Macromolecule Content

• Total Structure Weight: 15.95 kDa 
• Atom Count: 1117 
• Residue Count: 143 
• Unique protein chains: 2

1UEL

Solution structure of ubiquitin-like domain of hHR23B complexed with ubiquitin-interacting motif of proteasome subunit S5a

• DOI: 10.2210/pdb1UEL/pdb

• Classification: GENE REGULATION/protein binding
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2003-05-19 Released: 2004-02-10 
• Deposition Author(s): Fujiwara, K., Tenno, T., Jee, J.G., Sugasawa, K., Ohki, I., Kojima, C., Tochio, H., Hiroaki, H., Hanaoka, H., Shirakawa, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: The submitted conformer models are the 20 structures with the lowest 

Literature

Structure of the Ubiquitin-interacting Motif of S5a Bound to the Ubiquitin-like Domain of HR23B

Fujiwara, K., Tenno, T., Sugasawa, K., Jee, J.G., Ohki, I., Kojima, C., Tochio, H., Hiroaki, H., Hanaoka, F., Shirakawa, M.

(2004) J Biol Chem 279: 4760-4767

• PubMed: 14585839 
• DOI: 10.1074/jbc.M309448200
• Primary Citation of Related Structures:  
  1UEL


• PubMed Abstract: 
  

Ubiquitination, a modification in which single or multiple ubiquitin molecules are attached to a protein, serves signaling functions that control several cellular processes. The ubiquitination signal is recognized by downstream effectors, many of which carry a ubiquitin-interacting motif (UIM). Such interactions can be modulated by regulators carrying a ubiquitin-like (UbL) domain, which binds UIM by mimicking ubiquitination. Of them, HR23B regulates the proteasomal targeting of ubiquitinated substrates, DNA repair factors, and other proteins. Here we report the structure of the UIM of the proteasome subunit S5a bound to the UbL domain of HR23B. The UbL domain presents one hydrophobic and two polar contact sites for interaction with UIM. The residues in these contact sites are well conserved in ubiquitin, but ubiquitin also presents a histidine at the interface. The pH-dependent protonation of this residue interferes with the access of ubiquitin to the UIM and the ubiquitin-associated domain (UBA), and its mutation to a smaller residue increases the affinity of ubiquitin for UIM.

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Organizational Affiliation: 

Graduate School of Integrated Science, Yokohama City University, 1-7-29 Suehiro, Tsurumi, Yokohama, Kanagawa 230-0045, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
UV excision repair protein RAD23 homolog B	A	95	Homo sapiens	Mutation(s): 0  Gene Names: RAD23B
Find proteins for P54727 (Homo sapiens) Explore P54727  Go to UniProtKB:  P54727
NIH Common Fund Data Resources
PHAROS:  P54727 GTEx:  ENSG00000119318

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
26S proteasome non-ATPase regulatory subunit 4	B	48	Homo sapiens	Mutation(s): 0  Gene Names: PSMD4, MCB1
Find proteins for P55036 (Homo sapiens) Explore P55036  Go to UniProtKB:  P55036
NIH Common Fund Data Resources
PHAROS:  P55036 GTEx:  ENSG00000159352

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: The submitted conformer models are the 20 structures with the lowest 
• OLDERADO: 1UEL Olderado

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-05-19 
• Released Date: 2004-02-10 
Deposition Author(s): Fujiwara, K., Tenno, T., Jee, J.G., Sugasawa, K., Ohki, I., Kojima, C., Tochio, H., Hiroaki, H., Hanaoka, H., Shirakawa, M., RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Revision History 

• Version 1.0: 2004-02-10
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance