Cryo-EM structure of human p97 in complex with Npl4/Ufd1 and polyubiquitinated Ub-Eos (CHAPSO, Class 1, Close State)

Experimental Data Snapshot

  • Resolution: 3.09 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report

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Mechanistic insight into substrate processing and allosteric inhibition of human p97.

Pan, M.Yu, Y.Ai, H.Zheng, Q.Xie, Y.Liu, L.Zhao, M.

(2021) Nat Struct Mol Biol 28: 614-625

  • DOI: https://doi.org/10.1038/s41594-021-00617-2
  • Primary Citation of Related Structures:  
    7LMY, 7LMZ, 7LN0, 7LN1, 7LN2, 7LN3, 7LN4, 7LN5, 7LN6

  • PubMed Abstract: 

    p97 processes ubiquitinated substrates and plays a central role in cellular protein homeostasis. Here, we report a series of cryo-EM structures of the substrate-engaged human p97 complex with resolutions ranging from 2.9 to 3.8 Å that captured 'power-stroke'-like motions of both the D1 and D2 ATPase rings of p97. A key feature of these structures is the critical conformational changes of the intersubunit signaling (ISS) motifs, which tighten the binding of nucleotides and neighboring subunits and contribute to the spiral staircase conformation of the D1 and D2 rings. In addition, we determined the cryo-EM structure of human p97 in complex with NMS-873, a potent p97 inhibitor, at a resolution of 2.4 Å. The structures showed that NMS-873 binds at a cryptic groove in the D2 domain and interacts with the ISS motif, preventing its conformational change and thus blocking substrate translocation allosterically.

  • Organizational Affiliation

    Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA. panm@uchicago.edu.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transitional endoplasmic reticulum ATPase
A, B, C, D, E
A, B, C, D, E, F
806Homo sapiensMutation(s): 2 
Gene Names: VCP
UniProt & NIH Common Fund Data Resources
Find proteins for P55072 (Homo sapiens)
Explore P55072 
Go to UniProtKB:  P55072
GTEx:  ENSG00000165280 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55072
Sequence Annotations
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
polyubiquitinated Ub-Eos22Mus musculusMutation(s): 0 
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ATP (Subject of Investigation/LOI)
Query on ATP

Download Ideal Coordinates CCD File 
J [auth B]
M [auth C]
P [auth D]
Q [auth D]
T [auth E]
J [auth B],
M [auth C],
P [auth D],
Q [auth D],
T [auth E],
U [auth E],
X [auth F]
C10 H16 N5 O13 P3
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
H [auth A],
I [auth A],
K [auth B],
N [auth C],
Y [auth F]
C10 H15 N5 O10 P2
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
L [auth B]
O [auth C]
R [auth D]
S [auth D]
V [auth E]
L [auth B],
O [auth C],
R [auth D],
S [auth D],
V [auth E],
W [auth E],
Z [auth F]
Experimental Data & Validation

Experimental Data

  • Resolution: 3.09 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion

Structure Validation

View Full Validation Report

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-09-15
    Type: Initial release
  • Version 1.1: 2024-05-29
    Changes: Data collection