, Suen PH, Chen K, Doan ND, Shoulders MD. Curr Top Microbiol Immunol 414 1-25 (2018)
  27. Cryo-electron Microscopy Analysis of Structurally Heterogeneous Macromolecular Complexes. Jonić S. Comput Struct Biotechnol J 14 385-390 (2016)
  28. Electron Cryo-microscopy as a Tool for Structure-Based Drug Development. Merino F, Raunser S. Angew Chem Int Ed Engl 56 2846-2860 (2017)
  29. The PGC-1/ERR network and its role in precision oncology. De Vitto H, Bode AM, Dong Z. NPJ Precis Oncol 3 9 (2019)
  30. Advances in high-resolution cryo-EM of oligomeric enzymes. Vonck J, Mills DJ. Curr Opin Struct Biol 46 48-54 (2017)
  31. Current approach and novel perspectives in nasopharyngeal carcinoma: the role of targeting proteasome dysregulation as a molecular landmark in nasopharyngeal cancer. Yarza R, Bover M, Agulló-Ortuño MT, Iglesias-Docampo LC. J Exp Clin Cancer Res 40 202 (2021)
  32. Structure and Function of p97 and Pex1/6 Type II AAA+ Complexes. Saffert P, Enenkel C, Wendler P. Front Mol Biosci 4 33 (2017)
  33. While the revolution will not be crystallized, biochemistry reigns supreme. Takizawa Y, Binshtein E, Erwin AL, Pyburn TM, Mittendorf KF, Ohi MD. Protein Sci 26 69-81 (2017)
  34. Assessing heterogeneity in oligomeric AAA+ machines. Sysoeva TA. Cell Mol Life Sci 74 1001-1018 (2017)
  35. Structural Study of Heterogeneous Biological Samples by Cryoelectron Microscopy and Image Processing. White HE, Ignatiou A, Clare DK, Orlova EV. Biomed Res Int 2017 1032432 (2017)
  36. Atomic resolution structure determination by the cryo-EM method MicroED. Liu S, Hattne J, Reyes FE, Sanchez-Martinez S, Jason de la Cruz M, Shi D, Gonen T. Protein Sci 26 8-15 (2017)
  37. Visualization of biological macromolecules at near-atomic resolution: cryo-electron microscopy comes of age. Mitra AK. Acta Crystallogr F Struct Biol Commun 75 3-11 (2019)
  38. Effects of radiation damage in studies of protein-DNA complexes by cryo-EM. Mishyna M, Volokh O, Danilova Y, Gerasimova N, Pechnikova E, Sokolova OS. Micron 96 57-64 (2017)
  39. The functional importance of VCP to maintaining cellular protein homeostasis. Ahlstedt BA, Ganji R, Raman M. Biochem Soc Trans 50 1457-1469 (2022)
  40. Tools for the cryo-EM gold rush: going from the cryo-EM map to the atomistic model. Kim DN, Sanbonmatsu KY. Biosci Rep 37 BSR20170072 (2017)
  41. AAA+ proteins: one motor, multiple ways to work. Lin J, Shorter J, Lucius AL. Biochem Soc Trans 50 895-906 (2022)
  42. Insights into the Structure and Function of the Pex1/Pex6 AAA-ATPase in Peroxisome Homeostasis. Judy RM, Sheedy CJ, Gardner BM. Cells 11 2067 (2022)
  43. Using chemical inhibitors to probe AAA protein conformational dynamics and cellular functions. Steinman JB, Kapoor TM. Curr Opin Chem Biol 50 45-54 (2019)
  44. The Cryo-EM Effect: Structural Biology of Neurodegenerative Disease Proteostasis Factors. Creekmore BC, Chang YW, Lee EB. J Neuropathol Exp Neurol 80 494-513 (2021)
  45. Versatility of Approximating Single-Particle Electron Microscopy Density Maps Using Pseudoatoms and Approximation-Accuracy Control. Jonić S, Sorzano CO. Biomed Res Int 2016 7060348 (2016)
  46. Integration of Nanometer-Range Label-to-Label Distances and Their Distributions into Modelling Approaches. Jeschke G. Biomolecules 12 1369 (2022)
  47. Proteolytic control of genome integrity at the replication fork. Rageul J, Weinheimer AS, Park JJ, Kim H. DNA Repair (Amst) 81 102657 (2019)
  48. The Cure VCP Scientific Conference 2021: Molecular and clinical insights into neurodegeneration and myopathy linked to multisystem proteinopathy-1 (MSP-1). Johnson MA, Klickstein JA, Khanna R, Gou Y, Cure VCP Disease Research Consortium, Raman M. Neurobiol Dis 169 105722 (2022)
  49. Versatile control of the CDC48 segregase by the plant UBX-containing (PUX) proteins. Zhang J, Vancea AI, Shahul Hameed UF, Arold ST. Comput Struct Biotechnol J 19 3125-3132 (2021)
  50. Structural insights of the p97/VCP AAA+ ATPase: How adapter interactions coordinate diverse cellular functionality. Braxton JR, Southworth DR. J Biol Chem 299 105182 (2023)

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  1. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Punjani A, Rubinstein JL, Fleet DJ, Brubaker MA. Nat Methods 14 290-296 (2017)
  2. Breaking Cryo-EM Resolution Barriers to Facilitate Drug Discovery. Merk A, Bartesaghi A, Banerjee S, Falconieri V, Rao P, Davis MI, Pragani R, Boxer MB, Earl LA, Milne JLS, Subramaniam S. Cell 165 1698-1707 (2016)
  3. Molecular Mechanism of Substrate Processing by the Cdc48 ATPase Complex. Bodnar NO, Rapoport TA. Cell 169 722-735.e9 (2017)
  4. Substrate processing by the Cdc48 ATPase complex is initiated by ubiquitin unfolding. Twomey EC, Ji Z, Wales TE, Bodnar NO, Ficarro SB, Marto JA, Engen JR, Rapoport TA. Science 365 eaax1033 (2019)
  5. An atomic structure of the human 26S proteasome. Huang X, Luan B, Wu J, Shi Y. Nat Struct Mol Biol 23 778-785 (2016)
  6. Structure of the human 26S proteasome at a resolution of 3.9 Å. Schweitzer A, Aufderheide A, Rudack T, Beck F, Pfeifer G, Plitzko JM, Sakata E, Schulten K, Förster F, Baumeister W. Proc Natl Acad Sci U S A 113 7816-7821 (2016)
  7. Ubiquitin- and ATP-dependent unfoldase activity of P97/VCP•NPLOC4•UFD1L is enhanced by a mutation that causes multisystem proteinopathy. Blythe EE, Olson KC, Chau V, Deshaies RJ. Proc Natl Acad Sci U S A 114 E4380-E4388 (2017)
  8. Structure of the Cdc48 segregase in the act of unfolding an authentic substrate. Cooney I, Han H, Stewart MG, Carson RH, Hansen DT, Iwasa JH, Price JC, Hill CP, Shen PS. Science 365 502-505 (2019)
  9. ULK1 and ULK2 Regulate Stress Granule Disassembly Through Phosphorylation and Activation of VCP/p97. Wang B, Maxwell BA, Joo JH, Gwon Y, Messing J, Mishra A, Shaw TI, Ward AL, Quan H, Sakurada SM, Pruett-Miller SM, Bertorini T, Vogel P, Kim HJ, Peng J, Taylor JP, Kundu M. Mol Cell 74 742-757.e8 (2019)
  10. Structure of a AAA+ unfoldase in the process of unfolding substrate. Ripstein ZA, Huang R, Augustyniak R, Kay LE, Rubinstein JL. Elife 6 e25754 (2017)
  11. Expanded Coverage of the 26S Proteasome Conformational Landscape Reveals Mechanisms of Peptidase Gating. Eisele MR, Reed RG, Rudack T, Schweitzer A, Beck F, Nagy I, Pfeifer G, Plitzko JM, Baumeister W, Tomko RJ, Sakata E. Cell Rep 24 1301-1315.e5 (2018)
  12. The AAA ATPase Vps4 binds ESCRT-III substrates through a repeating array of dipeptide-binding pockets. Han H, Monroe N, Sundquist WI, Shen PS, Hill CP. Elife 6 e31324 (2017)
  13. Katanin spiral and ring structures shed light on power stroke for microtubule severing. Zehr E, Szyk A, Piszczek G, Szczesna E, Zuo X, Roll-Mecak A. Nat Struct Mol Biol 24 717-725 (2017)
  14. Pushing the resolution limit by correcting the Ewald sphere effect in single-particle Cryo-EM reconstructions. Zhu D, Wang X, Fang Q, Van Etten JL, Rossmann MG, Rao Z, Zhang X. Nat Commun 9 1552 (2018)
  15. Catastrophic disassembly of actin filaments via Mical-mediated oxidation. Grintsevich EE, Ge P, Sawaya MR, Yesilyurt HG, Terman JR, Zhou ZH, Reisler E. Nat Commun 8 2183 (2017)
  16. VCP inhibitors induce endoplasmic reticulum stress, cause cell cycle arrest, trigger caspase-mediated cell death and synergistically kill ovarian cancer cells in combination with Salubrinal. Bastola P, Neums L, Schoenen FJ, Chien J. Mol Oncol 10 1559-1574 (2016)
  17. Structure of the Cdc48 ATPase with its ubiquitin-binding cofactor Ufd1-Npl4. Bodnar NO, Kim KH, Ji Z, Wales TE, Svetlov V, Nudler E, Engen JR, Walz T, Rapoport TA. Nat Struct Mol Biol 25 616-622 (2018)
  18. Near-atomic cryo-EM imaging of a small protein displayed on a designed scaffolding system. Liu Y, Gonen S, Gonen T, Yeates TO. Proc Natl Acad Sci U S A 115 3362-3367 (2018)
  19. A Dynamic molecular basis for malfunction in disease mutants of p97/VCP. Schuetz AK, Kay LE. Elife 5 e20143 (2016)
  20. ATP hydrolysis-coupled peptide translocation mechanism of Mycobacterium tuberculosis ClpB. Yu H, Lupoli TJ, Kovach A, Meng X, Zhao G, Nathan CF, Li H. Proc Natl Acad Sci U S A 115 E9560-E9569 (2018)
  21. Precision medicine: the foundation of future cancer therapeutics. Shin SH, Bode AM, Dong Z. NPJ Precis Oncol 1 12 (2017)
  22. Atomic-level evidence for packing and positional amyloid polymorphism by segment from TDP-43 RRM2. Guenther EL, Ge P, Trinh H, Sawaya MR, Cascio D, Boyer DR, Gonen T, Zhou ZH, Eisenberg DS. Nat Struct Mol Biol 25 311-319 (2018)
  23. Cryo-EM structures of the archaeal PAN-proteasome reveal an around-the-ring ATPase cycle. Majumder P, Rudack T, Beck F, Danev R, Pfeifer G, Nagy I, Baumeister W. Proc Natl Acad Sci U S A 116 534-539 (2019)
  24. Action of a minimal contractile bactericidal nanomachine. Ge P, Scholl D, Prokhorov NS, Avaylon J, Shneider MM, Browning C, Buth SA, Plattner M, Chakraborty U, Ding K, Leiman PG, Miller JF, Zhou ZH. Nature 580 658-662 (2020)
  25. Direct visualization of degradation microcompartments at the ER membrane. Albert S, Wietrzynski W, Lee CW, Schaffer M, Beck F, Schuller JM, Salomé PA, Plitzko JM, Baumeister W, Engel BD. Proc Natl Acad Sci U S A 117 1069-1080 (2020)
  26. Mechanistic insight into substrate processing and allosteric inhibition of human p97. Pan M, Yu Y, Ai H, Zheng Q, Xie Y, Liu L, Zhao M. Nat Struct Mol Biol 28 614-625 (2021)
  27. Multisystem Proteinopathy Mutations in VCP/p97 Increase NPLOC4·UFD1L Binding and Substrate Processing. Blythe EE, Gates SN, Deshaies RJ, Martin A. Structure 27 1820-1829.e4 (2019)
  28. Unfolding the mechanism of the AAA+ unfoldase VAT by a combined cryo-EM, solution NMR study. Huang R, Ripstein ZA, Augustyniak R, Lazniewski M, Ginalski K, Kay LE, Rubinstein JL. Proc Natl Acad Sci U S A 113 E4190-9 (2016)
  29. SPT5 stabilization of promoter-proximal RNA polymerase II. Aoi Y, Takahashi YH, Shah AP, Iwanaszko M, Rendleman EJ, Khan NH, Cho BK, Goo YA, Ganesan S, Kelleher NL, Shilatifard A. Mol Cell 81 4413-4424.e5 (2021)
  30. Seesaw conformations of Npl4 in the human p97 complex and the inhibitory mechanism of a disulfiram derivative. Pan M, Zheng Q, Yu Y, Ai H, Xie Y, Zeng X, Wang C, Liu L, Zhao M. Nat Commun 12 121 (2021)
  31. Single-particle cryo-electron microscopy: Mathematical theory, computational challenges, and opportunities. Bendory T, Bartesaghi A, Singer A. IEEE Signal Process Mag 37 58-76 (2020)
  32. p97 Composition Changes Caused by Allosteric Inhibition Are Suppressed by an On-Target Mechanism that Increases the Enzyme's ATPase Activity. Her NG, Toth JI, Ma CT, Wei Y, Motamedchaboki K, Sergienko E, Petroski MD. Cell Chem Biol 23 517-528 (2016)
  33. An algorithm for estimation and correction of anisotropic magnification distortion of cryo-EM images without need of pre-calibration. Yu G, Li K, Liu Y, Chen Z, Wang Z, Yan R, Klose T, Tang L, Jiang W. J Struct Biol 195 207-215 (2016)
  34. p97 Disease Mutations Modulate Nucleotide-Induced Conformation to Alter Protein-Protein Interactions. Bulfer SL, Chou TF, Arkin MR. ACS Chem Biol 11 2112-2116 (2016)
  35. Cryo-EM structure of the essential ribosome assembly AAA-ATPase Rix7. Lo YH, Sobhany M, Hsu AL, Ford BL, Krahn JM, Borgnia MJ, Stanley RE. Nat Commun 10 513 (2019)
  36. Quantitative interaction mapping reveals an extended UBX domain in ASPL that disrupts functional p97 hexamers. Arumughan A, Roske Y, Barth C, Forero LL, Bravo-Rodriguez K, Redel A, Kostova S, McShane E, Opitz R, Faelber K, Rau K, Mielke T, Daumke O, Selbach M, Sanchez-Garcia E, Rocks O, Panáková D, Heinemann U, Wanker EE. Nat Commun 7 13047 (2016)
  37. EMBuilder: A Template Matching-based Automatic Model-building Program for High-resolution Cryo-Electron Microscopy Maps. Zhou N, Wang H, Wang J. Sci Rep 7 2664 (2017)
  38. A Sensitive Yellow Fever Virus Entry Reporter Identifies Valosin-Containing Protein (VCP/p97) as an Essential Host Factor for Flavivirus Uncoating. Ramanathan HN, Zhang S, Douam F, Mar KB, Chang J, Yang PL, Schoggins JW, Ploss A, Lindenbach BD. mBio 11 e00467-20 (2020)
  39. Emerging Cancer Therapeutic Targets in Protein Homeostasis. Bastola P, Oien DB, Cooley M, Chien J. AAPS J 20 94 (2018)
  40. Exploiting conformational plasticity in the AAA+ protein VCP/p97 to modify function. Schütz AK, Rennella E, Kay LE. Proc Natl Acad Sci U S A 114 E6822-E6829 (2017)
  41. Cooperative subunit dynamics modulate p97 function. Huang R, Ripstein ZA, Rubinstein JL, Kay LE. Proc Natl Acad Sci U S A 116 158-167 (2019)
  42. Benchmarking cryo-EM Single Particle Analysis Workflow. Kim LY, Rice WJ, Eng ET, Kopylov M, Cheng A, Raczkowski AM, Jordan KD, Bobe D, Potter CS, Carragher B. Front Mol Biosci 5 50 (2018)
  43. Specific mutations in the D1-D2 linker region of VCP/p97 enhance ATPase activity and confer resistance to VCP inhibitors. Bastola P, Wang F, Schaich MA, Gan T, Freudenthal BD, Chou TF, Chien J. Cell Death Discov 3 17065 (2017)
  44. Structural insights into ubiquitin recognition and Ufd1 interaction of Npl4. Sato Y, Tsuchiya H, Yamagata A, Okatsu K, Tanaka K, Saeki Y, Fukai S. Nat Commun 10 5708 (2019)
  45. Letter The democratization of cryo-EM. Stuart DI, Subramaniam S, Abrescia NG. Nat Methods 13 607-608 (2016)
  46. Designing a chemical inhibitor for the AAA protein spastin using active site mutations. Cupido T, Pisa R, Kelley ME, Kapoor TM. Nat Chem Biol 15 444-452 (2019)
  47. HEMNMA-3D: Cryo Electron Tomography Method Based on Normal Mode Analysis to Study Continuous Conformational Variability of Macromolecular Complexes. Harastani M, Eltsov M, Leforestier A, Jonic S. Front Mol Biosci 8 663121 (2021)
  48. A Non-Competitive Inhibitor of VCP/p97 and VPS4 Reveals Conserved Allosteric Circuits in Type I and II AAA ATPases. Pöhler R, Krahn JH, van den Boom J, Dobrynin G, Kaschani F, Eggenweiler HM, Zenke FT, Kaiser M, Meyer H. Angew Chem Int Ed Engl 57 1576-1580 (2018)
  49. Transmembrane helix hydrophobicity is an energetic barrier during the retrotranslocation of integral membrane ERAD substrates. Guerriero CJ, Reutter KR, Augustine AA, Preston GM, Weiberth KF, Mackie TD, Cleveland-Rubeor HC, Bethel NP, Callenberg KM, Nakatsukasa K, Grabe M, Brodsky JL. Mol Biol Cell 28 2076-2090 (2017)
  50. PTPN12/PTP-PEST Regulates Phosphorylation-Dependent Ubiquitination and Stability of Focal Adhesion Substrates in Invasive Glioblastoma Cells. Chen Z, Morales JE, Guerrero PA, Sun H, McCarty JH. Cancer Res 78 3809-3822 (2018)
  51. Selective Capture of Histidine-tagged Proteins from Cell Lysates Using TEM grids Modified with NTA-Graphene Oxide. Benjamin CJ, Wright KJ, Bolton SC, Hyun SH, Krynski K, Grover M, Yu G, Guo F, Kinzer-Ursem TL, Jiang W, Thompson DH. Sci Rep 6 32500 (2016)
  52. X-ray and cryo-EM structures of inhibitor-bound cytochrome bc1 complexes for structure-based drug discovery. Amporndanai K, Johnson RM, O'Neill PM, Fishwick CWG, Jamson AH, Rawson S, Muench SP, Hasnain SS, Antonyuk SV. IUCrJ 5 200-210 (2018)
  53. Phospho-Ser784-VCP Is Required for DNA Damage Response and Is Associated with Poor Prognosis of Chemotherapy-Treated Breast Cancer. Zhu C, Rogers A, Asleh K, Won J, Gao D, Leung S, Li S, Vij KR, Zhu J, Held JM, You Z, Nielsen TO, Shao J. Cell Rep 31 107745 (2020)
  54. Hybrid Electron Microscopy Normal Mode Analysis with Scipion. Harastani M, Sorzano COS, Jonić S. Protein Sci 29 223-236 (2020)
  55. Rational design of highly potent broad-spectrum enterovirus inhibitors targeting the nonstructural protein 2C. Bauer L, Manganaro R, Zonsics B, Hurdiss DL, Zwaagstra M, Donselaar T, Welter NGE, van Kleef RGDM, Lopez ML, Bevilacqua F, Raman T, Ferla S, Bassetto M, Neyts J, Strating JRPM, Westerink RHS, Brancale A, van Kuppeveld FJM. PLoS Biol 18 e3000904 (2020)
  56. Structural Details of Ufd1 Binding to p97 and Their Functional Implications in ER-Associated Degradation. Le LT, Kang W, Kim JY, Le OT, Lee SY, Yang JK. PLoS One 11 e0163394 (2016)
  57. An intrinsically disordered motif regulates the interaction between the p47 adaptor and the p97 AAA+ ATPase. Conicella AE, Huang R, Ripstein ZA, Nguyen A, Wang E, Löhr T, Schuck P, Vendruscolo M, Rubinstein JL, Kay LE. Proc Natl Acad Sci U S A 117 26226-26236 (2020)
  58. Analyzing Resistance to Design Selective Chemical Inhibitors for AAA Proteins. Pisa R, Cupido T, Steinman JB, Jones NH, Kapoor TM. Cell Chem Biol 26 1263-1273.e5 (2019)
  59. Interaction between the AAA+ ATPase p97 and its cofactor ataxin3 in health and disease: Nucleotide-induced conformational changes regulate cofactor binding. Rao MV, Williams DR, Cocklin S, Loll PJ. J Biol Chem 292 18392-18407 (2017)
  60. Active conformation of the p97-p47 unfoldase complex. Xu Y, Han H, Cooney I, Guo Y, Moran NG, Zuniga NR, Price JC, Hill CP, Shen PS. Nat Commun 13 2640 (2022)
  61. Development of a yeast internal-subunit eGFP labeling strategy and its application in subunit identification in eukaryotic group II chaperonin TRiC/CCT. Zang Y, Wang H, Cui Z, Jin M, Liu C, Han W, Wang Y, Cong Y. Sci Rep 8 2374 (2018)
  62. A covalent p97/VCP ATPase inhibitor can overcome resistance to CB-5083 and NMS-873 in colorectal cancer cells. Zhang G, Li S, Wang F, Jones AC, Goldberg AFG, Lin B, Virgil S, Stoltz BM, Deshaies RJ, Chou TF. Eur J Med Chem 213 113148 (2021)
  63. DeepHEMNMA: ResNet-based hybrid analysis of continuous conformational heterogeneity in cryo-EM single particle images. Hamitouche I, Jonic S. Front Mol Biosci 9 965645 (2022)
  64. Elucidating the structural basis for differing enzyme inhibitor potency by cryo-EM. Rawson S, Bisson C, Hurdiss DL, Fazal A, McPhillie MJ, Sedelnikova SE, Baker PJ, Rice DW, Muench SP. Proc Natl Acad Sci U S A 115 1795-1800 (2018)
  65. Shedding light on the expansion and diversification of the Cdc48 protein family during the rise of the eukaryotic cell. Kienle N, Kloepper TH, Fasshauer D. BMC Evol Biol 16 215 (2016)
  66. Simultaneous refinement of inaccurate local regions and overall structure in the CASP12 protein model refinement experiment. Lee GR, Heo L, Seok C. Proteins 86 Suppl 1 168-176 (2018)
  67. AAA+ ATPase p97/VCP mutants and inhibitor binding disrupt inter-domain coupling and subsequent allosteric activation. Caffrey B, Zhu X, Berezuk A, Tuttle K, Chittori S, Subramaniam S. J Biol Chem 297 101187 (2021)
  68. Compounds activating VCP D1 ATPase enhance both autophagic and proteasomal neurotoxic protein clearance. Wrobel L, Hill SM, Djajadikerta A, Fernandez-Estevez M, Karabiyik C, Ashkenazi A, Barratt VJ, Stamatakou E, Gunnarsson A, Rasmusson T, Miele EW, Beaton N, Bruderer R, Feng Y, Reiter L, Castaldi MP, Jarvis R, Tan K, Bürli RW, Rubinsztein DC. Nat Commun 13 4146 (2022)
  69. Optimization of Phenyl Indole Inhibitors of the AAA+ ATPase p97. LaPorte MG, Burnett JC, Colombo R, Bulfer SL, Alverez C, Chou TF, Neitz RJ, Green N, Moore WJ, Yue Z, Li S, Arkin MR, Wipf P, Huryn DM. ACS Med Chem Lett 9 1075-1081 (2018)
  70. Structural basis for inhibition of the AAA-ATPase Drg1 by diazaborine. Prattes M, Grishkovskaya I, Hodirnau VV, Rössler I, Klein I, Hetzmannseder C, Zisser G, Gruber CC, Gruber K, Haselbach D, Bergler H. Nat Commun 12 3483 (2021)
  71. Structural basis for nucleotide-modulated p97 association with the ER membrane. Tang WK, Zhang T, Ye Y, Xia D. Cell Discov 3 17045 (2017)
  72. Structural basis of ubiquitin-independent PP1 complex disassembly by p97. van den Boom J, Marini G, Meyer H, Saibil HR. EMBO J 42 e113110 (2023)
  73. Estimating the effect of finite depth of field in single-particle cryo-EM. Downing KH, Glaeser RM. Ultramicroscopy 184 94-99 (2018)
  74. Predicting the functional motions of p97 using symmetric normal modes. Na H, Song G. Proteins 84 1823-1835 (2016)
  75. Structural and Functional Analysis of Disease-Linked p97 ATPase Mutant Complexes. Nandi P, Li S, Columbres RCA, Wang F, Williams DR, Poh YP, Chou TF, Chiu PL. Int J Mol Sci 22 8079 (2021)
  76. Adaptor-Specific Antibody Fragment Inhibitors for the Intracellular Modulation of p97 (VCP) Protein-Protein Interactions. Jiang Z, Kuo YH, Zhong M, Zhang J, Zhou XX, Xing L, Wells JA, Wang Y, Arkin MR. J Am Chem Soc 144 13218-13225 (2022)
  77. Entropic Inhibition: How the Activity of a AAA+ Machine Is Modulated by Its Substrate-Binding Domain. Iljina M, Mazal H, Goloubinoff P, Riven I, Haran G. ACS Chem Biol 16 775-785 (2021)
  78. Fluoxetine targets an allosteric site in the enterovirus 2C AAA+ ATPase and stabilizes a ring-shaped hexameric complex. Hurdiss DL, El Kazzi P, Bauer L, Papageorgiou N, Ferron FP, Donselaar T, van Vliet ALW, Shamorkina TM, Snijder J, Canard B, Decroly E, Brancale A, Zeev-Ben-Mordehai T, Förster F, van Kuppeveld FJM, Coutard B. Sci Adv 8 eabj7615 (2022)
  79. Structural remodeling of AAA+ ATPase p97 by adaptor protein ASPL facilitates posttranslational methylation by METTL21D. Petrović S, Roske Y, Rami B, Phan MHQ, Panáková D, Heinemann U. Proc Natl Acad Sci U S A 120 e2208941120 (2023)
  80. Cryo-electron microscopy structure of a human PRMT5:MEP50 complex. Timm DE, Bowman V, Madsen R, Rauch C. PLoS One 13 e0193205 (2018)
  81. Cryo-electron microscopy structures of VCP/p97 reveal a new mechanism of oligomerization regulation. Yu G, Bai Y, Li K, Amarasinghe O, Jiang W, Zhang ZY. iScience 24 103310 (2021)
  82. Eeyarestatin I derivatives with improved aqueous solubility. Ding R, Zhang T, Xie J, Williams J, Ye Y, Chen L. Bioorg Med Chem Lett 26 5177-5181 (2016)
  83. Production of a New Plant-Based Milk from Adenanthera pavonina Seed and Evaluation of Its Nutritional and Health Benefits. Afolabi IS, Nwachukwu IC, Ezeoke CS, Woke RC, Adegbite OA, Olawole TD, Martins OC. Front Nutr 5 9 (2018)
  84. Reconstruction of 3D structures of MET antibodies from electron microscopy 2D class averages. Chen Q, Vieth M, Timm DE, Humblet C, Schneidman-Duhovny D, Chemmama IE, Sali A, Zeng W, Lu J, Liu L. PLoS One 12 e0175758 (2017)
  85. The Ufd1 cofactor determines the linkage specificity of polyubiquitin chain engagement by the AAA+ ATPase Cdc48. Williams C, Dong KC, Arkinson C, Martin A. Mol Cell 83 759-769.e7 (2023)
  86. The phosphorylation and dephosphorylation switch of VCP/p97 regulates the architecture of centrosome and spindle. Zhu K, Cai Y, Si X, Ye Z, Gao Y, Liu C, Wang R, Ma Z, Zhu H, Zhang L, Li S, Zhang H, Yue J. Cell Death Differ 29 2070-2088 (2022)
  87. Adapted ATPase domain communication overcomes the cytotoxicity of p97 inhibitors. Wei Y, Toth JI, Blanco GA, Bobkov AA, Petroski MD. J Biol Chem 293 20169-20180 (2018)
  88. Extreme parsimony in ATP consumption by 20S complexes in the global disassembly of single SNARE complexes. Kim C, Shon MJ, Kim SH, Eun GS, Ryu JK, Hyeon C, Jahn R, Yoon TY. Nat Commun 12 3206 (2021)
  89. Identification of Mg2+ ions next to nucleotides in cryo-EM maps using electrostatic potential maps. Wang J, Natchiar SK, Moore PB, Klaholz BP. Acta Crystallogr D Struct Biol 77 534-539 (2021)
  90. Single-particle cryo-EM reveals conformational variability of the oligomeric VCC β-barrel pore in a lipid bilayer. Sengupta N, Mondal AK, Mishra S, Chattopadhyay K, Dutta S. J Cell Biol 220 e202102035 (2021)
  91. The UBX domain in UBXD1 organizes ubiquitin binding at the C-terminus of the VCP/p97 AAA-ATPase. Blueggel M, Kroening A, Kracht M, van den Boom J, Dabisch M, Goehring A, Kaschani F, Kaiser M, Bayer P, Meyer H, Beuck C. Nat Commun 14 3258 (2023)
  92. Valosin-containing protein VCP/p97 is essential for the intracellular development of Leishmania and its survival under heat stress. Guedes Aguiar B, Padmanabhan PK, Dumas C, Papadopoulou B. Cell Microbiol 20 e12867 (2018)
  93. A novel storage system for cryoEM samples. Scapin G, Prosise WW, Wismer MK, Strickland C. J Struct Biol 199 84-86 (2017)
  94. Editorial Crystallography and the development of therapeutic medicines. Baker EN. IUCrJ 5 118-119 (2018)
  95. Data-driven determination of number of discrete conformations in single-particle cryo-EM. Zhou Y, Moscovich A, Bartesaghi A. Comput Methods Programs Biomed 221 106892 (2022)
  96. Probing allosteric interactions in homo-oligomeric molecular machines using solution NMR spectroscopy. Toyama Y, Kay LE. Proc Natl Acad Sci U S A 118 e2116325118 (2021)
  97. Anti-HCMV activity by an irreversible p97 inhibitor LC-1310. Wang Y, Soto-Acosta R, Ding R, Chen L, Geraghty RJ. Med Chem Res 30 440-448 (2021)
  98. Characterizing ATP processing by the AAA+ protein p97 at the atomic level. Shein M, Hitzenberger M, Cheng TC, Rout SR, Leitl KD, Sato Y, Zacharias M, Sakata E, Schütz AK. Nat Chem 16 363-372 (2024)
  99. In silico prediction, characterization, docking studies and molecular dynamics simulation of human p97 in complex with p37 cofactor. Mirzadeh A, Kobakhidze G, Vuillemot R, Jonic S, Rouiller I. BMC Mol Cell Biol 23 39 (2022)
  100. Structural dynamics of AAA + ATPase Drg1 and mechanism of benzo-diazaborine inhibition. Ma C, Wu D, Chen Q, Gao N. Nat Commun 13 6765 (2022)
  101. Synthesis and In Vitro Evaluation of 2-[3-(2-Aminoethyl)-1H-indol-1-yl]-N-benzylquinazolin-4-amine as a Novel p97/VCP Inhibitor Lead Capable of Inducing Apoptosis in Cancer Cells. Feng Q, Zheng J, Zhang J, Zhao M. ACS Omega 5 31784-31791 (2020)
  102. The cryo-EM structure of the human ERAD retrotranslocation complex. Rao B, Wang Q, Yao D, Xia Y, Li W, Xie Y, Li S, Cao M, Shen Y, Qin A, Zhao J, Cao Y. Sci Adv 9 eadi5656 (2023)
  103. A targeted covalent inhibitor of p97 with proteome-wide selectivity. Ye Z, Wang K, Chen L, Jin X, Chen H, Tang G, Yao SQ, Feng Z, Zhang CJ. Acta Pharm Sin B 12 982-989 (2022)
  104. Cdc48 influence on separase levels is independent of mitosis and suggests translational sensitivity of separase. Vijayakumari D, Müller J, Hauf S. Cell Rep 38 110554 (2022)
  105. Conserved L464 in p97 D1-D2 linker is critical for p97 cofactor regulated ATPase activity. Zhang X, Gui L, Li S, Nandi P, Columbres RC, Wong DE, Moen DR, Lin HJ, Chiu PL, Chou TF. Biochem J 478 3185-3204 (2021)
  106. Nuclear VCP drives colorectal cancer progression by promoting fatty acid oxidation. Huang Y, Wang F, Lin X, Li Q, Lu Y, Zhang J, Shen X, Tan J, Qin Z, Chen J, Chen X, Pan G, Wang X, Zeng Y, Yang S, Liu J, Xing F, Li K, Zhang H. Proc Natl Acad Sci U S A 120 e2221653120 (2023)
  107. Purification and cryo-EM structure determination of VCP/p97 dodecamers from mammalian and bacterial cells. Yu G, Bai Y, Zhang ZY. STAR Protoc 3 101339 (2022)
  108. Stoichiometry of Nucleotide Binding to Proteasome AAA+ ATPase Hexamer Established by Native Mass Spectrometry. Yu Y, Liu H, Yu Z, Witkowska HE, Cheng Y. Mol Cell Proteomics 19 1997-2015 (2020)
  109. Structural basis for recognition and methylation of p97 by METTL21D, a valosin-containing protein lysine methyltransferase. Nguyen TQ, Koh S, Kwon J, Jang S, Kang W, Yang JK. iScience 26 107222 (2023)
  110. Structure of the peroxisomal Pex1/Pex6 ATPase complex bound to a substrate. Rüttermann M, Koci M, Lill P, Geladas ED, Kaschani F, Klink BU, Erdmann R, Gatsogiannis C. Nat Commun 14 5942 (2023)
  111. Thicker Ice Improves the Integrity and Angular Distribution of CDC48A Hexamers on Cryo-EM Grids. Huntington B, Zhao L, Bron P, Shahul Hameed UF, Arold ST, Qureshi BM. Front Mol Biosci 9 890390 (2022)
  112. ATP hydrolysis captured in atomic detail. Elghobashi-Meinhardt N. Nat Chem 16 306-307 (2024)
  113. An Open-Source Storage Solution for Cryo-Electron Microscopy Samples. Ultee E, Schenkel F, Yang W, Brenzinger S, Depelteau JS, Briegel A. Microsc Microanal 24 60-63 (2018)
  114. An autosomal-dominant childhood-onset disorder associated with pathogenic variants in VCP. Mah-Som AY, Daw J, Huynh D, Wu M, Creekmore BC, Burns W, Skinner SA, Holla ØL, Smeland MF, Planes M, Uguen K, Redon S, Bierhals T, Scholz T, Denecke J, Mensah MA, Sczakiel HL, Tichy H, Verheyen S, Blatterer J, Schreiner E, Thies J, Lam C, Spaeth CG, Pena L, Ramsey K, Narayanan V, Seaver LH, Rodriguez D, Afenjar A, Burglen L, Lee EB, Chou TF, Weihl CC, Shinawi MS. Am J Hum Genet 110 1959-1975 (2023)
  115. Analysis of the Conformational Landscape of the N-Domains of the AAA ATPase p97: Disentangling the Continuous Conformational Variability in Partially Symmetrical Complexes. Valimehr S, Vuillemot R, Kazemi M, Jonic S, Rouiller I. Int J Mol Sci 25 3371 (2024)
  116. From structural polymorphism to structural metamorphosis of the coat protein of flexuous filamentous potato virus Y. Kavčič L, Kežar A, Koritnik N, Žnidarič MT, Klobučar T, Vičič Ž, Merzel F, Holden E, Benesch JLP, Podobnik M. Commun Chem 7 14 (2024)
  117. Inhibition of VCP modulates NF-κB signaling pathway to suppress multiple myeloma cell proliferation and osteoclast differentiation. Wei R, Cao Y, Wu H, Liu X, Jiang M, Luo X, Deng Z, Wang Z, Ke M, Zhu Y, Chen S, Gu C, Yang Y. Aging (Albany NY) 15 8220-8236 (2023)
  118. Interface-acting nucleotide controls polymerization dynamics at microtubule plus- and minus-ends. McCormick LA, Cleary JM, Hancock WO, Rice LM, Rice LM. Elife 12 RP89231 (2024)
  119. MDSPACE and MDTOMO Software for Extracting Continuous Conformational Landscapes from Datasets of Single Particle Images and Subtomograms Based on Molecular Dynamics Simulations: Latest Developments in ContinuousFlex Software Package. Vuillemot R, Harastani M, Hamitouche I, Jonic S. Int J Mol Sci 25 20 (2023)
  120. Optimization of 1,2,4-Triazole-Based p97 Inhibitors for the Treatment of Cancer. LaPorte MG, Alverez C, Chatterley A, Kovaliov M, Carder EJ, Houghton MJ, Lim C, Miller ER, Samankumara LP, Liang M, Kerrigan K, Yue Z, Li S, Tomaino F, Wang F, Green N, Stott GM, Srivastava A, Chou TF, Wipf P, Huryn DM. ACS Med Chem Lett 14 977-985 (2023)
  121. RecJ3/4-aRNase J form a Ubl-associated nuclease complex functioning in survival against DNA damage in Haloferax volcanii. Jia H, Dantuluri S, Margulies S, Smith V, Lever R, Allers T, Koh J, Chen S, Maupin-Furlow JA. mBio 14 e0085223 (2023)