6OA9

Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ATP

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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This is version 1.3 of the entry. See complete history. 


Literature

Substrate processing by the Cdc48 ATPase complex is initiated by ubiquitin unfolding.

Twomey, E.C., Ji, Z., Wales, T.E., Bodnar, N.O., Ficarro, S.B., Marto, J.A., Engen, J.R., Rapoport, T.A.

(2019) Science 365

  • DOI: https://doi.org/10.1126/science.aax1033
  • Primary Citation of Related Structures:  
    6OA9, 6OAA, 6OAB

  • PubMed Abstract: 

    • The Cdc48 adenosine triphosphatase (ATPase) (p97 or valosin-containing protein in mammals) and its cofactor Ufd1/Npl4 extract polyubiquitinated proteins from membranes or macromolecular complexes for subsequent degradation by the proteasome. How Cdc48 processes its diverse and often well-folded substrates is unclear ...

    The Cdc48 adenosine triphosphatase (ATPase) (p97 or valosin-containing protein in mammals) and its cofactor Ufd1/Npl4 extract polyubiquitinated proteins from membranes or macromolecular complexes for subsequent degradation by the proteasome. How Cdc48 processes its diverse and often well-folded substrates is unclear. Here, we report cryo-electron microscopy structures of the Cdc48 ATPase in complex with Ufd1/Npl4 and polyubiquitinated substrate. The structures show that the Cdc48 complex initiates substrate processing by unfolding a ubiquitin molecule. The unfolded ubiquitin molecule binds to Npl4 and projects its N-terminal segment through both hexameric ATPase rings. Pore loops of the second ring form a staircase that acts as a conveyer belt to move the polypeptide through the central pore. Inducing the unfolding of ubiquitin allows the Cdc48 ATPase complex to process a broad range of substrates.

    Organizational Affiliation: 

    Department of Cell Biology, Harvard Medical School, and Howard Hughes Medical Institute, 240 Longwood Avenue, Boston, MA 02115, USA. tom_rapoport@hms.harvard.edu.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Cell division control protein 48
A, B, C, D, E, F
A, B, C, D, E, F
835Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: CDC48, YDL126C
EC: 3.6.4.6
UniProt
Find proteins for P25694 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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Go to UniProtKB:  P25694
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UniProt GroupP25694
Protein Feature View
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinG [auth K],
H,
I [auth J]		76Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RPL40A, UBI1, YIL148W
UniProt
Find proteins for P0CH08 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP0CH08
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear protein localization protein 4J [auth G]580Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: NPL4, HRD4, YBR170C, YBR1231
UniProt
Find proteins for P33755 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
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UniProt GroupP33755
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.90 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR01GM052586
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesT32GM007753

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-03
    Type: Initial release
  • Version 1.1: 2019-07-10
    Changes: Data collection, Database references
  • Version 1.2: 2019-08-14
    Changes: Data collection, Database references
  • Version 1.3: 2019-11-20
    Changes: Author supporting evidence