Hofler A, Yu J, Yang J, Zhang Z, Chang L, McLaughlin SH, Grime GW, Garman EF, Boland A, Barford D
Nat Commun (2024) 15 pp. 10074-10074 [ DOI: doi:10.1038/s41467-024-54398-5 Pubmed: 39567505 ]
- F-box only protein 5 (50 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Fizzy-related protein homolog (55 kDa, Protein from Homo sapiens)
- Anaphase-promoting complex (apc/c) bound to co-activator cdh1 (1 MDa, Complex from Homo sapiens)
- Anaphase-promoting complex subunit 11 (9 kDa, Protein from Homo sapiens)
- Anaphase-promoting complex subunit 16 (11 kDa, Protein from Homo sapiens)
- Cell division cycle protein 27 homolog (91 kDa, Protein from Homo sapiens)
- Anaphase-promoting complex subunit 5 (85 kDa, Protein from Homo sapiens)
- Cell division cycle protein 23 homolog (68 kDa, Protein from Homo sapiens)
- Anaphase-promoting complex subunit 10 (21 kDa, Protein from Homo sapiens)
- Anaphase-promoting complex subunit 1 (216 kDa, Protein from Homo sapiens)
- Anaphase-promoting complex subunit cdc26 (9 kDa, Protein from Homo sapiens)
- Cell division cycle protein 16 homolog (71 kDa, Protein from Homo sapiens)
- Anaphase-promoting complex subunit 15 (14 kDa, Protein from Homo sapiens)
- Anaphase-promoting complex subunit 13 (8 kDa, Protein from Homo sapiens)
- Anaphase-promoting complex subunit 7 (66 kDa, Protein from Homo sapiens)
- Anaphase-promoting complex subunit 4 (93 kDa, Protein from Homo sapiens)
- Anaphase-promoting complex subunit 2 (93 kDa, Protein from Homo sapiens)
Outer kinetochore Ndc80-Dam1 alpha/beta-tubulin complex
Resolution: 3.54 Å
EM Method: Single-particle
Fitted PDBs: 8qau
Q-score: 0.343
Muir KW, Batters C, Dendooven T, Yang J, Zhang Z, Burt A, Barford D
bioRxiv (2023) [ DOI: doi:10.1101/2023.07.20.549907 ]
- Dash complex subunit dam1 (38 kDa, Protein from Saccharomyces cerevisiae)
- Guanosine-5'-diphosphate (443 Da, Ligand)
- Kinetochore protein nuf2 (53 kDa, Protein from Saccharomyces cerevisiae)
- Outer kinetochore ndc80-nuf2 ch domains bound to dam1 in complex with alpha-beta tubulin (Complex from Saccharomyces cerevisiae)
- Guanosine-5'-triphosphate (523 Da, Ligand)
- Tubulin alpha-1a chain (50 kDa, Protein from Sus scrofa)
- Kinetochore protein ndc80 (80 kDa, Protein from Saccharomyces cerevisiae)
- Tubulin beta chain (49 kDa, Protein from Sus scrofa)
- Magnesium ion (24 Da, Ligand)
- Taxol (853 Da, Ligand)
Structure of the human outer kinetochore KMN network complex
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 8ppr
Q-score: 0.341
Yatskevich S, Yang J, Bellini D, Zhang Z, Barford D
Nat Struct Mol Biol (2024) 31 pp. 874-883 [ DOI: doi:10.1038/s41594-024-01249-y Pubmed: 38459127 ]
- Kinetochore scaffold 1 (265 kDa, Protein from Homo sapiens)
- Protein mis12 homolog (24 kDa, Protein from Homo sapiens)
- Kinetochore protein spc25 (26 kDa, Protein from Homo sapiens)
- Water (18 Da, Ligand)
- Kinetochore protein spc24 (22 kDa, Protein from Homo sapiens)
- Zw10 interactor (31 kDa, Protein from Homo sapiens)
- Kinetochore-associated protein dsn1 homolog (40 kDa, Protein from Homo sapiens)
- Outer kinetochore kmn network junction complex (Complex from Homo sapiens)
- Kinetochore-associated protein nsl1 homolog (32 kDa, Protein from Homo sapiens)
- Polyamine-modulated factor 1 (23 kDa, Protein from Homo sapiens)
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8s4g, 9gaw
Q-score: 0.37
Hofler A, Yu J, Yang J, Zhang Z, Chang L, McLaughlin SH, Grime GW, Garman EF, Boland A, Barford D
Nat Commun (2024) 15 pp. 10074-10074 [ DOI: doi:10.1038/s41467-024-54398-5 Pubmed: 39567505 ]
- F-box only protein 5 (50 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Fizzy-related protein homolog (55 kDa, Protein from Homo sapiens)
- Anaphase-promoting complex (apc/c) bound to co-activator cdh1 (1 MDa, Complex from Homo sapiens)
- Anaphase-promoting complex subunit 11 (9 kDa, Protein from Homo sapiens)
- Anaphase-promoting complex subunit 16 (11 kDa, Protein from Homo sapiens)
- Cell division cycle protein 27 homolog (91 kDa, Protein from Homo sapiens)
- Anaphase-promoting complex subunit 5 (85 kDa, Protein from Homo sapiens)
- Cell division cycle protein 23 homolog (68 kDa, Protein from Homo sapiens)
- Anaphase-promoting complex subunit 10 (21 kDa, Protein from Homo sapiens)
- Anaphase-promoting complex subunit 1 (216 kDa, Protein from Homo sapiens)
- Anaphase-promoting complex subunit cdc26 (9 kDa, Protein from Homo sapiens)
- Cell division cycle protein 16 homolog (71 kDa, Protein from Homo sapiens)
- Anaphase-promoting complex subunit 15 (14 kDa, Protein from Homo sapiens)
- Anaphase-promoting complex subunit 13 (8 kDa, Protein from Homo sapiens)
- Anaphase-promoting complex subunit 7 (66 kDa, Protein from Homo sapiens)
- Anaphase-promoting complex subunit 4 (93 kDa, Protein from Homo sapiens)
- Anaphase-promoting complex subunit 2 (93 kDa, Protein from Homo sapiens)
The cryo-EM structure of human sphingomyelin synthase-related protein in complex with ceramide
Resolution: 3.45 Å
EM Method: Single-particle
Fitted PDBs: 8ijq
Q-score: 0.461
Resolution: 3.29 Å
EM Method: Single-particle
Fitted PDBs: 8ijr
Q-score: 0.485
Hu K, Zhang Q, Chen Y, Yang J, Xia Y, Rao B, Li S, Shen Y, Cao M, Lu H, Qin A, Jiang XC, Yao D, Zhao J, Zhou L, Cao Y
Nat Struct Mol Biol (2024) 31 pp. 884-895 [ DOI: doi:10.1038/s41594-024-01237-2 Pubmed: 38388831 ]
- Phosphoric acid mono-(2-amino-ethyl) ester (141 Da, Ligand)
- Sphingomyelin synthase-related protein 1 (48 kDa, Protein from Homo sapiens)
- The cryo-em structure of human sphingomyelin synthase-related protein in complex with diacylglycerol/phosphoethanolamine (Complex from Homo sapiens)
- (2s)-1-(hexadecanoyloxy)-3-hydroxypropan-2-yl (11z)-octadec-11-enoate (594 Da, Ligand)
Resolution: 3.74 Å
EM Method: Single-particle
Fitted PDBs: 8w9w
Q-score: 0.377
Hu K, Zhang Q, Chen Y, Yang J, Xia Y, Rao B, Li S, Shen Y, Cao M, Lu H, Qin A, Jiang XC, Yao D, Zhao J, Zhou L, Cao Y
Nat Struct Mol Biol (2024) 31 pp. 884-895 [ DOI: doi:10.1038/s41594-024-01237-2 Pubmed: 38388831 ]
- Phosphoric acid mono-(2-amino-ethyl) ester (141 Da, Ligand)
- Sphingomyelin synthase-related protein 1 (31 kDa, Protein from Homo sapiens)
- The cryo-em structure of human sphingomyelin synthase-related protein in complex with ceramide/phosphoethanolamine (Complex from Homo sapiens)
- ~{n}-[(~{z},2~{s},3~{r})-1,3-bis(oxidanyl)heptadec-4-en-2-yl]dodecanamide (467 Da, Ligand)
Cryo-EM structure of the apo Anaphase-promoting complex/cyclosome (APC/C) at 3.2 Angstrom resolution
Resolution: 3.2 Å
EM Method: Single-particle
Fitted PDBs: 8pkp
Q-score: 0.409
Hofler A, Yu J, Yang J, Zhang Z, Chang L, McLaughlin SH, Grime GW, Garman EF, Boland A, Barford D
Nat Commun (2024) 15 pp. 10074-10074 [ DOI: doi:10.1038/s41467-024-54398-5 Pubmed: 39567505 ]
- Zinc ion (65 Da, Ligand)
- Apo anaphase-promoting complex (apc/c) (1 MDa, Complex from Homo sapiens)
- Anaphase-promoting complex subunit 11 (9 kDa, Protein from Homo sapiens)
- Anaphase-promoting complex subunit 16 (11 kDa, Protein from Homo sapiens)
- Cell division cycle protein 27 homolog (91 kDa, Protein from Homo sapiens)
- Anaphase-promoting complex subunit 4 (93 kDa, Protein from Homo sapiens)
- Anaphase-promoting complex subunit 5 (85 kDa, Protein from Homo sapiens)
- Cell division cycle protein 23 homolog (68 kDa, Protein from Homo sapiens)
- Anaphase-promoting complex subunit cdc26 (9 kDa, Protein from Homo sapiens)
- Anaphase-promoting complex subunit 1 (216 kDa, Protein from Homo sapiens)
- Anaphase-promoting complex subunit 10 (21 kDa, Protein from Homo sapiens)
- Anaphase-promoting complex subunit 13 (8 kDa, Protein from Homo sapiens)
- Anaphase-promoting complex subunit 15 (14 kDa, Protein from Homo sapiens)
- Anaphase-promoting complex subunit 7 (63 kDa, Protein from Homo sapiens)
- Cell division cycle protein 16 homolog (71 kDa, Protein from Homo sapiens)
- Anaphase-promoting complex subunit 2 (93 kDa, Protein from Homo sapiens)
The 5-MTHF-bound BRIL-SLC19A1/Fab/Nb ternary complex
Resolution: 3.54 Å
EM Method: Single-particle
Fitted PDBs: 8hij
Q-score: 0.296
Dang Y, Zhou D, Du X, Zhao H, Lee CH, Yang J, Wang Y, Qin C, Guo Z, Zhang Z
Cell Discov (2022) 8 pp. 141-141 [ Pubmed: 36575193 DOI: doi:10.1038/s41421-022-00508-w ]
- Anti-bril fab light chain (25 kDa, Protein from Homo sapiens)
- The 5-mthf-bound bril-slc19a1/fab/nb ternary complex (Complex from Homo sapiens)
- Bril-slc19a1 chimera (75 kDa, Protein from Homo sapiens)
- Anti-fab nanobody (16 kDa, Protein from Lama glama)
- N-[4-({[(6s)-2-amino-4-hydroxy-5-methyl-5,6,7,8-tetrahydropteridin-6-yl]methyl}amino)benzoyl]-l-glutamic acid (459 Da, Ligand)
- Anti-bril fab heavy chain (27 kDa, Protein from Homo sapiens)
The TPP-bound BRIL-SLC19A1/Fab/Nb ternary complex
Resolution: 3.72 Å
EM Method: Single-particle
Fitted PDBs: 8hik
Q-score: 0.249
Dang Y, Zhou D, Du X, Zhao H, Lee CH, Yang J, Wang Y, Qin C, Guo Z, Zhang Z
Cell Discov (2022) 8 pp. 141-141 [ Pubmed: 36575193 DOI: doi:10.1038/s41421-022-00508-w ]
- Thiamine diphosphate (425 Da, Ligand)
- The tpp-bound bril-slc19a1/fab/nb ternary complex (Complex from Homo sapiens)
- Anti-bril fab light chain (25 kDa, Protein from Homo sapiens)
- Bril-slc19a1 chimera (75 kDa, Protein from Homo sapiens)
- Anti-fab nanobody (16 kDa, Protein from Lama glama)
- Anti-bril fab heavy chain (27 kDa, Protein from Homo sapiens)