Lodwick JE, Shen R, Erramilli S, Xie Y, Roganowicz K, Kossiakoff AA, Zhao M
bioRxiv (2024) [ Pubmed: 38979142 DOI: doi:10.1101/2024.06.27.601040 ]
- Major vault protein (99 kDa, Protein from Homo sapiens)
- Oligomerized human mvp (7 MDa, Complex from Homo sapiens)
Human Vault Cage in complex with NAD+
Lodwick JE, Shen R, Erramilli S, Xie Y, Roganowicz K, Kossiakoff AA, Zhao M
bioRxiv (2024) [ Pubmed: 38979142 DOI: doi:10.1101/2024.06.27.601040 ]
Human Vault Cage in complex with the MINT domain of PARP4
Lodwick JE, Shen R, Erramilli S, Xie Y, Roganowicz K, Kossiakoff AA, Zhao M
bioRxiv (2024) [ Pubmed: 38979142 DOI: doi:10.1101/2024.06.27.601040 ]
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 (8 kDa, Protein from Homo sapiens)
- 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))
- Zinc ion (65 Da, Ligand)
- N-degron (4 kDa, Protein from Saccharomyces cerevisiae S288C)
- Yeast ubr1 in complex with ubc2 and n-degron (Complex from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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 ]
- Zinc ion (65 Da, Ligand)
- Ubiquitin (8 kDa, Protein from Homo sapiens)
- Monoubiquitinated n-degron (4 kDa, Protein from Saccharomyces cerevisiae S288C)
- 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)
- E3 ubiquitin-protein ligase ubr1 (225 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- Ubiquitin-conjugating enzyme e2 2 (19 kDa, Protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
- 2-(ethylamino)ethane-1-thiol (105 Da, Ligand)
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 [ DOI: doi:10.1038/s41594-021-00617-2 Pubmed: 34262183 ]
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 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)
- 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 [ DOI: doi:10.1038/s41594-021-00617-2 Pubmed: 34262183 ]
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- 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)
- 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 [ DOI: doi:10.1038/s41594-021-00617-2 Pubmed: 34262183 ]
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Polyubiquitinated ub-eos (1 kDa, Protein from Mus musculus)
- Human p97 in complex with npl4/ufd1 and k48-linked polyubiquitinated ub-eos in the presence of atp (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 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 [ DOI: doi:10.1038/s41594-021-00617-2 Pubmed: 34262183 ]
- Magnesium ion (24 Da, Ligand)
- Adenosine-5'-diphosphate (427 Da, Ligand)
- Adenosine-5'-triphosphate (507 Da, Ligand)
- Polyubiquitinated ub-eos (1 kDa, Protein from Mus musculus)
- Human p97 in complex with npl4/ufd1 and k48-linked polyubiquitinated ub-eos in the presence of atp (Complex from Homo sapiens)
- Transitional endoplasmic reticulum atpase (89 kDa, Protein from Homo sapiens)