Bre1(mRBD-RING)/Rad6-Ub/nucleosome complex
Resolution: 3.44 Å
EM Method: Single-particle
Fitted PDBs: 8ieg
Q-score: 0.393
Deng Z, Ai H, Sun M, Tong Z, Du Y, Qu Q, Zhang L, Xu Z, Tao S, Shi Q, Li JB, Pan M, Liu L
Mol Cell (2023) 83 pp. 3080-3094.e14 [ Pubmed: 37633270 DOI: doi:10.1016/j.molcel.2023.08.001 ]
- Zinc ion (65 Da, Ligand)
- Histone h3.1 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 2 (16 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Bre1(mrbd-ring)/rad6-ub in complex with nucleosome (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- E3 ubiquitin-protein ligase bre1 (7 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Histone h4 (9 kDa, Protein from Homo sapiens)
RNF20-RNF40/hRad6A-Ub/nucleosome complex
Resolution: 3.12 Å
EM Method: Single-particle
Fitted PDBs: 8iej
Q-score: 0.461
Deng Z, Ai H, Sun M, Tong Z, Du Y, Qu Q, Zhang L, Xu Z, Tao S, Shi Q, Li JB, Pan M, Liu L
Mol Cell (2023) 83 pp. 3080-3094.e14 [ Pubmed: 37633270 DOI: doi:10.1016/j.molcel.2023.08.001 ]
- E3 ubiquitin-protein ligase bre1b (7 kDa, Protein from Homo sapiens)
- Zinc ion (65 Da, Ligand)
- Histone h3.1 (11 kDa, Protein from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Histone h2a type 1-b/e (11 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- Histone h2b type 1-k (10 kDa, Protein from Homo sapiens)
- Rnf20-rnf40/hrad6a-ub in complex with nucleosome (Complex from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 a (17 kDa, Protein from Homo sapiens)
- Dna (147-mer) (45 kDa, DNA from Homo sapiens)
- E3 ubiquitin-protein ligase bre1a (7 kDa, Protein from Homo sapiens)
- Histone h4 (9 kDa, Protein from Homo sapiens)
Structure of yeast Ubr1 in complex with Ubc2 and N-degron
Resolution: 3.35 Å
EM Method: Single-particle
Fitted PDBs: 7mex
Q-score: 0.45
Pan M, Zheng Q, Wang T, Liang L, Mao J, Zuo C, Ding R, Ai H, Xie Y, Si D, Yu Y, Liu L, Zhao M
Nature (2021) 600 pp. 334-338 [ Pubmed: 34789879 DOI: doi:10.1038/s41586-021-04097-8 ]
- Zinc ion (65 Da, Ligand)
- E3 ubiquitin-protein ligase ubr1 (225 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Ubiquitin-conjugating enzyme e2 2 (17 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Yeast ubr1 in complex with ubc2 and n-degron (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- N-degron (4 kDa, Protein from Saccharomyces cerevisiae S288C)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
Structure of yeast Ubr1 in complex with Ubc2 and monoubiquitinated N-degron
Resolution: 3.67 Å
EM Method: Single-particle
Fitted PDBs: 7mey
Q-score: 0.407
Pan M, Zheng Q, Wang T, Liang L, Mao J, Zuo C, Ding R, Ai H, Xie Y, Si D, Yu Y, Liu L, Zhao M
Nature (2021) 600 pp. 334-338 [ Pubmed: 34789879 DOI: doi:10.1038/s41586-021-04097-8 ]
- 2-(ethylamino)ethane-1-thiol (105 Da, Ligand)
- Zinc ion (65 Da, Ligand)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- E3 ubiquitin-protein ligase ubr1 (225 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Monoubiquitinated n-degron (4 kDa, Protein from Saccharomyces cerevisiae S288C)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 2 (19 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Yeast ubr1 in complex with ubc2 and monoubiquitinated n-degron (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Cryo-EM structure of human p97 in complex with NMS-873 in the presence of ATP, Npl4/Ufd1, and Ub6
Resolution: 2.4 Å
EM Method: Single-particle
Fitted PDBs: 7lmy
Q-score: 0.512
Pan M, Yu Y, Ai H, Zheng Q, Xie Y, Liu L, Zhao M
Nat Struct Mol Biol (2021) 28 pp. 614-625 [ Pubmed: 34262183 DOI: doi:10.1038/s41594-021-00617-2 ]
- 3-[3-cyclopentylsulfanyl-5-[[3-methyl-4-(4-methylsulfonylphenyl)phenoxy]methyl]-1,2,4-triazol-4-yl]pyridine (520 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Human p97 in complex with nms-873 in the presence of atp, npl4/ufd1, and k48-linked ub6 (Complex from Homo sapiens)
- Transitional endoplasmic reticulum atpase (89 kDa, Protein from Homo sapiens)
Cryo-EM structure of human p97 in complex with Npl4/Ufd1 and Ub6 (Class 1)
Resolution: 3.06 Å
EM Method: Single-particle
Fitted PDBs: 7lmz
Q-score: 0.389
Pan M, Yu Y, Ai H, Zheng Q, Xie Y, Liu L, Zhao M
Nat Struct Mol Biol (2021) 28 pp. 614-625 [ Pubmed: 34262183 DOI: doi:10.1038/s41594-021-00617-2 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Transitional endoplasmic reticulum atpase (89 kDa, Protein from Homo sapiens)
- Human p97 in complex with npl4/ufd1 and k48-linked ub6 in the presence of atp (Complex from Homo sapiens)
- Hexa-ubiquitin (783 Da, Protein from Homo sapiens)
Cryo-EM structure of human p97 in complex with Npl4/Ufd1 and Ub6 (Class 2)
Resolution: 2.98 Å
EM Method: Single-particle
Fitted PDBs: 7ln0
Q-score: 0.413
Pan M, Yu Y, Ai H, Zheng Q, Xie Y, Liu L, Zhao M
Nat Struct Mol Biol (2021) 28 pp. 614-625 [ Pubmed: 34262183 DOI: doi:10.1038/s41594-021-00617-2 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Transitional endoplasmic reticulum atpase (89 kDa, Protein from Homo sapiens)
- Human p97 in complex with npl4/ufd1 and k48-linked ub6 in the presence of atp (Complex from Homo sapiens)
- Hexa-ubiquitin (783 Da, Protein from Homo sapiens)
Cryo-EM structure of human p97 in complex with Npl4/Ufd1 and Ub6 (Class 3)
Resolution: 3.4 Å
EM Method: Single-particle
Fitted PDBs: 7ln1
Q-score: 0.382
Pan M, Yu Y, Ai H, Zheng Q, Xie Y, Liu L, Zhao M
Nat Struct Mol Biol (2021) 28 pp. 614-625 [ Pubmed: 34262183 DOI: doi:10.1038/s41594-021-00617-2 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Transitional endoplasmic reticulum atpase (89 kDa, Protein from Homo sapiens)
- Human p97 in complex with npl4/ufd1 and k48-linked ub6 in the presence of atp (Complex from Homo sapiens)
- Hexa-ubiquitin (783 Da, Protein from Homo sapiens)
Cryo-EM structure of human p97 in complex with Npl4/Ufd1 and polyubiquitinated Ub-Eos (FOM, Class 1)
Resolution: 3.63 Å
EM Method: Single-particle
Fitted PDBs: 7ln2
Q-score: 0.302
Pan M, Yu Y, Ai H, Zheng Q, Xie Y, Liu L, Zhao M
Nat Struct Mol Biol (2021) 28 pp. 614-625 [ Pubmed: 34262183 DOI: doi:10.1038/s41594-021-00617-2 ]
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Human p97 in complex with npl4/ufd1 and k48-linked polyubiquitinated ub-eos in the presence of atp (Complex from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- Polyubiquitinated ub-eos (1 kDa, Protein from Mus musculus)
- Transitional endoplasmic reticulum atpase (89 kDa, Protein from Homo sapiens)