Crystal structure of the UBC domain of baculoviral IAP repeat-containing protein 6

Experimental Data Snapshot

  • Resolution: 2.01 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 

wwPDB Validation   3D Report Full Report

This is version 1.2 of the entry. See complete history


A human ubiquitin conjugating enzyme (E2)-HECT E3 ligase structure-function screen.

Sheng, Y.Hong, J.H.Doherty, R.Srikumar, T.Shloush, J.Avvakumov, G.V.Walker, J.R.Xue, S.Neculai, D.Wan, J.W.Kim, S.K.Arrowsmith, C.H.Raught, B.Dhe-Paganon, S.

(2012) Mol Cell Proteomics 11: 329-341

  • DOI: https://doi.org/10.1074/mcp.O111.013706
  • Primary Citation of Related Structures:  
    1Y6L, 1YH2, 1YRV, 1ZDN, 1ZUO, 2A4D, 2A7L, 2AWF, 2F4W, 2OB4, 2QGX, 2Z5D, 3BZH, 3CEG

  • PubMed Abstract: 

    Here we describe a systematic structure-function analysis of the human ubiquitin (Ub) E2 conjugating proteins, consisting of the determination of 15 new high-resolution three-dimensional structures of E2 catalytic domains, and autoubiquitylation assays for 26 Ub-loading E2s screened against a panel of nine different HECT (homologous to E6-AP carboxyl terminus) E3 ligase domains. Integration of our structural and biochemical data revealed several E2 surface properties associated with Ub chain building activity; (1) net positive or neutral E2 charge, (2) an "acidic trough" located near the catalytic Cys, surrounded by an extensive basic region, and (3) similarity to the previously described HECT binding signature in UBE2L3 (UbcH7). Mass spectrometry was used to characterize the autoubiquitylation products of a number of functional E2-HECT pairs, and demonstrated that HECT domains from different subfamilies catalyze the formation of very different types of Ub chains, largely independent of the E2 in the reaction. Our data set represents the first comprehensive analysis of E2-HECT E3 interactions, and thus provides a framework for better understanding the molecular mechanisms of ubiquitylation.

  • Organizational Affiliation

    Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Baculoviral IAP repeat-containing protein 6
A, B
323Homo sapiensMutation(s): 0 
Gene Names: BIRC6KIAA1289
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NR09 (Homo sapiens)
Explore Q9NR09 
Go to UniProtKB:  Q9NR09
GTEx:  ENSG00000115760 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NR09
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 2.01 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.211 
  • R-Value Observed: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.199α = 90
b = 97.815β = 90
c = 129.888γ = 90
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2008-04-01
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-11-28
    Changes: Database references