8B5R

p97-p37-SPI substrate complex


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 2.1 of the entry. See complete history


Literature

Structural basis of ubiquitin-independent PP1 complex disassembly by p97.

van den Boom, J.Marini, G.Meyer, H.Saibil, H.R.

(2023) EMBO J 42: e113110-e113110

  • DOI: https://doi.org/10.15252/embj.2022113110
  • Primary Citation of Related Structures:  
    8B5R

  • PubMed Abstract: 

    The AAA+-ATPase p97 (also called VCP or Cdc48) unfolds proteins and disassembles protein complexes in numerous cellular processes, but how substrate complexes are loaded onto p97 and disassembled is unclear. Here, we present cryo-EM structures of p97 in the process of disassembling a protein phosphatase-1 (PP1) complex by extracting an inhibitory subunit from PP1. We show that PP1 and its partners SDS22 and inhibitor-3 (I3) are loaded tightly onto p97, surprisingly via a direct contact of SDS22 with the p97 N-domain. Loading is assisted by the p37 adapter that bridges two adjacent p97 N-domains underneath the substrate complex. A stretch of I3 is threaded into the central channel of the spiral-shaped p97 hexamer, while other elements of I3 are still attached to PP1. Thus, our data show how p97 arranges a protein complex between the p97 N-domain and central channel, suggesting a hold-and-extract mechanism for p97-mediated disassembly.


  • Organizational Affiliation

    Molecular Biology I, Center of Medical Biotechnology, Faculty of Biology, University of Duisburg-Essen, Essen, Germany.


Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transitional endoplasmic reticulum ATPase
A, B, C, D, E
A, B, C, D, E, F
812Homo sapiensMutation(s): 0 
Gene Names: VCP
EC: 3.6.4.6
UniProt & NIH Common Fund Data Resources
Find proteins for P55072 (Homo sapiens)
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Go to UniProtKB:  P55072
GTEx:  ENSG00000165280 
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UniProt GroupP55072
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  • Reference Sequence

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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
I3 sequence being threaded through the p97 channelG [auth I]22Homo sapiensMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Serine/threonine-protein phosphatase PP1-gamma catalytic subunitH [auth P]323Homo sapiensMutation(s): 0 
Gene Names: PPP1CC
EC: 3.1.3.16
UniProt & NIH Common Fund Data Resources
Find proteins for P36873 (Homo sapiens)
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Go to UniProtKB:  P36873
GTEx:  ENSG00000186298 
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UniProt GroupP36873
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Protein phosphatase 1 regulatory subunit 7I [auth S]360Homo sapiensMutation(s): 0 
Gene Names: PPP1R7SDS22
UniProt & NIH Common Fund Data Resources
Find proteins for Q15435 (Homo sapiens)
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PHAROS:  Q15435
GTEx:  ENSG00000115685 
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UniProt GroupQ15435
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  • Reference Sequence

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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
UBX domain-containing protein 2BJ [auth X]11Homo sapiensMutation(s): 0 
Gene Names: UBXN2B
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Find proteins for Q14CS0 (Homo sapiens)
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PHAROS:  Q14CS0
GTEx:  ENSG00000215114 
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UniProt GroupQ14CS0
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
UBX domain-containing protein 2BK [auth Y]86Homo sapiensMutation(s): 0 
Gene Names: UBXN2B
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Find proteins for Q14CS0 (Homo sapiens)
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Go to UniProtKB:  Q14CS0
PHAROS:  Q14CS0
GTEx:  ENSG00000215114 
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UniProt GroupQ14CS0
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 6.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487:

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom106249/Z/14/Z
Wellcome TrustUnited Kingdom202679/Z/16/Z
Wellcome TrustUnited Kingdom206166/Z/17/Z

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-07
    Type: Initial release
  • Version 2.0: 2023-06-14
    Changes: Atomic model, Database references
  • Version 2.1: 2023-07-26
    Changes: Database references