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)
- 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)
- Transitional endoplasmic reticulum atpase (89 kDa, Protein from Homo sapiens)
- P97/vcp aaa+ atpase r155h mutant/nsc804515 (536 kDa, Complex from Homo sapiens)
Resolution: 3.14 Å
EM Method: Single-particle
Fitted PDBs: 8cyi
Q-score: 0.451
Zhou W, Yadav GP, Yang X, Qin F, Li C, Jiang QX
Commun Biol (2022) 5 pp. 1054-1054 [ Pubmed: 36192627 DOI: doi:10.1038/s42003-022-03991-9 ]
- 5'-deoxy-5'-methylthioadenosine (297 Da, Ligand)
- Methylosome protein 50 (33 kDa, Protein from Homo sapiens)
- N-[(2-aminoquinolin-7-yl)methyl]-9-(2-hydroxyethyl)-2,3,4,9-tetrahydro-1h-carbazole-6-carboxamide (414 Da, Ligand)
- Complex of prmt5 and mep50 in the presence of mta and a novel inhibitor (11-2f) (440 kDa, Complex from Homo sapiens)
- Protein arginine n-methyltransferase 5 (72 kDa, Protein from Homo sapiens)
Structure of VSD4-NaV1.7-NaVPas channel chimera bound to the hybrid inhibitor GNE-9296
Resolution: 3.1 Å
EM Method: Single-particle
Fitted PDBs: 8f0s
Q-score: 0.614
Kschonsak M, Jao CC, Arthur CP, Rohou AL, Bergeron P, Ortwine DF, McKerrall SJ, Hackos DH, Deng L, Chen J, Li T, Dragovich PS, Volgraf M, Wright MR, Payandeh J, Ciferri C, Tellis JC
eLife (2023) 12 [ Pubmed: 36975198 DOI: doi:10.7554/eLife.84151 ]
- Sodium channel protein pafpc1,sodium channel protein type 9 subunit alpha chimera (184 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (744 Da, Ligand)
- Beta-diguetoxin-dc1a (8 kDa, Protein from Diguetia canities)
- Cholesterol hemisuccinate (486 Da, Ligand)
- 5-chloro-4-(cyclopentylmethoxy)-n-(4-{[(1s,2s)-2-(dimethylamino)cyclohexyl]amino}-2-fluorobenzene-1-sulfonyl)-2-fluorobenzamide (570 Da, Ligand)
- Vsd4-nav1.7-navpas channel chimera bound to the hybrid inhibitor gne-9296 (Complex from Homo sapiens)
CryoEM Structure of NLRP3 NACHT domain in complex with G2394
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 8etr
Q-score: 0.488
McBride C, Trzoss L, Povero D, Lazic M, Ambrus-Aikelin G, Santini A, Pranadinata R, Bain G, Stansfield R, Stafford JA, Veal J, Takahashi R, Ly J, Chen S, Liu L, Nespi M, Blake R, Katewa A, Kleinheinz T, Sujatha-Bhaskar S, Ramamoorthi N, Sims J, McKenzie B, Chen M, Ultsch M, Johnson M, Murray J, Ciferri C, Staben ST, Townsend MJ, Stivala CE
J Med Chem (2022) 65 pp. 14721-14739 [ DOI: doi:10.1021/acs.jmedchem.2c01250 Pubmed: 36279149 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- (6s,8r)-n-[(1,2,3,5,6,7-hexahydro-s-indacen-4-yl)carbamoyl]-6-(methylamino)-6,7-dihydro-5h-pyrazolo[5,1-b][1,3]oxazine-3-sulfonamide (431 Da, Ligand)
- Nlrp3 nacht domain (120 kDa, Complex from Homo sapiens)
- Magnesium ion (24 Da, Ligand)
- Nacht, lrr and pyd domains-containing protein 3 (63 kDa, Protein from Homo sapiens)
Harrison JJEK, Passos DO, Bruhn JF, Bauman JD, Tuberty L, DeStefano JJ, Ruiz FX, Lyumkis D, Arnold E
Sci Adv (2022) 8 pp. eabn9874-eabn9874 [ Pubmed: 35857464 DOI: doi:10.1126/sciadv.abn9874 ]
Subtomogram averaging of Rubiscos along the shell of Halothiobacillus carboxysome
Ni T, Sun Y, Burn W, Al-Hazeem MMJ, Zhu Y, Yu X, Liu LN, Zhang P
Nat Commun (2022) 13 pp. 4299-4299 [ DOI: doi:10.1038/s41467-022-32004-w Pubmed: 35879301 ]
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 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Thrombomodulin (55 kDa, Protein from Homo sapiens)
- Fab msl-109 heavy chain (27 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 ul128 (19 kDa, Protein from Human betaherpesvirus 5)
- Envelope glycoprotein l (30 kDa, Protein from Human betaherpesvirus 5)
- Envelope glycoprotein ul130 (28 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)
- Envelope glycoprotein h (87 kDa, Protein from Human betaherpesvirus 5)
- Fab 13h11 light chain (25 kDa, Protein from Homo sapiens)
- Fab msl-109 light chain (28 kDa, Protein from Homo sapiens)
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 ]
- Fab 8i21 light chain (25 kDa, Protein from Homo sapiens)
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Calcium ion (40 Da, Ligand)
- Envelope protein ul128 (19 kDa, Protein from Human betaherpesvirus 5)
- Envelope glycoprotein l (30 kDa, Protein from Human betaherpesvirus 5)
- Envelope glycoprotein ul130 (28 kDa, Protein from Human betaherpesvirus 5)
- Fab 8i21 heavy chain (26 kDa, Protein from Homo sapiens)
- Neuropilin-2 (98 kDa, Protein from Homo sapiens)
- 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)
- Fab 13h11 heavy chain (26 kDa, Protein from Homo sapiens)
- Envelope protein ul131a (15 kDa, Protein from Human betaherpesvirus 5)
- Envelope glycoprotein h (87 kDa, Protein from Human betaherpesvirus 5)
- Fab 13h11 light chain (25 kDa, Protein from Homo sapiens)
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 h (Protein from Human betaherpesvirus 5)
- Fab 13h11 heavy chain (Protein from Homo sapiens)
- Hcmv envelope glycoprotein ul128 (Protein from Human betaherpesvirus 5)
- Hcmv envelope glycoprotein ul130 (Protein from Human betaherpesvirus 5)
- Hcmv envelope glycoprotein l (Protein from Human betaherpesvirus 5)
- Fab 13h11 light chain (Protein from Homo sapiens)
- 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 8i21 light chain (Protein from Homo sapiens)
- Hcmv envelope glycoprotein ul131a (Protein from Human betaherpesvirus 5)
- Fab 8i21 heavy chain (Protein from Homo sapiens)
- Neuropilin-2 (Protein from Homo sapiens)
Resolution: 3.65 Å
EM Method: Single-particle
Fitted PDBs: 7lwd
Q-score: 0.466
Plenge P, Yang D, Salomon K, Laursen L, Kalenderoglou IE, Newman AH, Gouaux E, Coleman JA, Loland CJ
Nat Commun (2021) 12 pp. 5063-5063 [ Pubmed: 34417466 DOI: doi:10.1038/s41467-021-25363-3 ]
- 2-acetamido-2-deoxy-beta-d-glucopyranose (221 Da, Ligand)
- Serotonin transporter (Complex from Homo sapiens)
- 8b6 antibody (Complex from Mus musculus)
- 3-(5h-dibenzo[b,f]azepin-5-yl)-n,n-dimethylpropan-1-amine (280 Da, Ligand)
- Light chain antibody fragment (11 kDa, Protein from Mus musculus)
- Heavy chain antibody fragment (12 kDa, Protein from Mus musculus)
- 5-{4-[4-(5-cyano-1h-indol-3-yl)butyl]piperazin-1-yl}-1-benzofuran-2-carboxamide (441 Da, Ligand)
- Serotonin transporter 8b6 fab complex (105 kDa, Complex)
- Sodium-dependent serotonin transporter (61 kDa, Protein from Homo sapiens)