8FCN

Cryo-EM structure of p97:UBXD1 VIM-only state


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

The p97/VCP adaptor UBXD1 drives AAA+ remodeling and ring opening through multi-domain tethered interactions.

Braxton, J.R.Altobelli, C.R.Tucker, M.R.Tse, E.Thwin, A.C.Arkin, M.R.Southworth, D.R.

(2023) Nat Struct Mol Biol 30: 2009-2019

  • DOI: https://doi.org/10.1038/s41594-023-01126-0
  • Primary Citation of Related Structures:  
    8FCL, 8FCM, 8FCN, 8FCO, 8FCP, 8FCQ, 8FCR, 8FCT

  • PubMed Abstract: 

    p97, also known as valosin-containing protein, is an essential cytosolic AAA+ (ATPases associated with diverse cellular activities) hexamer that unfolds substrate polypeptides to support protein homeostasis and macromolecular disassembly. Distinct sets of p97 adaptors guide cellular functions but their roles in direct control of the hexamer are unclear. The UBXD1 adaptor localizes with p97 in critical mitochondria and lysosome clearance pathways and contains multiple p97-interacting domains. Here we identify UBXD1 as a potent p97 ATPase inhibitor and report structures of intact human p97-UBXD1 complexes that reveal extensive UBXD1 contacts across p97 and an asymmetric remodeling of the hexamer. Conserved VIM, UBX and PUB domains tether adjacent protomers while a connecting strand forms an N-terminal domain lariat with a helix wedged at the interprotomer interface. An additional VIM-connecting helix binds along the second (D2) AAA+ domain. Together, these contacts split the hexamer into a ring-open conformation. Structures, mutagenesis and comparisons to other adaptors further reveal how adaptors containing conserved p97-remodeling motifs regulate p97 ATPase activity and structure.


  • Organizational Affiliation

    Graduate Program in Chemistry and Chemical Biology, University of California San Francisco, San Francisco, CA, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
UBX domain-containing protein 6441Homo sapiensMutation(s): 0 
Gene Names: UBXN6UBXD1UBXDC2
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BZV1 (Homo sapiens)
Explore Q9BZV1 
Go to UniProtKB:  Q9BZV1
PHAROS:  Q9BZV1
GTEx:  ENSG00000167671 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BZV1
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 ATPase806Homo sapiensMutation(s): 0 
Gene Names: VCP
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
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
M [auth F]
N [auth F]
O [auth E]
P [auth E]
Q [auth D]
M [auth F],
N [auth F],
O [auth E],
P [auth E],
Q [auth D],
R [auth D],
S [auth C],
T [auth C],
U [auth B],
V [auth B],
W [auth A],
X [auth A]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.95 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM138690

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-21
    Type: Initial release
  • Version 1.1: 2023-11-15
    Changes: Data collection, Database references
  • Version 1.2: 2023-11-22
    Changes: Database references
  • Version 1.3: 2023-12-20
    Changes: Database references