7US2

PARL-cleaved Skd3 (human ClpB) E455Q Nucleotide Binding Domain hexamer bound to ATPgammaS, open conformation


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.76 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

Dodecamer assembly of a metazoan AAA + chaperone couples substrate extraction to refolding.

Gupta, A.Lentzsch, A.M.Siegel, A.Yu, Z.Chio, U.S.Cheng, Y.Shan, S.O.

(2023) Sci Adv 9: eadf5336-eadf5336

  • DOI: https://doi.org/10.1126/sciadv.adf5336
  • Primary Citation of Related Structures:  
    7US2

  • PubMed Abstract: 

    Ring-forming AAA + chaperones solubilize protein aggregates and protect organisms from proteostatic stress. In metazoans, the AAA + chaperone Skd3 in the mitochondrial intermembrane space (IMS) is critical for human health and efficiently refolds aggregated proteins, but its underlying mechanism is poorly understood. Here, we show that Skd3 harbors both disaggregase and protein refolding activities enabled by distinct assembly states. High-resolution structures of Skd3 hexamers in distinct conformations capture ratchet-like motions that mediate substrate extraction. Unlike previously described disaggregases, Skd3 hexamers further assemble into dodecameric cages in which solubilized substrate proteins can attain near-native states. Skd3 mutants defective in dodecamer assembly retain disaggregase activity but are impaired in client refolding, linking the disaggregase and refolding activities to the hexameric and dodecameric states of Skd3, respectively. We suggest that Skd3 is a combined disaggregase and foldase, and this property is particularly suited to meet the complex proteostatic demands in the mitochondrial IMS.


  • Organizational Affiliation

    Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Caseinolytic peptidase B protein homolog
A, B, C, D, E
A, B, C, D, E, F
581Homo sapiensMutation(s): 0 
Gene Names: CLPBHSP78SKD3
EC: 3.6.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q9H078 (Homo sapiens)
Explore Q9H078 
Go to UniProtKB:  Q9H078
PHAROS:  Q9H078
GTEx:  ENSG00000162129 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9H078
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
SubstrateG [auth P]14Homo sapiensMutation(s): 0 
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
AGS (Subject of Investigation/LOI)
Query on AGS

Download Ideal Coordinates CCD File 
H [auth A]
J [auth B]
L [auth C]
N [auth D]
P [auth E]
H [auth A],
J [auth B],
L [auth C],
N [auth D],
P [auth E],
R [auth F]
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER
C10 H16 N5 O12 P3 S
NLTUCYMLOPLUHL-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

Download Ideal Coordinates CCD File 
I [auth A]
K [auth B]
M [auth C]
O [auth D]
Q [auth E]
I [auth A],
K [auth B],
M [auth C],
O [auth D],
Q [auth E],
S [auth F]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.76 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/Office of the DirectorUnited StatesOD021741
National Institutes of Health/Office of the DirectorUnited StatesOD026881
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM129541
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM136321
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM137463
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM140847

Revision History  (Full details and data files)

  • Version 1.0: 2023-04-26
    Type: Initial release
  • Version 1.1: 2023-11-08
    Changes: Data collection, Database references