Biological Assembly 1  

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

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 25.42 kDa 
• Atom Count: 1435 
• Modelled Residue Count: 188 
• Deposited Residue Count: 230 
• Unique protein chains: 2

1YX6

Solution Structure of S5a UIM-2/Ubiquitin Complex

• PDB DOI: 10.2210/pdb1YX6/pdb
• BMRB: 6233

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


• Deposited: 2005-02-19 Released: 2005-04-19 
• Deposition Author(s): Wang, Q., Young, P., Walters, K.J.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 18 
• Selection Criteria: back calculated data agree with experimental NOESY spectrum 

Literature

Structure of S5a Bound to Monoubiquitin Provides a Model for Polyubiquitin Recognition

Wang, Q., Young, P., Walters, K.J.

(2005) J Mol Biol 348: 727-739

• PubMed: 15826667 
• DOI: 10.1016/j.jmb.2005.03.007
• Primary Citation of Related Structures:  
  1YX4, 1YX5, 1YX6


• PubMed Abstract: 
  

Ubiquitin is a key regulatory molecule in diverse cellular events. How cells determine the outcome of ubiquitylation remains unclear; however, a likely determinant is the specificity of ubiquitin receptor proteins for polyubiquitin chains of certain length and linkage. Proteasome subunit S5a contains two ubiquitin-interacting motifs (UIMs) through which it recruits ubiquitylated substrates to the proteasome for their degradation. Here, we report the structure of S5a (196-306) alone and complexed with two monoubiquitin molecules. This construct contains the two UIMs of S5a and we reveal their different ubiquitin-binding mechanisms and provide a rationale for their unique specificities for different ubiquitin-like domains. Furthermore, we provide direct evidence that S5a (196-306) binds either K63-linked or K48-linked polyubiquitin, and in both cases prefers longer chains. On the basis of these results we present a model for how S5a and other ubiquitin-binding proteins recognize polyubiquitin.

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Organizational Affiliation: 

Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota, 6-155 Jackson Hall, 321 Church St SE, Minneapolis, MN 55455, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 4	A	132	Homo sapiens	Mutation(s): 0  Gene Names: PSMD4, MCB1
UniProt & NIH Common Fund Data Resources
Find proteins for P55036 (Homo sapiens) Explore P55036  Go to UniProtKB:  P55036
PHAROS:  P55036

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	B	98	Homo sapiens	Mutation(s): 0  Gene Names: UBC
UniProt & NIH Common Fund Data Resources
Find proteins for P0CG48 (Homo sapiens) Explore P0CG48  Go to UniProtKB:  P0CG48
PHAROS:  P0CG48

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 20 
• Conformers Submitted: 18 
• Selection Criteria: back calculated data agree with experimental NOESY spectrum 
• OLDERADO: 1YX6 Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-02-19 
• Released Date: 2005-04-19 
Deposition Author(s): Wang, Q., Young, P., Walters, K.J.

Revision History  

• Version 1.0: 2005-04-19
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2022-03-02
  Changes: Database references, Derived calculations