7MHS

Structure of p97 (subunits A to E) with substrate engaged

  • Classification: HYDROLASE
  • Organism(s): Homo sapiens
  • Mutation(s): No 

  • Deposited: 2021-04-15 Released: 2022-05-11 
  • Deposition Author(s): Xu, Y., Han, H., Cooney, I., Hill, C.P., Shen, P.S.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Active conformation of the p97-p47 unfoldase complex.

Xu, Y.Han, H.Cooney, I.Guo, Y.Moran, N.G.Zuniga, N.R.Price, J.C.Hill, C.P.Shen, P.S.

(2022) Nat Commun 13: 2640-2640

  • DOI: https://doi.org/10.1038/s41467-022-30318-3
  • Primary Citation of Related Structures:  
    7MHS

  • PubMed Abstract: 

    The p97 AAA+ATPase is an essential and abundant regulator of protein homeostasis that plays a central role in unfolding ubiquitylated substrates. Here we report two cryo-EM structures of human p97 in complex with its p47 adaptor. One of the conformations is six-fold symmetric, corresponds to previously reported structures of p97, and lacks bound substrate. The other structure adopts a helical conformation, displays substrate running in an extended conformation through the pore of the p97 hexamer, and resembles structures reported for other AAA unfoldases. These findings support the model that p97 utilizes a "hand-over-hand" mechanism in which two residues of the substrate are translocated for hydrolysis of two ATPs, one in each of the two p97 AAA ATPase rings. Proteomics analysis supports the model that one p97 complex can bind multiple substrate adaptors or binding partners, and can process substrates with multiple types of ubiquitin modification.


  • Organizational Affiliation

    Department of Biochemistry, 15 N. Medical Drive East, University of Utah, Salt Lake City, UT, 84112, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Transitional endoplasmic reticulum ATPase
A, B, C, D, E
806Homo sapiensMutation(s): 0 
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:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Unknown substrateF [auth G]22Homo sapiensMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download Ideal Coordinates CCD File 
BA [auth D]
EA [auth E]
FA [auth E]
G [auth A]
J [auth A]
BA [auth D],
EA [auth E],
FA [auth E],
G [auth A],
J [auth A],
M [auth B],
P [auth B],
S [auth C],
V [auth C],
Y [auth D]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
BEF
Query on BEF

Download Ideal Coordinates CCD File 
CA [auth D]
H [auth A]
K [auth A]
N [auth B]
Q [auth B]
CA [auth D],
H [auth A],
K [auth A],
N [auth B],
Q [auth B],
T [auth C],
W [auth C],
Z [auth D]
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
MG
Query on MG

Download Ideal Coordinates CCD File 
AA [auth D]
DA [auth D]
I [auth A]
L [auth A]
O [auth B]
AA [auth D],
DA [auth D],
I [auth A],
L [auth A],
O [auth B],
R [auth B],
U [auth C],
X [auth C]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.60 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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 StatesGM133772
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesP50AI150464

Revision History  (Full details and data files)

  • Version 1.0: 2022-05-11
    Type: Initial release
  • Version 1.1: 2022-11-23
    Changes: Database references