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

  • 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); 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: 2.0013 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.185 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1016/j.cell.2016.05.037
  • Primary Citation of Related Structures:  

  • 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 ...

    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 Biochemistry and Biophysics and Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA.,Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.,Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria. Electronic address: jan-michael.peters@imp.ac.at.,Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, 02115, USA.,Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany. Electronic address: hstark1@gwdg.de.,Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, Memphis, TN 38105, USA.,Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA.,Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S3E1, Canada.,Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, Memphis, TN 38105, USA. Electronic address: brenda.schulman@stjude.org.,Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Anaphase-promoting complex subunit 11
A, D
70Homo sapiensMutation(s): 0 
Gene Names: ANAPC11
Find proteins for Q9NYG5 (Homo sapiens)
Go to Gene View: ANAPC11
Go to UniProtKB:  Q9NYG5
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Polyubiquitin-B
B, C
84Homo sapiensMutation(s): 0 
Gene Names: UBB
Find proteins for P0CG47 (Homo sapiens)
Go to Gene View: UBB
Go to UniProtKB:  P0CG47
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, D
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0013 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.185 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 131.066α = 90.00
b = 35.193β = 120.42
c = 72.768γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
HKL-2000data reduction
PHENIXrefinement
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



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
ALSACUnited 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 

  • Version 1.0: 2016-06-15
    Type: Initial release
  • Version 1.1: 2017-09-06
    Type: Author supporting evidence, Derived calculations
  • Version 1.2: 2017-09-27
    Type: Author supporting evidence
  • Version 1.3: 2019-11-20
    Type: Author supporting evidence