Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 6-mer - A2B2C2 

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

Macromolecule Content

• Total Structure Weight: 65.34 kDa 
• Atom Count: 4389 
• Modelled Residue Count: 558 
• Deposited Residue Count: 580 
• Unique protein chains: 3

4AUQ

Structure of BIRC7-UbcH5b-Ub complex.

• PDB DOI: 10.2210/pdb4AUQ/pdb

• Classification: LIGASE/LIGASE/SIGNALLING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2012-05-21 Released: 2012-08-15 
• Deposition Author(s): Dou, H., Buetow, L., Sibbet, G.J., Cameron, K., Huang, D.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 0.249 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 

Literature

Birc7-E2 Ubiquitin Conjugate Structure Reveals the Mechanism of Ubiquitin Transfer by a Ring Dimer.

Dou, H., Buetow, L., Sibbet, G.J., Cameron, K., Huang, D.T.

(2012) Nat Struct Mol Biol 19: 876

• PubMed: 22902369 
• DOI: 10.1038/nsmb.2379
• Primary Citation of Related Structures:  
  4AUQ


• PubMed Abstract: 
  

Certain RING ubiquitin ligases (E3s) dimerize to facilitate ubiquitin (Ub) transfer from ubiquitin-conjugating enzyme (E2) to substrate, but structural evidence on how this process promotes Ub transfer is lacking. Here we report the structure of the human dimeric RING domain from BIRC7 in complex with the E2 UbcH5B covalently linked to Ub (UbcH5B∼Ub). The structure reveals extensive noncovalent donor Ub interactions with UbcH5B and both subunits of the RING domain dimer that stabilize the globular body and C-terminal tail of Ub. Mutations that disrupt these noncovalent interactions or RING dimerization reduce UbcH5B∼Ub binding affinity and ubiquitination activity. Moreover, NMR analyses demonstrate that BIRC7 binding to UbcH5B∼Ub induces peak-shift perturbations in the donor Ub consistent with the crystallographically-observed Ub interactions. Our results provide structural insights into how dimeric RING E3s recruit E2∼Ub and optimize the donor Ub configuration for transfer.

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Organizational Affiliation: 

The Beatson Institute for Cancer Research, Garscube Estate, Switchback Road, Glasgow, G61 1BD, United Kingdom.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UBIQUITIN-CONJUGATING ENZYME E2 D2	A, D	147	Homo sapiens	Mutation(s): 3  Gene Names: UBE2D2, PUBC1, UBC4, UBC5B, UBCH4, UBCH5B EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt), 2.3.2.24 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P62837 (Homo sapiens) Explore P62837  Go to UniProtKB:  P62837
PHAROS:  P62837 GTEx:  ENSG00000131508

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 7	B, E	62	Homo sapiens	Mutation(s): 0  Gene Names: BIRC7, KIAP, LIVIN, MLIAP, RNF50, UNQ5800/PRO19607/PRO21344 EC: 6.3.2 (PDB Primary Data), 2.3.2.27 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96CA5 (Homo sapiens) Explore Q96CA5  Go to UniProtKB:  Q96CA5
PHAROS:  Q96CA5 GTEx:  ENSG00000101197

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
POLYUBIQUITIN-C	C, F	81	Homo sapiens	Mutation(s): 0  Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
PHAROS:  P0CG48

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	G [auth B], H [auth B], I [auth E], J [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 0.249 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.64	α = 90
b = 100.64	β = 90
c = 123.899	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-05-21 
• Released Date: 2012-08-15 
Deposition Author(s): Dou, H., Buetow, L., Sibbet, G.J., Cameron, K., Huang, D.T.

Revision History  

• Version 1.0: 2012-08-15
  Type: Initial release
  
• Version 1.1: 2012-09-26
  Changes: Database references
• Version 1.2: 2019-07-31
  Changes: Advisory, Data collection, Derived calculations