3OLM

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

• PDB DOI: https://doi.org/10.2210/pdb3OLM/pdb

• Classification: LIGASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2010-08-26 Released: 2011-03-23 
• Deposition Author(s): Kim, H.C., Steffen, A., Chen, J., Huibregtse, J.M.

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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 

Starting Model: experimental

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

• PubMed: 21399621 
• DOI: https://doi.org/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. 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Macromolecule Content

• Total Structure Weight: 59.21 kDa 
• Atom Count: 4,074 
• Modelled Residue Count: 486 
• Deposited Residue Count: 508 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
E3 ubiquitin-protein ligase RSP5	A	429	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: RSP5, MDP1, NPI1, YER125W, SYGP-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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	B [auth D]	79	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: UBI4, SCD2, YLL039C
UniProt
Find proteins for P0CG63 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P0CG63  Go to UniProtKB:  P0CG63

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 = 161.57	α = 90
b = 50.331	β = 116.72
c = 79.684	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-23 
Deposition Author(s): Kim, H.C., Steffen, A., Chen, J., Huibregtse, J.M.

Revision History  

• 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
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Refinement description