USP1-UAF1 bound to Lys63-linked diubiquitin
Resolution: 3.04 Å
EM Method: Single-particle
Fitted PDBs: 9hnw
Q-score: 0.422
Keijzer N, Sixma TK, Sakoltchik J
To Be Published
- Polyubiquitin-b (8 kDa, Protein from Homo sapiens)
- Usp1-uaf1 bound to lys63-linked diubiquitin (Complex from Homo sapiens)
- Ubiquitin carboxyl-terminal hydrolase 1 (91 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Wd repeat-containing protein 48 (80 kDa, Protein from Homo sapiens)
- Polyubiquitin-b (8 kDa, Protein from Homo sapiens)
Cryo-EM structure of USP1-UAF1-Ubiquitin in complex with TNG348
Simoneau A, Pratt CB, Wu HJ, Rajeswaran SS, Comer CG, Sudsakorn S, Zhang W, Liu S, Meier SR, Choi AH, Khendu T, Stowe H, Shen B, Whittington DA, Chen Y, Yu Y, Mallender WD, Feng T, Andersen JN, Maxwell JP, Throner S
Mol.Cancer Ther. (2025) [ DOI: doi:10.1158/1535-7163.MCT-24-0515 Pubmed: 39886906 ]
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- 2-(4-cyclopropyl-6-methoxypyrimidin-5-yl)-9-({4-[1-methyl-4-(trifluoromethyl)-1h-imidazol-2-yl]phenyl}methyl)-7-(2,2,2-trifluoroethyl)-7,9-dihydro-8h-purin-8-imine (603 Da, Ligand)
- Wd repeat-containing protein 48 (77 kDa, Protein from Homo sapiens)
- Usp1-uaf1-ub complex with tng348 (174 kDa, Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- 3-(methanesulfonyl)propan-1-amine (137 Da, Ligand)
- Ubiquitin carboxyl-terminal hydrolase 1 (88 kDa, Protein from Homo sapiens)
USP1 bound to KSQ-4279 and ubiquitin conjugated to FANCD2 (focused refinement)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 9fci
Q-score: 0.525
Rennie ML, Gundogdu M, Arkinson C, Liness S, Frame S, Walden H
J Med Chem (2024) 67 pp. 15557-15568 [ Pubmed: 39190802 DOI: doi:10.1021/acs.jmedchem.4c01184 ]
- Ubiquitin carboxyl-terminal hydrolase 1 (88 kDa, Protein from Homo sapiens)
- Polyubiquitin-c (8 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- 6-(4-cyclopropyl-6-methoxy-pyrimidin-5-yl)-1-[[4-[1-propan-2-yl-4-(trifluoromethyl)imidazol-2-yl]phenyl]methyl]pyrazolo[3,4-d]pyrimidine (534 Da, Ligand)
- Usp1 bound to ksq-4279 and ubiquitin conjugated to fancd2 (Complex from Homo sapiens)
USP1 bound to ML323 and ubiquitin conjugated to FANCD2 (ordered subset, focused refinement)
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 9fcj
Q-score: 0.618
Rennie ML, Gundogdu M, Arkinson C, Liness S, Frame S, Walden H
J Med Chem (2024) 67 pp. 15557-15568 [ Pubmed: 39190802 DOI: doi:10.1021/acs.jmedchem.4c01184 ]
- Ubiquitin carboxyl-terminal hydrolase 1 (88 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- 5-methyl-2-(2-propan-2-ylphenyl)-~{n}-[[4-(1,2,3-triazol-1-yl)phenyl]methyl]pyrimidin-4-amine (384 Da, Ligand)
- Polyubiquitin-c (8 kDa, Protein from Homo sapiens)
- Usp1 bound to ml323 and ubiquitin conjugated to fancd2 (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
Cryo-EM structure of USP16 bound to H2AK119Ub nucleosome
Resolution: 3.05 Å
EM Method: Single-particle
Fitted PDBs: 8wg5
Q-score: 0.306
Ai H, He Z, Deng Z, Chu GC, Shi Q, Tong Z, Li JB, Pan M, Liu L
Nat Struct Mol Biol (2024) 31 pp. 1745-1755 [ Pubmed: 38918638 DOI: doi:10.1038/s41594-024-01342-2 ]
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Histone h2a type 1-b/e (12 kDa, Protein from Homo sapiens)
- Ubiquitin b (8 kDa, Protein from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
- Complex of usp16 bound to h2ak119ub nucleosome (Complex from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Ubiquitin carboxyl-terminal hydrolase 16 (93 kDa, Protein from Homo sapiens)
- Histone h3.1 (11 kDa, Protein from Homo sapiens)
USP1 bound to ubiquitin conjugated to FANCD2 (focused refinement)
Resolution: 2.5 Å
EM Method: Single-particle
Fitted PDBs: 7zh3
Q-score: 0.662
Rennie ML, Arkinson C, Chaugule VK, Walden H
Sci Adv (2022) 8 pp. eabq6353-eabq6353 [ DOI: doi:10.1126/sciadv.abq6353 Pubmed: 36170365 ]
- Usp1(c90s) bound to ubiquitin conjugated to fancd2 (Complex)
- Ubiquitin-60s ribosomal protein l40 (Complex from Homo sapiens)
- Ubiquitin carboxyl-terminal hydrolase 1 (88 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Ubiquitin-60s ribosomal protein l40 (8 kDa, Protein from Homo sapiens)
- Ubiquitin carboxyl-terminal hydrolase 1 (Complex from Homo sapiens)
USP1 bound to ML323 and ubiquitin conjugated to FANCD2 (focused refinement)
Resolution: 2.49 Å
EM Method: Single-particle
Fitted PDBs: 7zh4
Q-score: 0.657
Rennie ML, Arkinson C, Chaugule VK, Walden H
Sci Adv (2022) 8 pp. eabq6353-eabq6353 [ Pubmed: 36170365 DOI: doi:10.1126/sciadv.abq6353 ]
- Zinc ion (65 Da, Ligand)
- Water (18 Da, Ligand)
- Ubiquitin-60s ribosomal protein l40 (8 kDa, Protein from Homo sapiens)
- Usp1 bound to ml323 and ubiquitin conjugated to fancd2 (Complex from Homo sapiens)
- Ubiquitin carboxyl-terminal hydrolase 1 (88 kDa, Protein from Homo sapiens)
- 5-methyl-2-(2-propan-2-ylphenyl)-~{n}-[[4-(1,2,3-triazol-1-yl)phenyl]methyl]pyrimidin-4-amine (384 Da, Ligand)
Rennie ML, Arkinson C, Chaugule VK, Walden H
Sci Adv (2022) 8 pp. eabq6353-eabq6353 [ DOI: doi:10.1126/sciadv.abq6353 Pubmed: 36170365 ]
- Fanconi anemia group d2 protein (Protein from Homo sapiens)
- Fanconi anemia group i protein, fanconi anemia group d2 protein with ubiquitin conjugated to k561, ubiquitin carboxyl-terminal hydrolase 1, wd repeat-containing protein 48 (Complex from Homo sapiens)
- Fanconi anemia group i protein (Protein from Homo sapiens)
- Usp1(c90s)-uaf1 bound to fanci and mono-ubiquitinated fancd2 with dsdna and ml323 (Complex)
- Polyubiquitin-c (Protein from Homo sapiens)
- Dna (61-mer) (DNA from synthetic construct)
- Ubiquitin carboxyl-terminal hydrolase 1 (Protein from Homo sapiens)
- Wd repeat-containing protein 48 (Protein from Homo sapiens)
Resolution: 2.8 Å
EM Method: Single-particle
Fitted PDBs: 8a9j
Q-score: 0.553
Rennie ML, Arkinson C, Chaugule VK, Walden H
Sci Adv (2022) 8 pp. eabq6353-eabq6353 [ DOI: doi:10.1126/sciadv.abq6353 Pubmed: 36170365 ]
- Usp1(c90s)-uaf1 bound to fanci and mono-ubiquitinated fancd2 with dsdna (Complex)
- Wd repeat-containing protein 48 (78 kDa, Protein from Homo sapiens)
- Ubiquitin carboxyl-terminal hydrolase 1 (88 kDa, Protein from Homo sapiens)
- Fanconi anemia group i protein, fanconi anemia group d2 protein with ubiquitin conjugated to k561, ubiquitin carboxyl-terminal hydrolase 1, wd repeat-containing protein 48 (Complex from Homo sapiens)
- Fanconi anemia group d2 protein (164 kDa, Protein from Homo sapiens)
- Polyubiquitin-c (8 kDa, Protein from Homo sapiens)
- Dna (61-mer) (5 kDa, DNA from synthetic construct)
- Zinc ion (65 Da, Ligand)
- Fanconi anemia group i protein (150 kDa, Protein from Homo sapiens)
Structure of USP14-bound human 26S proteasome in substrate-inhibited state SB_USP14
Resolution: 3.5 Å
EM Method: Single-particle
Fitted PDBs: 7w3i
Q-score: 0.358
Zhang S, Zou S, Yin D, Zhao L, Finley D, Wu Z, Mao Y
Nature (2022) 605 pp. 567-574 [ DOI: doi:10.1038/s41586-022-04671-8 Pubmed: 35477760 ]
- Proteasome subunit beta type-4 (29 kDa, Protein from Homo sapiens)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Usp14 (Complex)
- Isoform 2 of 26s proteasome regulatory subunit 8 (44 kDa, Protein from Homo sapiens)
- Proteasome subunit beta type-1 (26 kDa, Protein from Homo sapiens)
- 26s proteasome non-atpase regulatory subunit 2 (100 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Proteasome subunit beta type-3 (22 kDa, Protein from Homo sapiens)
- Proteasome subunit beta type-2 (22 kDa, Protein from Homo sapiens)
- Proteasome subunit alpha type-6 (27 kDa, Protein from Homo sapiens)
- Proteasome subunit alpha type-3 (28 kDa, Protein from Homo sapiens)
- 26s protease regulatory subunit 6a (49 kDa, Protein from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 26s proteasome non-atpase regulatory subunit 1 (105 kDa, Protein from Homo sapiens)
- 26s protease regulatory subunit 4 (49 kDa, Protein from Homo sapiens)
- 26s proteasome (Complex from Homo sapiens)
- 26s proteasome non-atpase regulatory subunit 11 (47 kDa, Protein from Homo sapiens)
- Proteasome subunit beta type-7 (30 kDa, Protein from Homo sapiens)
- Isoform long of proteasome subunit alpha type-1 (30 kDa, Protein from Homo sapiens)
- 26s proteasome regulatory subunit 10b (45 kDa, Protein from Homo sapiens)
- 26s proteasome non-atpase regulatory subunit 13 (42 kDa, Protein from Homo sapiens)
- 26s proteasome non-atpase regulatory subunit 3 (61 kDa, Protein from Homo sapiens)
- 26s proteasome non-atpase regulatory subunit 12 (52 kDa, Protein from Homo sapiens)
- 26s proteasome non-atpase regulatory subunit 14 (34 kDa, Protein from Homo sapiens)
- 26s proteasome non-atpase regulatory subunit 8 (39 kDa, Protein from Homo sapiens)
- 26s proteasome (1 MDa, Complex from Homo sapiens)
- 26s protease regulatory subunit 7 (48 kDa, Protein from Homo sapiens)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Ubiquitin carboxyl-terminal hydrolase 14 (56 kDa, Protein from Homo sapiens)
- 26s proteasome non-atpase regulatory subunit 6 (45 kDa, Protein from Homo sapiens)
- 26s proteasome non-atpase regulatory subunit 7 (37 kDa, Protein from Homo sapiens)
- Proteasome subunit alpha type-5 (26 kDa, Protein from Homo sapiens)
- 26s proteasome non-atpase regulatory subunit 4 (40 kDa, Protein from Homo sapiens)
- 26s proteasome complex subunit dss1 (8 kDa, Protein from Homo sapiens)
- Proteasome subunit beta type-6 (25 kDa, Protein from Homo sapiens)
- 26s protease regulatory subunit 6b (47 kDa, Protein from Homo sapiens)
- Proteasome subunit alpha type-4 (29 kDa, Protein from Homo sapiens)
- Proteasome subunit alpha type-2 (25 kDa, Protein from Homo sapiens)
- Proteasome subunit alpha type-7 (27 kDa, Protein from Homo sapiens)
- Proteasome subunit beta type-5 (28 kDa, Protein from Homo sapiens)