4YII | pdb_00004yii

Structure of an APC2-UBCH10 complex reveals distinctive cullin-RING ligase mechanism for Anaphase-promoting complex/Cyclosome

• PDB DOI: https://doi.org/10.2210/pdb4YII/pdb

• Classification: ligase/cell cycle
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-03-02 Released: 2015-04-08 
• Deposition Author(s): Brown, N.G., Cho, S.E., Schulman, B.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.199 (Depositor) 

Starting Models: experimental

Literature

Crystal Structure of E2 Complex

Brown, N.G., Cho, S.E., Schulman, B.A.

(2015) Proc Natl Acad Sci U S A 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 27.62 kDa 
• Atom Count: 1,768 
• Modeled Residue Count: 217 
• Deposited Residue Count: 245 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 C	A [auth U]	155	Homo sapiens	Mutation(s): 0  Gene Names: UBE2C, UBCH10 EC: 6.3.2.19 (PDB Primary Data), 2.3.2.24 (UniProt), 2.3.2.23 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O00762 (Homo sapiens) Explore O00762  Go to UniProtKB:  O00762
PHAROS:  O00762 GTEx:  ENSG00000175063

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Anaphase-promoting complex subunit 2	B [auth A]	90	Homo sapiens	Mutation(s): 0  Gene Names: ANAPC2, APC2, KIAA1406
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UJX6 (Homo sapiens) Explore Q9UJX6  Go to UniProtKB:  Q9UJX6
PHAROS:  Q9UJX6 GTEx:  ENSG00000176248

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.245 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.199 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 133.113	α = 90
b = 33.188	β = 100.12
c = 51.963	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-08 
Deposition Author(s): Brown, N.G., Cho, S.E., Schulman, B.A.

Revision History  

• Version 1.0: 2015-04-08
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description, Source and taxonomy