Biological Assembly 1  

 3D View: Structure | Electron Density

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

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

Macromolecule Content

• Total Structure Weight: 18.05 kDa 
• Atom Count: 1449 
• Modelled Residue Count: 152 
• Deposited Residue Count: 157 
• Unique protein chains: 1

3L1Y

Crystal structure of human UBC4 E2 conjugating enzyme

• DOI: 10.2210/pdb3L1Y/pdb

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


• Deposited: 2009-12-14 Released: 2010-05-05 
• Deposition Author(s): Benirschke, R., Thompson, J.R., Mer, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.229 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 

Literature

Molecular Basis for the Association of Human E4B U Box Ubiquitin Ligase with E2-Conjugating Enzymes UbcH5c and Ubc4.

Benirschke, R.C., Thompson, J.R., Nomine, Y., Wasielewski, E., Juranic, N., Macura, S., Hatakeyama, S., Nakayama, K.I., Botuyan, M.V., Mer, G.

(2010) Structure 18: 955-965

• PubMed: 20696396 
• DOI: 10.1016/j.str.2010.04.017
• Primary Citation of Related Structures:  
  3L1X, 3L1Y, 3L1Z, 2KRE


• PubMed Abstract: 
  

Human E4B, also called UFD2a, is a U box-containing protein that functions as an E3 ubiquitin ligase and an E4 polyubiquitin chain elongation factor. E4B is thought to participate in the proteasomal degradation of misfolded or damaged proteins through association with chaperones. The U box domain is an anchor site for E2 ubiquitin-conjugating enzymes, but little is known of the binding mechanism. Using X-ray crystallography and NMR spectroscopy, we determined the structures of E4B U box free and bound to UbcH5c and Ubc4 E2s. Whereas previously characterized U box domains are homodimeric, we show that E4B U box is a monomer stabilized by a network of hydrogen bonds identified from scalar coupling measurements. These structural studies, complemented by calorimetry- and NMR-based binding assays, suggest an allosteric regulation of UbcH5c and Ubc4 by E4B U box and provide a molecular basis to understand how the ubiquitylation machinery involving E4B assembles.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin-conjugating enzyme E2 D2	A	157	Homo sapiens	Mutation(s): 0  Gene Names: UBE2D2, UBC4, UBCH5B, PUBC1, UBC5B, UBCH4 EC: 6.3.2.19 (PDB Primary Data), 2.3.2.23 (UniProt), 2.3.2.24 (UniProt)
Find proteins for P62837 (Homo sapiens) Explore P62837  Go to UniProtKB:  P62837
NIH Common Fund Data Resources
PHAROS:  P62837 GTEx:  ENSG00000131508

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free: 0.229 
• R-Value Work: 0.187 
• R-Value Observed: 0.189 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 28.23	α = 90
b = 59.12	β = 106.73
c = 45.24	γ = 90

Software Package:

Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-12-14 
• Released Date: 2010-05-05 
Deposition Author(s): Benirschke, R., Thompson, J.R., Mer, G.

Revision History  

• Version 1.0: 2010-05-05
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance