4R2Y

Crystal structure of APC11 RING domain

• PDB DOI:  https://doi.org/10.2210/pdb4R2Y/pdb

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


• Deposited: 2014-08-13 Released: 2014-10-29 
• Deposition Author(s): Brown, N.G., Watson, E.R., Weissmann, F., Jarvis, M.A., Vanderlinden, R., Grace, C.R.R., Frye, J.J., Dube, P., Qiao, R., Petzold, G., Cho, S.E., Alsharif, O., Bao, J., Zheng, J., Nourse, A., Kurinov, I., Peters, J.M., Stark, H., Schulman, B.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.229 
• R-Value Work: 0.192 
• R-Value Observed: 0.195 

Literature

Mechanism of Polyubiquitination by Human Anaphase-Promoting Complex: RING Repurposing for Ubiquitin Chain Assembly.

Brown, N.G., Watson, E.R., Weissmann, F., Jarvis, M.A., VanderLinden, R., Grace, C.R., Frye, J.J., Qiao, R., Dube, P., Petzold, G., Cho, S.E., Alsharif, O., Bao, J., Davidson, I.F., Zheng, J.J., Nourse, A., Kurinov, I., Peters, J.M., Stark, H., Schulman, B.A.

(2014) Mol Cell 56: 246-260

• PubMed: 25306923 
• DOI: https://doi.org/10.1016/j.molcel.2014.09.009
• Primary Citation of Related Structures:  
  2MT5, 4R2Y


• PubMed Abstract: 
  

Polyubiquitination by E2 and E3 enzymes is a predominant mechanism regulating protein function. Some RING E3s, including anaphase-promoting complex/cyclosome (APC), catalyze polyubiquitination by sequential reactions with two different E2s. An initiating E2 ligates ubiquitin to an E3-bound substrate. Another E2 grows a polyubiquitin chain on the ubiquitin-primed substrate through poorly defined mechanisms. Here we show that human APC's RING domain is repurposed for dual functions in polyubiquitination. The canonical RING surface activates an initiating E2-ubiquitin intermediate for substrate modification. However, APC engages and activates its specialized ubiquitin chain-elongating E2 UBE2S in ways that differ from current paradigms. During chain assembly, a distinct APC11 RING surface helps deliver a substrate-linked ubiquitin to accept another ubiquitin from UBE2S. Our data define mechanisms of APC/UBE2S-mediated polyubiquitination, reveal diverse functions of RING E3s and E2s, and provide a framework for understanding distinctive RING E3 features specifying ubiquitin chain elongation.

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Organizational Affiliation: 

Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA; Howard Hughes Medical Institute, St. Jude Children's Research Hospital, Memphis, TN 38105, USA. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 5 assigned by authors and generated by PISA (software)

Biological Assembly 6  

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 6 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 32.41 kDa 
• Atom Count: 2,250 
• Modelled Residue Count: 250 
• Deposited Residue Count: 272 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit 11	A, B, C, D	68	Homo sapiens	Mutation(s): 0  Gene Names: ANAPC11, HSPC214
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NYG5 (Homo sapiens) Explore Q9NYG5  Go to UniProtKB:  Q9NYG5
PHAROS:  Q9NYG5

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], F [auth A], G [auth A], H [auth B], I [auth B], J [auth B], K [auth C], L [auth C], M [auth C], N [auth D], O [auth D], P [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.229 
• R-Value Work: 0.192 
• R-Value Observed: 0.195 
• Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.446	α = 90
b = 39.876	β = 108.49
c = 65.038	γ = 90

Software Package:

Software Name	Purpose
XDS-RAPD	data collection
SHELXS	phasing
PHENIX	refinement
XDS-RAPD	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-29 
Deposition Author(s): Brown, N.G., Watson, E.R., Weissmann, F., Jarvis, M.A., Vanderlinden, R., Grace, C.R.R., Frye, J.J., Dube, P., Qiao, R., Petzold, G., Cho, S.E., Alsharif, O., Bao, J., Zheng, J., Nourse, A., Kurinov, I., Peters, J.M., Stark, H., Schulman, B.A.

Revision History  

• Version 1.0: 2014-10-29
  Type: Initial release
  
• Version 1.1: 2014-11-19
  Changes: Database references