8UA0

Cdc48-Shp1 unfolding native substrate, Class 8

  • Classification: CHAPERONE
  • Organism(s): Saccharomyces cerevisiae
  • Mutation(s): No 

  • Deposited: 2023-09-20 Released: 2024-11-06 
  • Deposition Author(s): Cooney, I., Schubert, H.L., Cedeno, K., Carson, R., Fisher, O.N., Price, J.C., 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), National Institutes of Health/National Institute on Aging (NIH/NIA), National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Visualization of the Cdc48 AAA+ ATPase protein unfolding pathway.

Cooney, I.Schubert, H.L.Cedeno, K.Fisher, O.N.Carson, R.Price, J.C.Hill, C.P.Shen, P.S.

(2024) Nat Commun 15: 7505-7505

  • DOI: https://doi.org/10.1038/s41467-024-51835-3
  • Primary Citation of Related Structures:  
    8U7T, 8U8I, 8U9C, 8U9P, 8U9Q, 8U9Z, 8UA0, 8UA1, 8UAA, 8UB4

  • PubMed Abstract: 

    The Cdc48 AAA+ ATPase is an abundant and essential enzyme that unfolds substrates in multiple protein quality control pathways. The enzyme includes two conserved AAA+ ATPase motor domains, D1 and D2, that assemble as hexameric rings with D1 stacked above D2. Here, we report an ensemble of native structures of Cdc48 affinity purified from budding yeast lysate in complex with the adaptor Shp1 in the act of unfolding substrate. Our analysis reveals a continuum of structural snapshots that spans the entire translocation cycle. These data uncover elements of Shp1-Cdc48 interactions and support a 'hand-over-hand' mechanism in which the sequential movement of individual subunits is closely coordinated. D1 hydrolyzes ATP and disengages from substrate prior to D2, while D2 rebinds ATP and re-engages with substrate prior to D1, thereby explaining the dominant role played by the D2 motor in substrate translocation/unfolding.


  • Organizational Affiliation

    Department of Biochemistry, University of Utah, Salt Lake City, UT, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Cell division control protein 48
A, B, C, D, E
A, B, C, D, E, F
835Saccharomyces cerevisiaeMutation(s): 0 
EC: 3.6.4.6
UniProt
Find proteins for P25694 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P25694 
Go to UniProtKB:  P25694
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25694
Sequence Annotations
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  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Substrate22Saccharomyces cerevisiaeMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
08T
Query on 08T

Download Ideal Coordinates CCD File 
H [auth A]
J [auth A]
L [auth B]
N [auth B]
P [auth C]
H [auth A],
J [auth A],
L [auth B],
N [auth B],
P [auth C],
R [auth C],
V [auth F]
[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium
C10 H14 Be F3 N5 O10 P2
WOGYHYSOODLXII-KWIZKVQNSA-J
ADP (Subject of Investigation/LOI)
Query on ADP

Download Ideal Coordinates CCD File 
T [auth D],
U [auth D]
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
MG (Subject of Investigation/LOI)
Query on MG

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

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.50 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 StatesR35 GM133772
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesU54 AI170856
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01 GM112080
National Institutes of Health/National Institute on Aging (NIH/NIA)United StatesR01 AG066874
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesF31 CA254427

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release