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 8YKA | pdb_00008yka

Cryo-EM structure of P97-VCPIP1 complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report

Validation slider image for 8YKA

This is version 1.2 of the entry. See complete history. 

Literature

Molecular Basis of VCPIP1 and P97/VCP Interaction Reveals Its Functions in Post-Mitotic Golgi Reassembly.

Liao, T., Li, R., Lu, P., Liu, Y., Yang, R., Guo, H., Wu, Z., Wang, R., Yuan, L., Hu, Z., Gao, H., Li, F.

(2024) Adv Sci (Weinh) 11: e2403417-e2403417

  • DOI: https://doi.org/10.1002/advs.202403417
  • Primary Citation Related Structures: 
    8YKA

  • PubMed Abstract: 

    The VCPIP1-P97/VCP (Valosin-Containing Protein) complex is required for post-mitotic Golgi cisternae reassembly and maintenance in interphase. However, the organization and mechanism of this complex in regulating Golgi membrane fusion is still elusive. Here, the cryo-electron microscopy (cryo-EM) structures of the human VCPIP1-P97/VCP complex are presented. These studies reveal that three independent VCPIP1 molecules sit over the C-terminal substrate exit tunnel formed by P97/VCP homo-hexamer, resulting in an unusual C3 to C6 symmetric barrel architecture. The UFD1 (unknown function domain 1) from VCPIP1, but not the N-terminal OTU domain and the C-terminal UBL domain, docks to the two adjacent D2 domains of P97/VCP, allosterically causing the cofactors binding domain-NTDs (N-terminal domains) of P97/VCP in a "UP" and D1 domain in an ATPase competent conformation. Conversely, VCPIP1 bound P97/VCP hexamer favors the binding of P47, and thus the intact SNARE complex, promoting Golgi membrane fusion. These studies not only reveal the unexpected organization of humanVCPIP1-P97/VCP complex, but also provide new insights into the mechanism of VCPIP1-P97/VCP mediated Golgi apparatus reassembly, which is a fundamental cellular event for protein and lipid processing.


  • Organizational Affiliation: 
    • MOE Key Laboratory of Rare Pediatric Diseases, Center for Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, 410013, China.

Macromolecule Content 

  • Total Structure Weight: 703.42 kDa 
  • Atom Count: 49,386 
  • Modeled Residue Count: 6,291 
  • Deposited Residue Count: 6,291 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transitional endoplasmic reticulum ATPase764Homo sapiensMutation(s): 0 
Gene Names: VCP, HEL-220, HEL-S-70
EC: 3.6.4.6
UniProt & NIH Common Fund Data Resources
Find proteins for P55072 (Homo sapiens)
Explore P55072 
Go to UniProtKB:  P55072
PHAROS:  P55072
GTEx:  ENSG00000165280 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55072
Sequence Annotations
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Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Deubiquitinating protein VCPIP1G [auth 2],
H [auth 3],
I [auth 1]
569Homo sapiensMutation(s): 0 
Gene Names: VCPIP1, KIAA1850, VCIP135
EC: 3.4.19.12
UniProt & NIH Common Fund Data Resources
Find proteins for Q96JH7 (Homo sapiens)
Explore Q96JH7 
Go to UniProtKB:  Q96JH7
PHAROS:  Q96JH7
GTEx:  ENSG00000175073 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96JH7
Sequence Annotations
Expand
Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.45 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX

Structure Validation

View Full Validation Report



Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Natural Science Foundation of China (NSFC)China32370742
National Natural Science Foundation of China (NSFC)China32271258

Revision History  (Full details and data files)

  • Version 1.0: 2024-10-02
    Type: Initial release
  • Version 1.1: 2024-11-20
    Changes: Data collection, Database references, Structure summary
  • Version 1.2: 2025-07-02
    Changes: Data collection