6OAA

Cdc48-Npl4 complex processing poly-ubiquitinated substrate in the presence of ADP-BeFx, state 1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report


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: 10.1126/science.aax1033
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The Cdc48 ATPase (p97 or VCP in mammals) and its cofactor Ufd1/Npl4 extract poly-ubiquitinated proteins from membranes or macromolecular complexes for subsequent degradation by the proteasome. How Cdc48 processes its diverse and often well-folded sub ...

    The Cdc48 ATPase (p97 or VCP in mammals) and its cofactor Ufd1/Npl4 extract poly-ubiquitinated 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-EM structures of the Cdc48 ATPase in complex with Ufd1/Npl4 and poly-ubiquitinated 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 Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA.,Department of Cell Biology, Harvard Medical School, and Howard Hughes Medical Institute, 240 Longwood Avenue, Boston, Massachusetts 02115, USA.,Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.,Department of Cancer Biology, Department of Oncologic Pathology, and Blais Proteomics Center, Dana-Farber Cancer Institute, Boston, MA 02115, USA.,Department of Cell Biology, Harvard Medical School, and Howard Hughes Medical Institute, 240 Longwood Avenue, Boston, Massachusetts 02115, USA. tom_rapoport@hms.harvard.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Cell division control protein 48
B, C, D, E
835Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: CDC48
EC: 3.6.4.6
Find proteins for P25694 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P25694
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear protein localization protein 4
G
580Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: NPL4 (HRD4)
Find proteins for P33755 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P33755
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Ubiquitin
H
76Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: RPL40A (UBI1)
Find proteins for P0CH08 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P0CH08
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download SDF File 
Download CCD File 
B, C, E
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
BEF
Query on BEF

Download SDF File 
Download CCD File 
B, C, D
BERYLLIUM TRIFLUORIDE ION
Be F3
OGIAHMCCNXDTIE-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 4.1 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report or Ramachandran Plots



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 

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