[English] 日本語
Yorodumi Papers
- Database of articles cited by EMDB/PDB/SASBDB data -

+
Search query

Keywords
Structure methods
Author
Journal
IF

-
Structure paper

TitleStructural basis of VCP-VCPIP1-p47 ternary complex in Golgi maintenance.
Journal, issue, pagesNat Commun, Vol. 16, Issue 1, Page 8025, Year 2025
Publish dateAug 28, 2025
AuthorsBinita Shah / Moritz Hunkeler / Ariana Bratt / Hong Yue / Isabella Jaen Maisonet / Eric S Fischer / Sara J Buhrlage /
PubMed AbstractVCP/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). ...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.
External linksNat Commun / PubMed:40877265 / PubMed Central
MethodsEM (single particle)
Resolution2.3 - 4.0 Å
Structure data

48499

9mpq

EMDB-48499, PDB-9mpq:
Cryo-EM structure of VCP (consensus)
Method: EM (single particle) / Resolution: 2.3 Å

48500

9mpr

EMDB-48500, PDB-9mpr:
Cryo-EM structure of three VCPIP1 VCPIDs bound to VCP
Method: EM (single particle) / Resolution: 2.9 Å

48501

9mps

EMDB-48501, PDB-9mps:
Cryo-EM structure of VCPIP1 VCPID bound to VCP D2 domain dimer (with extra D2 domain)
Method: EM (single particle) / Resolution: 2.9 Å

48502

9mpt

EMDB-48502, PDB-9mpt:
Cryo-EM structure of VCPIP1 UBX domain bound to VCP N-domain (with D1 domain)
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-48503: Cryo-EM structure of VCP bound to VCPIP1 UBX and VCPID (with stalk region)
Method: EM (single particle) / Resolution: 2.9 Å

EMDB-48504: Cryo-EM structure of VCP bound to p47 UBX domain and VCPIP1 VCPIDs (with stalk region)
Method: EM (single particle) / Resolution: 2.63 Å

48505

9mpu

EMDB-48505, PDB-9mpu:
Cryo-EM structure of p47 bound to VCP N-domain (with D1 domain)
Method: EM (single particle) / Resolution: 4.0 Å

48506

9mpv

EMDB-48506, PDB-9mpv:
Cryo-EM structure of three VCPIP1 VCPIDs bound to VCP
Method: EM (single particle) / Resolution: 3.1 Å

Source
  • homo sapiens (human)
KeywordsHYDROLASE / double-ring hexameric complex / valosin containing protein / ATPase / VCP / mammalian / DUB / deubiquitinase / deubiquitinating enzyme / VCIP135 / p97 / VCPIP1 / VCPID / UBX / p47 / adapter / SHP

+
About Yorodumi Papers

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi Papers

Database of articles cited by EMDB/PDB/SASBDB data

  • Database of articles cited by EMDB, PDB, and SASBDB entries
  • Using PubMed data

Related info.:EMDB / PDB / SASBDB / Yorodumi / EMN Papers / Changes in new EM Navigator and Yorodumi

Read more