5JG6

APC11-Ubv shows role of noncovalent RING-Ubiquitin interactions in processive multiubiquitination and Ubiquitin chain elongation by APC/C

  • Classification: CELL CYCLE
  • Organism(s): Homo sapiens
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2016-04-19 Released: 2016-06-15 
  • Deposition Author(s): Brown, N.G., Zhang, W., Yu, S., Miller, D.J., Sidhu, S.S., Schulman, B.A.
  • Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Cancer Institute (NIH/NCI), St. Jude Children's Research Hospital (ALSAC), Howard Hughes Medical Institute (HHMI), Canadian Institutes of Health Research (CIHR), Leukemia & Lymphoma Society, Jane Coffin Childs Memorial Fund

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 

Starting Models: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.5 of the entry. See complete history


Literature

Dual RING E3 Architectures Regulate Multiubiquitination and Ubiquitin Chain Elongation by APC/C.

Brown, N.G.VanderLinden, R.Watson, E.R.Weissmann, F.Ordureau, A.Wu, K.P.Zhang, W.Yu, S.Mercredi, P.Y.Harrison, J.S.Davidson, I.F.Qiao, R.Lu, Y.Dube, P.Brunner, M.R.Grace, C.R.Miller, D.J.Haselbach, D.Jarvis, M.A.Yamaguchi, M.Yanishevski, D.Petzold, G.Sidhu, S.S.Kuhlman, B.Kirschner, M.W.Harper, J.W.Peters, J.M.Stark, H.Schulman, B.A.

(2016) Cell 165: 1440-1453

  • DOI: https://doi.org/10.1016/j.cell.2016.05.037
  • Primary Citation of Related Structures:  
    5JG6, 5L9T, 5L9U

  • PubMed Abstract: 

    Protein ubiquitination involves E1, E2, and E3 trienzyme cascades. E2 and RING E3 enzymes often collaborate to first prime a substrate with a single ubiquitin (UB) and then achieve different forms of polyubiquitination: multiubiquitination of several sites and elongation of linkage-specific UB chains. Here, cryo-EM and biochemistry show that the human E3 anaphase-promoting complex/cyclosome (APC/C) and its two partner E2s, UBE2C (aka UBCH10) and UBE2S, adopt specialized catalytic architectures for these two distinct forms of polyubiquitination. The APC/C RING constrains UBE2C proximal to a substrate and simultaneously binds a substrate-linked UB to drive processive multiubiquitination. Alternatively, during UB chain elongation, the RING does not bind UBE2S but rather lures an evolving substrate-linked UB to UBE2S positioned through a cullin interaction to generate a Lys11-linked chain. Our findings define mechanisms of APC/C regulation, and establish principles by which specialized E3-E2-substrate-UB architectures control different forms of polyubiquitination.


  • Organizational Affiliation

    Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Anaphase-promoting complex subunit 11
A, D
70Homo sapiensMutation(s): 0 
Gene Names: ANAPC11HSPC214
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NYG5 (Homo sapiens)
Explore Q9NYG5 
Go to UniProtKB:  Q9NYG5
PHAROS:  Q9NYG5
GTEx:  ENSG00000141552 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NYG5
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Polyubiquitin-B
B, C
84Homo sapiensMutation(s): 0 
Gene Names: UBB
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG47 (Homo sapiens)
Explore P0CG47 
Go to UniProtKB:  P0CG47
PHAROS:  P0CG47
GTEx:  ENSG00000170315 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0CG47
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.187 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 131.066α = 90
b = 35.193β = 120.42
c = 72.768γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

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 StatesR37GM065930
National Institutes of Health/National Cancer Institute (NIH/NCI)United StatesP30CA021765
St. Jude Children's Research Hospital (ALSAC)United States--
Howard Hughes Medical Institute (HHMI)United States--
Canadian Institutes of Health Research (CIHR)CanadaMOP#111149
Canadian Institutes of Health Research (CIHR)Canada136956
Leukemia & Lymphoma SocietyUnited States--
Jane Coffin Childs Memorial FundUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2016-06-15
    Type: Initial release
  • Version 1.1: 2017-09-06
    Changes: Author supporting evidence, Derived calculations
  • Version 1.2: 2017-09-27
    Changes: Author supporting evidence
  • Version 1.3: 2019-11-20
    Changes: Author supporting evidence
  • Version 1.4: 2020-01-08
    Changes: Author supporting evidence
  • Version 1.5: 2023-09-27
    Changes: Data collection, Database references, Refinement description