9MPU | pdb_00009mpu

Cryo-EM structure of p47 bound to VCP N-domain (with D1 domain)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Starting Models: experimental, in silico
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wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Structural basis of VCP-VCPIP1-p47 ternary complex in Golgi maintenance.

Shah, B.Hunkeler, M.Bratt, A.Yue, H.Jaen Maisonet, I.Fischer, E.S.Buhrlage, S.J.

(2025) Nat Commun 16: 8025-8025

  • DOI: https://doi.org/10.1038/s41467-025-63161-3
  • Primary Citation of Related Structures:  
    9MPQ, 9MPR, 9MPS, 9MPT, 9MPU, 9MPV

  • PubMed Abstract: 

    VCP/p97 regulates a wide range of cellular processes, including post-mitotic Golgi reassembly. In this context, VCP is assisted by p47, an adapter protein, and VCPIP1, a deubiquitylase (DUB). However, how they organize into a functional ternary complex to promote Golgi assembly remains unknown. Here, we use cryo-EM to characterize both VCP-VCPIP1 and VCP-VCPIP1-p47 complexes. We show that VCPIP1 engages VCP through two interfaces: one involving the N-domain of VCP and the UBX domain of VCPIP1, and the other involving the VCP D2 domains and a region of VCPIP1 we refer to as VCPID. The p47 UBX domain competitively binds to the VCP N-domain, while not affecting VCPID binding. We show that VCPID is critical for VCP-mediated enhancement of DUB activity and proper Golgi assembly. The ternary structure along with biochemical and cellular data provides new insights into the complex interplay of VCP with its co-factors.


  • Organizational Affiliation
    • Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
NSFL1 cofactor p47A [auth B]393Homo sapiensMutation(s): 0 
Gene Names: NSFL1CUBXN2C
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UNZ2 (Homo sapiens)
Explore Q9UNZ2 
Go to UniProtKB:  Q9UNZ2
PHAROS:  Q9UNZ2
GTEx:  ENSG00000088833 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9UNZ2
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Transitional endoplasmic reticulum ATPaseB [auth A]832Homo sapiensMutation(s): 0 
Gene Names: VCPHEL-220HEL-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
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.6.0
MODEL REFINEMENTPHENIX1.21.1_5286

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 CA262188
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesR01 CA233800
National Institutes of Health/National Cancer Institute (NIH/NCI)United States5F31 CA281197

Revision History  (Full details and data files)

  • Version 1.0: 2025-10-15
    Type: Initial release