Biological Assembly 1  

 3D View: Structure | 1D-3D View | Validation Report

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 16.76 kDa 
• Atom Count: 1178 
• Modelled Residue Count: 147 
• Deposited Residue Count: 147 
• Unique protein chains: 1

1W4U

NMR solution structure of the ubiquitin conjugating enzyme UbcH5B

• PDB DOI: 10.2210/pdb1W4U/pdb
• BMRB: 6277

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


• Deposited: 2004-07-29 Released: 2004-11-10 
• Deposition Author(s): Houben, K., Dominguez, C., Van Schaik, F.M.A., Timmers, H.T.M., Bonvin, A.M.J.J., Boelens, R.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 10 
• Selection Criteria: LOWEST ENERGY 

Literature

Solution Structure of the Ubiquitin-Conjugating Enzyme Ubch5B

Houben, K., Dominguez, C., Van Schaik, F.M.A., Timmers, H.T.M., Bonvin, A.M.J.J., Boelens, R.

(2004) J Mol Biol 344: 513

• PubMed: 15522302 
• DOI: 10.1016/j.jmb.2004.09.054
• Primary Citation of Related Structures:  
  1W4U


• PubMed Abstract: 
  

The ubiquitination pathway is the main pathway for protein degradation in eukaryotic cells. The attachment of ubiquitin to a substrate protein is catalyzed by three types of enzymes, namely a ubiquitin activating enzyme (E1), a ubiquitin-conjugating enzyme (E2), and a ubiquitin ligase (E3). Here, the structure of the human ubiquitin-conjugating enzyme (E2) UbcH5B has been solved by a combination of homology modeling, NMR relaxation data and automated NOE assignments. Comparison to E2 structures solved previously by X-ray crystallography or NMR shows in all cases the same compact fold, but differences are observed in the orientation of both N and C-terminal alpha-helices. The N-terminal helix that is involved in binding to ubiquitin ligases (E3) displays a different position, which could have consequences for precise E2-E3 recognition. In addition, multiple conformations of the side-chain of Asn77 are found in solution, which contrasts the single hydrogen-bonded conformation in the crystal structures of E2 enzymes. The possible implication of this conformational freedom of Asn77 for its catalytic function is discussed.

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Organizational Affiliation: 

Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UBIQUITIN-CONJUGATING ENZYME E2-17 KDA 2	A	147	Homo sapiens	Mutation(s): 0  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

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 50 
• Conformers Submitted: 10 
• Selection Criteria: LOWEST ENERGY 
• OLDERADO: 1W4U Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-07-29 
• Released Date: 2004-11-10 
Deposition Author(s): Houben, K., Dominguez, C., Van Schaik, F.M.A., Timmers, H.T.M., Bonvin, A.M.J.J., Boelens, R.

Revision History  

• Version 1.0: 2004-11-10
  Type: Initial release
  
• Version 1.1: 2017-04-19
  Changes: Atomic model, Other