3OLM

Structure and Function of a Ubiquitin Binding Site within the Catalytic Domain of a HECT Ubiquitin Ligase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure and function of a HECT domain ubiquitin-binding site.

Kim, H.C.Steffen, A.M.Oldham, M.L.Chen, J.Huibregtse, J.M.

(2011) EMBO Rep 12: 334-341

  • DOI: 10.1038/embor.2011.23
  • Primary Citation of Related Structures:  
    3OLM

  • PubMed Abstract: 
  • The Rsp5 ubiquitin ligase contains a non-covalent binding site for ubiquitin within the amino-terminal lobe (N-lobe) of the HECT domain, and the X-ray crystal structure of the HECT-ubiquitin complex has been determined. Hydrophobic patch residues of ubiquitin (L8, I44, V70) were crucial for interaction with Rsp5, and amino-acid alterations at the Rsp5-binding interface resulted in defects in polyubiquitination ...

    The Rsp5 ubiquitin ligase contains a non-covalent binding site for ubiquitin within the amino-terminal lobe (N-lobe) of the HECT domain, and the X-ray crystal structure of the HECT-ubiquitin complex has been determined. Hydrophobic patch residues of ubiquitin (L8, I44, V70) were crucial for interaction with Rsp5, and amino-acid alterations at the Rsp5-binding interface resulted in defects in polyubiquitination. Our results support a model in which the N-lobe-binding site acts to localize and orient the distal end of the ubiquitin chain to promote conjugation of the next ubiquitin molecule.


    Organizational Affiliation

    Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
E3 ubiquitin-protein ligase RSP5A429Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: RSP5MDP1NPI1YER125WSYGP-ORF41
EC: 6.3.2 (PDB Primary Data), 2.3.2.26 (UniProt)
UniProt
Find proteins for P39940 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P39940 
Go to UniProtKB:  P39940
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
UbiquitinB [auth D]79Saccharomyces cerevisiaeMutation(s): 0 
Gene Names: UBI4SCD2YLL039C
UniProt
Find proteins for P0CG63 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P0CG63 
Go to UniProtKB:  P0CG63
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.272 
  • R-Value Work: 0.220 
  • R-Value Observed: 0.223 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 161.57α = 90
b = 50.331β = 116.72
c = 79.684γ = 90
Software Package:
Software NamePurpose
Blu-Icedata 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: 2011-03-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-09-25
    Changes: Derived calculations