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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 [ DOI: doi:10.1038/s41586-021-04097-8 Pubmed: 34789879 ]
- 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)
- E3 ubiquitin-protein ligase ubr1 (225 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Zinc ion (65 Da, Ligand)
- 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 [ DOI: doi:10.1038/s41586-021-04097-8 Pubmed: 34789879 ]
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Yeast ubr1 in complex with ubc2 and monoubiquitinated n-degron (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Ubiquitin-conjugating enzyme e2 2 (19 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Monoubiquitinated n-degron (4 kDa, Protein from Saccharomyces cerevisiae S288C)
- E3 ubiquitin-protein ligase ubr1 (225 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 2-(ethylamino)ethane-1-thiol (105 Da, Ligand)
- Zinc ion (65 Da, Ligand)
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)
- Human p97 in complex with nms-873 in the presence of atp, npl4/ufd1, and k48-linked ub6 (Complex from Homo sapiens)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Magnesium ion (24 Da, Ligand)
- 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 ]
- Hexa-ubiquitin (783 Da, Protein from Homo sapiens)
- Human p97 in complex with npl4/ufd1 and k48-linked ub6 in the presence of atp (Complex from Homo sapiens)
- 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)
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 ]
- Hexa-ubiquitin (783 Da, Protein from Homo sapiens)
- Human p97 in complex with npl4/ufd1 and k48-linked ub6 in the presence of atp (Complex from Homo sapiens)
- 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)
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 ]
- Hexa-ubiquitin (783 Da, Protein from Homo sapiens)
- Human p97 in complex with npl4/ufd1 and k48-linked ub6 in the presence of atp (Complex from Homo sapiens)
- 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)
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)
- Transitional endoplasmic reticulum atpase (89 kDa, Protein from Homo sapiens)
- Polyubiquitinated ub-eos (1 kDa, Protein from Mus musculus)
Cryo-EM structure of human p97 in complex with Npl4/Ufd1 and polyubiquitinated Ub-Eos (FOM, Class 2)
Resolution: 3.45 Å
EM Method: Single-particle
Fitted PDBs: 7ln3
Q-score: 0.322
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)
- Transitional endoplasmic reticulum atpase (89 kDa, Protein from Homo sapiens)
- Polyubiquitinated ub-eos (1 kDa, Protein from Mus musculus)
Cryo-EM structure of human p97 in complex with Npl4/Ufd1 and polyubiquitinated Ub-Eos (FOM, Class 3)
Resolution: 3.0 Å
EM Method: Single-particle
Fitted PDBs: 7ln4
Q-score: 0.377
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)
- Transitional endoplasmic reticulum atpase (89 kDa, Protein from Homo sapiens)
- Polyubiquitinated ub-eos (1 kDa, Protein from Mus musculus)
Resolution: 3.09 Å
EM Method: Single-particle
Fitted PDBs: 7ln5
Q-score: 0.415
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)
- Transitional endoplasmic reticulum atpase (89 kDa, Protein from Homo sapiens)
- Polyubiquitinated ub-eos (1 kDa, Protein from Mus musculus)