5VHH

Conformational Landscape of the p28-Bound Human Proteasome Regulatory Particle


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Conformational Landscape of the p28-Bound Human Proteasome Regulatory Particle.

Lu, Y.Wu, J.Dong, Y.Chen, S.Sun, S.Ma, Y.B.Ouyang, Q.Finley, D.Kirschner, M.W.Mao, Y.

(2017) Mol Cell 67: 322-333.e6

  • DOI: https://doi.org/10.1016/j.molcel.2017.06.007
  • Primary Citation of Related Structures:  
    5VGZ, 5VHF, 5VHH, 5VHI, 5VHJ, 5VHM, 5VHN, 5VHO, 5VHP, 5VHQ, 5VHR, 5VHS

  • PubMed Abstract: 

    The proteasome holoenzyme is activated by its regulatory particle (RP) consisting of two subcomplexes, the lid and the base. A key event in base assembly is the formation of a heterohexameric ring of AAA-ATPases, which is guided by at least four RP assembly chaperones in mammals: PAAF1, p28/gankyrin, p27/PSMD9, and S5b. Using cryogenic electron microscopy, we analyzed the non-AAA structure of the p28-bound human RP at 4.5 Å resolution and determined seven distinct conformations of the Rpn1-p28-AAA subcomplex within the p28-bound RP at subnanometer resolutions. Remarkably, the p28-bound AAA ring does not form a channel in the free RP and spontaneously samples multiple "open" and "closed" topologies at the Rpt2-Rpt6 and Rpt3-Rpt4 interfaces. Our analysis suggests that p28 assists the proteolytic core particle to select a specific conformation of the ATPase ring for RP engagement and is released in a shoehorn-like fashion in the last step of the chaperone-mediated proteasome assembly.


  • Organizational Affiliation

    State Key Laboratory for Artificial Microstructures and Mesoscopic Physics, Institute of Condensed Matter Physics, School of Physics, Center for Quantitative Biology, Peking University, Beijing 100871, China.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 7352Homo sapiensMutation(s): 0 
Gene Names: PSMC2MSS1
UniProt & NIH Common Fund Data Resources
Find proteins for P35998 (Homo sapiens)
Explore P35998 
Go to UniProtKB:  P35998
PHAROS:  P35998
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP35998
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 4340Homo sapiensMutation(s): 0 
Gene Names: PSMC1
UniProt
Find proteins for P62191 (Homo sapiens)
Explore P62191 
Go to UniProtKB:  P62191
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62191
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 8385Homo sapiensMutation(s): 0 
Gene Names: PSMC5SUG1
UniProt & NIH Common Fund Data Resources
Find proteins for P62195 (Homo sapiens)
Explore P62195 
Go to UniProtKB:  P62195
PHAROS:  P62195
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62195
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6B368Homo sapiensMutation(s): 0 
Gene Names: PSMC4MIP224TBP7
UniProt & NIH Common Fund Data Resources
Find proteins for P43686 (Homo sapiens)
Explore P43686 
Go to UniProtKB:  P43686
PHAROS:  P43686
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP43686
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 10B379Homo sapiensMutation(s): 0 
Gene Names: PSMC6SUG2
UniProt
Find proteins for P62333 (Homo sapiens)
Explore P62333 
Go to UniProtKB:  P62333
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62333
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6A380Homo sapiensMutation(s): 0 
Gene Names: PSMC3TBP1
UniProt & NIH Common Fund Data Resources
Find proteins for P17980 (Homo sapiens)
Explore P17980 
Go to UniProtKB:  P17980
PHAROS:  P17980
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP17980
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 1G [auth U]935Homo sapiensMutation(s): 0 
Gene Names: PSMD1
UniProt & NIH Common Fund Data Resources
Find proteins for Q99460 (Homo sapiens)
Explore Q99460 
Go to UniProtKB:  Q99460
PHAROS:  Q99460
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ99460
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 3H [auth V]488Homo sapiensMutation(s): 0 
Gene Names: PSMD3
UniProt & NIH Common Fund Data Resources
Find proteins for O43242 (Homo sapiens)
Explore O43242 
Go to UniProtKB:  O43242
PHAROS:  O43242
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO43242
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 12I [auth W]456Homo sapiensMutation(s): 0 
Gene Names: PSMD12
UniProt & NIH Common Fund Data Resources
Find proteins for O00232 (Homo sapiens)
Explore O00232 
Go to UniProtKB:  O00232
PHAROS:  O00232
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00232
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 11J [auth X]385Homo sapiensMutation(s): 0 
Gene Names: PSMD11
UniProt & NIH Common Fund Data Resources
Find proteins for O00231 (Homo sapiens)
Explore O00231 
Go to UniProtKB:  O00231
PHAROS:  O00231
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00231
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 6K [auth Y]378Homo sapiensMutation(s): 0 
Gene Names: PSMD6KIAA0107PFAAP4
UniProt & NIH Common Fund Data Resources
Find proteins for Q15008 (Homo sapiens)
Explore Q15008 
Go to UniProtKB:  Q15008
PHAROS:  Q15008
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ15008
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 7L [auth Z]286Homo sapiensMutation(s): 0 
Gene Names: PSMD7MOV34L
UniProt & NIH Common Fund Data Resources
Find proteins for P51665 (Homo sapiens)
Explore P51665 
Go to UniProtKB:  P51665
PHAROS:  P51665
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP51665
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 13M [auth a]374Homo sapiensMutation(s): 0 
Gene Names: PSMD13
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNM6 (Homo sapiens)
Explore Q9UNM6 
Go to UniProtKB:  Q9UNM6
PHAROS:  Q9UNM6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UNM6
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 4N [auth b]191Homo sapiensMutation(s): 0 
Gene Names: PSMD4MCB1
UniProt & NIH Common Fund Data Resources
Find proteins for P55036 (Homo sapiens)
Explore P55036 
Go to UniProtKB:  P55036
PHAROS:  P55036
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55036
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 14O [auth c]287Homo sapiensMutation(s): 0 
Gene Names: PSMD14POH1
EC: 3.4.19
UniProt & NIH Common Fund Data Resources
Find proteins for O00487 (Homo sapiens)
Explore O00487 
Go to UniProtKB:  O00487
PHAROS:  O00487
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO00487
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 8P [auth d]257Homo sapiensMutation(s): 0 
Gene Names: PSMD8
UniProt & NIH Common Fund Data Resources
Find proteins for P48556 (Homo sapiens)
Explore P48556 
Go to UniProtKB:  P48556
PHAROS:  P48556
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP48556
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome complex subunit SEM1Q [auth e]70Homo sapiensMutation(s): 0 
Gene Names: SEM1C7orf76DSS1SHFDG1SHFM1
UniProt & NIH Common Fund Data Resources
Find proteins for P60896 (Homo sapiens)
Explore P60896 
Go to UniProtKB:  P60896
PHAROS:  P60896
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP60896
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 10R [auth G]223Homo sapiensMutation(s): 0 
Gene Names: PSMD10
UniProt & NIH Common Fund Data Resources
Find proteins for O75832 (Homo sapiens)
Explore O75832 
Go to UniProtKB:  O75832
PHAROS:  O75832
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75832
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 2S [auth f]848Homo sapiensMutation(s): 0 
Gene Names: PSMD2TRAP2
UniProt & NIH Common Fund Data Resources
Find proteins for Q13200 (Homo sapiens)
Explore Q13200 
Go to UniProtKB:  Q13200
PHAROS:  Q13200
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13200
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
T [auth c]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2017-08-23
    Type: Initial release
  • Version 1.1: 2018-08-22
    Changes: Data collection, Database references
  • Version 1.2: 2023-08-16
    Changes: Data collection, Database references, Other