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): 10 

  • 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; National Institutes of Health/National Cancer Institute; ALSAC; Howard Hughes Medical Institute; Canadian Institutes of Health Research; 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 1.2 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:  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 ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Anaphase-promoting complex subunit 11
A, D
70Homo sapiensGene 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 sapiensGene 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
HKL-2000data scaling
PHASERphasing
HKL-2000data reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR37GM065930
National Institutes of Health/National Cancer InstituteUnited StatesP30CA021765
ALSACUnited States--
Howard Hughes Medical InstituteUnited States--
Canadian Institutes of Health ResearchCanadaMOP#111149
Canadian Institutes of Health ResearchCanada136956
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