5VHF

Conformational Landscape of the p28-Bound Human Proteasome Regulatory Particle


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 5.70 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

    Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 10A [auth G]223Homo sapiensMutation(s): 0 
Gene Names: PSMD10
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GTEx:  ENSG00000101843 
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 7B [auth A]352Homo sapiensMutation(s): 0 
Gene Names: PSMC2MSS1
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GTEx:  ENSG00000161057 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 4C [auth B]340Homo sapiensMutation(s): 0 
Gene Names: PSMC1
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GTEx:  ENSG00000100764 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 8D [auth C]385Homo sapiensMutation(s): 0 
Gene Names: PSMC5SUG1
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GTEx:  ENSG00000087191 
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6BE [auth D]368Homo sapiensMutation(s): 0 
Gene Names: PSMC4MIP224TBP7
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GTEx:  ENSG00000013275 
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 10BF [auth E]379Homo sapiensMutation(s): 0 
Gene Names: PSMC6SUG2
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GTEx:  ENSG00000100519 
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Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome regulatory subunit 6AG [auth F]380Homo sapiensMutation(s): 0 
Gene Names: PSMC3TBP1
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GTEx:  ENSG00000165916 
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Entity ID: 8
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 1H [auth U]841Homo sapiensMutation(s): 0 
Gene Names: PSMD1
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GTEx:  ENSG00000173692 
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Entity ID: 9
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 3I [auth V]183Homo sapiensMutation(s): 0 
Gene Names: PSMD3
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GTEx:  ENSG00000108344 
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Entity ID: 10
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 12J [auth W]456Homo sapiensMutation(s): 0 
Gene Names: PSMD12
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GTEx:  ENSG00000197170 
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Entity ID: 11
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 11K [auth X]385Homo sapiensMutation(s): 0 
Gene Names: PSMD11
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GTEx:  ENSG00000108671 
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Entity ID: 12
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 6L [auth Y]378Homo sapiensMutation(s): 0 
Gene Names: PSMD6KIAA0107PFAAP4
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GTEx:  ENSG00000163636 
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Entity ID: 13
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 7M [auth Z]286Homo sapiensMutation(s): 0 
Gene Names: PSMD7MOV34L
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GTEx:  ENSG00000103035 
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Entity ID: 14
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 13N [auth a]374Homo sapiensMutation(s): 0 
Gene Names: PSMD13
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GTEx:  ENSG00000185627 
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Entity ID: 15
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 4O [auth b]191Homo sapiensMutation(s): 0 
Gene Names: PSMD4MCB1
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GTEx:  ENSG00000159352 
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Entity ID: 16
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 14P [auth c]287Homo sapiensMutation(s): 0 
Gene Names: PSMD14POH1
EC: 3.4.19
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GTEx:  ENSG00000115233 
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Entity ID: 17
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 8Q [auth d]136Homo sapiensMutation(s): 0 
Gene Names: PSMD8
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GTEx:  ENSG00000099341 
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Entity ID: 18
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome complex subunit SEM1R [auth e]70Homo sapiensMutation(s): 0 
Gene Names: SEM1C7orf76DSS1SHFDG1SHFM1
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GTEx:  ENSG00000127922 
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Entity ID: 19
MoleculeChains Sequence LengthOrganismDetailsImage
26S proteasome non-ATPase regulatory subunit 2S [auth f]848Homo sapiensMutation(s): 0 
Gene Names: PSMD2TRAP2
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GTEx:  ENSG00000175166 
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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: 5.70 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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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