Human p97/VCP R155H mutant structure with a triazole inhibitor (NSC804515)
Nandi P, DeVore K, Wang F, Li S, Walker JD, Truong TT, LaPorte MG, Wipf P, Schlager H, McCleerey J, Paquette W, Columbres RCA, Gan T, Poh YP, Fromme P, Flint AJ, Wolf M, Huryn DM, Chou TF, Chiu PL
Commun Chem (2024) 7 pp. 177-177 [ DOI: doi:10.1038/s42004-024-01267-3 Pubmed: 39122922 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Transitional endoplasmic reticulum atpase (89 kDa, Protein from Homo sapiens)
- N-[3-(2,5-difluoro-4-{[(4m)-5-(hexylsulfanyl)-4-(pyridin-3-yl)-4h-1,2,4-triazol-3-yl]methoxy}phenyl)prop-2-yn-1-yl]propanamide (513 Da, Ligand)
- P97/vcp aaa+ atpase r155h mutant/nsc804515 (536 kDa, Complex from Homo sapiens)
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7t4r
Q-score: 0.429
Kschonsak M, Johnson MC, Schelling R, Green EM, Rouge L, Ho H, Patel N, Kilic C, Kraft E, Arthur CP, Rohou AL, Comps-Agrar L, Martinez-Martin N, Perez L, Payandeh J, Ciferri C
Sci Adv (2022) 8 pp. eabm2536-eabm2536 [ Pubmed: 35275719 DOI: doi:10.1126/sciadv.abm2536 ]
- Envelope glycoprotein ul130 (28 kDa, Protein from Human betaherpesvirus 5)
- Envelope glycoprotein l (30 kDa, Protein from Human betaherpesvirus 5)
- Envelope glycoprotein h (87 kDa, Protein from Human betaherpesvirus 5)
- Fab 13h11 heavy chain (26 kDa, Protein from Homo sapiens)
- Fab msl-109 light chain (28 kDa, Protein from Homo sapiens)
- Complex of 2x hcmv pentamer gh, gl, ul128, ul130, ul131a bound to 1x thbd and 2x fabs of human neutralizing antibodies msl-109 and 13h11 (590 kDa, Complex)
- Envelope protein ul131a (15 kDa, Protein from Human betaherpesvirus 5)
- Fab 13h11 light chain (25 kDa, Protein from Homo sapiens)
- Envelope protein ul128 (19 kDa, Protein from Human betaherpesvirus 5)
- Thrombomodulin (55 kDa, Protein from Homo sapiens)
- Fab msl-109 heavy chain (27 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 7t4s
Q-score: 0.57
Kschonsak M, Johnson MC, Schelling R, Green EM, Rouge L, Ho H, Patel N, Kilic C, Kraft E, Arthur CP, Rohou AL, Comps-Agrar L, Martinez-Martin N, Perez L, Payandeh J, Ciferri C
Sci Adv (2022) 8 pp. eabm2536-eabm2536 [ Pubmed: 35275719 DOI: doi:10.1126/sciadv.abm2536 ]
- Envelope glycoprotein ul130 (28 kDa, Protein from Human betaherpesvirus 5)
- Envelope glycoprotein l (30 kDa, Protein from Human betaherpesvirus 5)
- Envelope glycoprotein h (87 kDa, Protein from Human betaherpesvirus 5)
- Fab 13h11 heavy chain (26 kDa, Protein from Homo sapiens)
- Envelope protein ul131a (15 kDa, Protein from Human betaherpesvirus 5)
- Fab 8i21 heavy chain (26 kDa, Protein from Homo sapiens)
- Neuropilin-2 (98 kDa, Protein from Homo sapiens)
- Fab 8i21 light chain (25 kDa, Protein from Homo sapiens)
- Fab 13h11 light chain (25 kDa, Protein from Homo sapiens)
- Envelope protein ul128 (19 kDa, Protein from Human betaherpesvirus 5)
- Pentameric complex of hcmv proteins gh, gl, ul128, ul130, ul131a bound to neuropilin 2 and fabs of human neutralizing antibodies 8i21 and 13h11 (360 kDa, Complex)
- Calcium ion (40 Da, Ligand)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
Kschonsak M, Johnson MC, Schelling R, Green EM, Rouge L, Ho H, Patel N, Kilic C, Kraft E, Arthur CP, Rohou AL, Comps-Agrar L, Martinez-Martin N, Perez L, Payandeh J, Ciferri C
Sci Adv (2022) 8 pp. eabm2536-eabm2536 [ Pubmed: 35275719 DOI: doi:10.1126/sciadv.abm2536 ]
- Hcmv envelope glycoprotein ul131a (Protein from Human betaherpesvirus 5)
- Hcmv envelope glycoprotein l (Protein from Human betaherpesvirus 5)
- Neuropilin-2 (Protein from Homo sapiens)
- Fab 8i21 heavy chain (Protein from Homo sapiens)
- Fab 13h11 light chain (Protein from Homo sapiens)
- Hcmv envelope glycoprotein ul128 (Protein from Human betaherpesvirus 5)
- Fab 8i21 light chain (Protein from Homo sapiens)
- Hcmv envelope glycoprotein h (Protein from Human betaherpesvirus 5)
- Complex of 2x hcmv pentamer proteins gh, gl, ul128, ul130, ul131a bound to neuropilin 2 and 2x fabs of human neutralizing antibodies 8i21 and 13h11 (720 kDa, Complex)
- Fab 13h11 heavy chain (Protein from Homo sapiens)
- Hcmv envelope glycoprotein ul130 (Protein from Human betaherpesvirus 5)
Cryo-EM of the SLFN12-PDE3A complex: Consensus subset model
Resolution: 3.22 Å
EM Method: Single-particle
Fitted PDBs: 7lrd
Q-score: 0.434
Garvie CW, Wu X, Papanastasiou M, Lee S, Fuller J, Schnitzler GR, Horner SW, Baker A, Zhang T, Mullahoo JP, Westlake L, Hoyt SH, Toetzl M, Ranaghan MJ, de Waal L, McGaunn J, Kaplan B, Piccioni F, Yang X, Lange M, Tersteegen A, Raymond D, Lewis TA, Carr SA, Cherniack AD, Lemke CT, Meyerson M, Greulich H
Nat Commun (2021) 12 pp. 4375-4375 [ DOI: doi:10.1038/s41467-021-24495-w Pubmed: 34272366 ]
- Magnesium ion (24 Da, Ligand)
- Manganese (ii) ion (54 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- (4~{r})-3-[4-(diethylamino)-3-[oxidanyl(oxidanylidene)-$l^{4}-azanyl]phenyl]-4-methyl-4,5-dihydro-1~{h}-pyridazin-6-one (305 Da, Ligand)
- Schlafen family member 12 (67 kDa, Protein from Homo sapiens)
- Slfn12-pde3a complex, consensus subset model (Complex from Homo sapiens)
- Cgmp-inhibited 3',5'-cyclic phosphodiesterase a (57 kDa, Protein from Homo sapiens)
Structure of human TRPA1 in complex with antagonist compound 21
Resolution: 3.05 Å
EM Method: Single-particle
Fitted PDBs: 7jup
Q-score: 0.522
Terrett JA, Chen H, Shore DG, Villemure E, Larouche-Gauthier R, Dery M, Beaumier F, Constantineau-Forget L, Grand-Maitre C, Lepissier L, Ciblat S, Sturino C, Chen Y, Hu B, Lu A, Wang Y, Cridland AP, Ward SI, Hackos DH, Reese RM, Shields SD, Chen J, Balestrini A, Riol-Blanco L, Lee WP, Liu J, Suto E, Wu X, Zhang J, Ly JQ, La H, Johnson K, Baumgardner M, Chou KJ, Rohou A, Rouge L, Safina BS, Magnuson S, Volgraf M
J Med Chem (2021) 64 pp. 3843-3869 [ Pubmed: 33749283 DOI: doi:10.1021/acs.jmedchem.0c02023 ]
Human AAA+ ATPase VCP mutant - T76A, AMP-PNP-bound form, Conformation I
Resolution: 3.3 Å
EM Method: Single-particle
Fitted PDBs: 7bpa
Q-score: 0.512
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. (2022) [ Pubmed: 35430615 DOI: doi:10.1038/s41418-022-01000-4 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Transitional endoplasmic reticulum atpase (89 kDa, Protein from Homo sapiens)
- Phosphoaminophosphonic acid-adenylate ester (506 Da, Ligand)
- Transitional endoplasmic reticulum atpase, vcp. (97 MDa, Complex from Homo sapiens)
Structure of human TRPA1 in complex with inhibitor GDC-0334
Resolution: 3.6 Å
EM Method: Single-particle
Fitted PDBs: 6wj5
Q-score: 0.471
Balestrini A, Joseph V, Dourado M, Reese RM, Shields SD, Rouge L, Bravo DD, Chernov-Rogan T, Austin CD, Chen H, Wang L, Villemure E, Shore DGM, Verma VA, Hu B, Chen Y, Leong L, Bjornson C, Hotzel K, Gogineni A, Lee WP, Suto E, Wu X, Liu J, Zhang J, Gandham V, Wang J, Payandeh J, Ciferri C, Estevez A, Arthur CP, Kortmann J, Wong RL, Heredia JE, Doerr J, Jung M, Vander Heiden JA, Roose-Girma M, Tam L, Barck KH, Carano RAD, Ding HT, Brillantes B, Tam C, Yang X, Gao SS, Ly JQ, Liu L, Chen L, Liederer BM, Lin JH, Magnuson S, Chen J, Hackos DH, Elstrott J, Rohou A, Safina BS, Volgraf M, Bauer RN, Riol-Blanco L
J Exp Med (2021) 218 [ DOI: doi:10.1084/jem.20201637 Pubmed: 33620419 ]
- Transient receptor potential cation channel subfamily a member 1 (72 kDa, Protein from Homo sapiens)
- (4r,5s)-4-fluoro-1-[(4-fluorophenyl)sulfonyl]-5-methyl-n-({5-(trifluoromethyl)-2-[2-(trifluoromethyl)pyrimidin-5-yl]pyridin-4-yl}methyl)-l-prolinamide (609 Da, Ligand)
- Trpa1 bound by inhibitor gdc-0334 (Complex from Homo sapiens)
Structure of human TRPA1 in complex with agonist GNE551
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 6x2j
Q-score: 0.509
Liu C, Reese R, Vu S, Rouge L, Shields SD, Kakiuchi-Kiyota S, Chen H, Johnson K, Shi YP, Chernov-Rogan T, Greiner DMZ, Kohli PB, Hackos D, Brillantes B, Tam C, Li T, Wang J, Safina B, Magnuson S, Volgraf M, Payandeh J, Zheng J, Rohou A, Chen J
Neuron (2021) 109 pp. 273-284.e4 [ Pubmed: 33152265 DOI: doi:10.1016/j.neuron.2020.10.014 ]
GCGR-Gs signaling complex bound to a designed glucagon derivative
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 6wpw
Q-score: 0.518
Hilger D, Kumar KK, Hu H, Pedersen MF, O'Brien ES, Giehm L, Jennings C, Eskici G, Inoue A, Lerch M, Mathiesen JM, Skiniotis G, Kobilka BK
Science (2020) 369 [ DOI: doi:10.1126/science.aba3373 Pubmed: 32732395 ]
- Designed glucagon derivative (Complex from synthetic construct)
- Guanine nucleotide-binding protein g(i)/g(s)/g(t) subunit beta-1 (39 kDa, Protein from Homo sapiens)
- Nb35 (15 kDa, Protein from Lama glama)
- Guanine nucleotide-binding protein g(i)/g(s)/g(o) subunit gamma-2 (7 kDa, Protein from Homo sapiens)
- Gcgr (Complex from Homo sapiens)
- Nb35 (Complex from Lama glama)
- Gcgr-gs signaling complex bound to a designed glucagon derivative (163 kDa, Complex)
- Guanine nucleotide-binding protein g(s) subunit alpha isoforms short (44 kDa, Protein from Homo sapiens)
- Glucagon derivative zp3780 (3 kDa, Protein from synthetic construct)
- Gs (Complex from Homo sapiens)
- Glucagon receptor (56 kDa, Protein from Homo sapiens)