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 [ DOI: doi:10.1021/acs.jmedchem.4c01184 Pubmed: 39190802 ]
- Usp1 bound to ksq-4279 and ubiquitin conjugated to fancd2 (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Ubiquitin carboxyl-terminal hydrolase 1 (88 kDa, Protein from Homo sapiens)
- Polyubiquitin-c (8 kDa, Protein from Homo sapiens)
- 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 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 [ DOI: doi:10.1021/acs.jmedchem.4c01184 Pubmed: 39190802 ]
- Usp1 bound to ml323 and ubiquitin conjugated to fancd2 (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Water (18 Da, Ligand)
- Ubiquitin carboxyl-terminal hydrolase 1 (88 kDa, Protein from Homo sapiens)
- Polyubiquitin-c (8 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)
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 [ Pubmed: 36170365 DOI: doi:10.1126/sciadv.abq6353 ]
- Ubiquitin carboxyl-terminal hydrolase 1 (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Ubiquitin carboxyl-terminal hydrolase 1 (88 kDa, Protein from Homo sapiens)
- Ubiquitin-60s ribosomal protein l40 (Complex from Homo sapiens)
- Usp1(c90s) bound to ubiquitin conjugated to fancd2 (Complex)
- Ubiquitin-60s ribosomal protein l40 (8 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
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 carboxyl-terminal hydrolase 1 (88 kDa, Protein from Homo sapiens)
- Usp1 bound to ml323 and ubiquitin conjugated to fancd2 (Complex from Homo sapiens)
- Ubiquitin-60s ribosomal protein l40 (8 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 [ Pubmed: 36170365 DOI: doi:10.1126/sciadv.abq6353 ]
- Usp1(c90s)-uaf1 bound to fanci and mono-ubiquitinated fancd2 with dsdna and ml323 (Complex)
- Dna (61-mer) (DNA from synthetic construct)
- Polyubiquitin-c (Protein from Homo sapiens)
- Fanconi anemia group i protein (Protein from Homo sapiens)
- Fanconi anemia group d2 protein (Protein from Homo sapiens)
- Ubiquitin carboxyl-terminal hydrolase 1 (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)
- 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 [ Pubmed: 36170365 DOI: doi:10.1126/sciadv.abq6353 ]
- Fanconi anemia group i protein (150 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Ubiquitin carboxyl-terminal hydrolase 1 (88 kDa, Protein 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)
- Wd repeat-containing protein 48 (78 kDa, Protein from Homo sapiens)
- Usp1(c90s)-uaf1 bound to fanci and mono-ubiquitinated fancd2 with dsdna (Complex)
- 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)
Cryo-EM structure of USP1-UAF1 bound to mono-ubiquitinated FANCD2, and FANCI
Resolution: 3.7 Å
EM Method: Single-particle
Fitted PDBs: 7ay1
Q-score: 0.432
Rennie ML, Arkinson C, Chaugule VK, Toth R, Walden H
Nat Struct Mol Biol (2021) 28 pp. 356-364 [ DOI: doi:10.1038/s41594-021-00576-8 Pubmed: 33795880 ]
- Fanconi anemia group i protein (150 kDa, Protein from Homo sapiens)
- Enzyme substrate complex of usp1-uaf1 and fanci-fancd2ub (Complex from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Enzyme substrate complex of usp1-uaf1 and fanci-fancd2ub-dsdna (490 kDa, Complex)
- Ubiquitin carboxyl-terminal hydrolase 1 (88 kDa, Protein from Homo sapiens)
- Fanconi anemia group d2 protein (164 kDa, Protein from Homo sapiens)
- Dna (61-mer) (5 kDa, DNA from synthetic construct)
- Wd repeat-containing protein 48 (78 kDa, Protein from Homo sapiens)
- Dna (Complex from synthetic construct)
- Ubiquitin-60s ribosomal protein l40 (8 kDa, Protein from Homo sapiens)
Cryo-EM structure of the C2S2-type PSII-LHCII supercomplex from Chlamydomonas reihardtii
Resolution: 2.7 Å
EM Method: Single-particle
Fitted PDBs: 6kac
Q-score: 0.569
Sheng X, Watanabe A, Li A, Kim E, Song C, Murata K, Song D, Minagawa J, Liu Z
Nat Plants (2019) 5 pp. 1320-1330 [ Pubmed: 31768031 DOI: doi:10.1038/s41477-019-0543-4 ]
- Chlorophyll a-b binding protein cp29 (29 kDa, Protein from Chlamydomonas reinhardtii)
- Predicted protein (19 kDa, Protein from Chlamydomonas reinhardtii)
- Cytochrome b559 subunit beta (4 kDa, Protein from Chlamydomonas reinhardtii)
- Chlorophyll a-b binding protein, chloroplastic (27 kDa, Protein from Chlamydomonas reinhardtii)
- Chlorophyll a-b binding protein, chloroplastic (27 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii reaction center protein k (5 kDa, Protein from Chlamydomonas reinhardtii)
- Unindentified stromal protein (usp) (2 kDa, Protein from Chlamydomonas reinhardtii)
- 4.1 kda photosystem ii subunit (9 kDa, Protein from Chlamydomonas reinhardtii)
- 2,3-dimethyl-5-(3,7,11,15,19,23,27,31,35-nonamethyl-2,6,10,14,18,22,26,30,34-hexatriacontanonaenyl-2,5-cyclohexadiene-1,4-dione-2,3-dimethyl-5-solanesyl-1,4-benzoquinone (749 Da, Ligand)
- Beta-carotene (536 Da, Ligand)
- Photosystem ii reaction center protein m (3 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii cp47 reaction center protein (56 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii protein d1 (39 kDa, Protein from Chlamydomonas reinhardtii)
- Bicarbonate ion (61 Da, Ligand)
- (1r,3r)-6-{(3e,5e,7e,9e,11e,13e,15e,17e)-18-[(1s,4r,6r)-4-hydroxy-2,2,6-trimethyl-7-oxabicyclo[4.1.0]hept-1-yl]-3,7,12,16-tetramethyloctadeca-1,3,5,7,9,11,13,15,17-nonaenylidene}-1,5,5-trimethylcyclohexane-1,3-diol (600 Da, Ligand)
- Chlorophyll a-b binding protein, chloroplastic (26 kDa, Protein from Chlamydomonas reinhardtii)
- Fe (ii) ion (55 Da, Ligand)
- Chlorophyll b (907 Da, Ligand)
- 1,2-dipalmitoyl-phosphatidyl-glycerole (722 Da, Ligand)
- Photosystem ii cp43 reaction center protein (50 kDa, Protein from Chlamydomonas reinhardtii)
- Chlorophyll a-b binding protein, chloroplastic (30 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii reaction center protein z (6 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii reaction center protein i (4 kDa, Protein from Chlamydomonas reinhardtii)
- Water (18 Da, Ligand)
- 10 kda photosystem ii polypeptide psbr (potential) (1 kDa, Protein from Chlamydomonas reinhardtii)
- Chloride ion (35 Da, Ligand)
- Photosystem ii reaction center protein j (4 kDa, Protein from Chlamydomonas reinhardtii)
- Oxygen-evolving enhancer protein 3, chloroplastic (21 kDa, Protein from Chlamydomonas reinhardtii)
- 1,2-di-o-acyl-3-o-[6-deoxy-6-sulfo-alpha-d-glucopyranosyl]-sn-glycerol (795 Da, Ligand)
- Pheophytin a (871 Da, Ligand)
- Photosystem ii reaction center w protein, chloroplastic (12 kDa, Protein from Chlamydomonas reinhardtii)
- Digalactosyl diacyl glycerol (dgdg) (949 Da, Ligand)
- Cytochrome b559 subunit alpha (9 kDa, Protein from Chlamydomonas reinhardtii)
- (3s,5r,6s,3's,5'r,6's)-5,6,5',6'-diepoxy-5,6,5',6'- tetrahydro-beta,beta-carotene-3,3'-diol (600 Da, Ligand)
- 1,2-distearoyl-monogalactosyl-diglyceride (787 Da, Ligand)
- Photosystem ii reaction center protein l (4 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii reaction center protein t (3 kDa, Protein from Chlamydomonas reinhardtii)
- (3r,3'r,6s)-4,5-didehydro-5,6-dihydro-beta,beta-carotene-3,3'-diol (568 Da, Ligand)
- Photosystem ii reaction center protein h (9 kDa, Protein from Chlamydomonas reinhardtii)
- Protoporphyrin ix containing fe (616 Da, Ligand)
- Oxygen-evolving enhancer protein 1, chloroplastic (30 kDa, Protein from Chlamydomonas reinhardtii)
- Dodecyl-alpha-d-maltoside (510 Da, Ligand)
- Ca-mn4-o5 cluster (339 Da, Ligand)
- The c2s2-type psii-lhcii supercomplex (Complex from Chlamydomonas reinhardtii)
- Photosystem ii reaction center protein ycf12 (3 kDa, Protein from Chlamydomonas reinhardtii)
- Chlorophyll a (893 Da, Ligand)
- Oxygen-evolving enhancer protein 2, chloroplastic (25 kDa, Protein from Chlamydomonas reinhardtii)
- Photosystem ii d2 protein (39 kDa, Protein from Chlamydomonas reinhardtii)