3L1Z

Crystal structure of the U-BOX domain of human E4B ubiquitin ligase in complex with UBCH5C E2 ubiquitin conjugating enzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.17 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.236 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


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

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

  • 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.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin-conjugating enzyme E2 D3157Homo sapiensMutation(s): 0 
Gene Names: UBE2D3UBCH5C
EC: 6.3.2.19
UniProt & NIH Common Fund Data Resources
Find proteins for P61077 (Homo sapiens)
Explore P61077 
Go to UniProtKB:  P61077
GTEx:  ENSG00000109332 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP61077
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Ubiquitin conjugation factor E4 B100Homo sapiensMutation(s): 0 
Gene Names: UBE4BHDNB1KIAA0684UFD2
UniProt & NIH Common Fund Data Resources
Find proteins for O95155 (Homo sapiens)
Explore O95155 
Go to UniProtKB:  O95155
GTEx:  ENSG00000130939 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO95155
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.17 Å
  • R-Value Free: 0.279 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.236 
  • Space Group: P 6 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 142.708α = 90
b = 142.708β = 90
c = 83.133γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2011-12-28
    Changes: Derived calculations
  • Version 1.3: 2023-09-06
    Changes: Data collection, Database references, Refinement description