2KSN | pdb_00002ksn

Solution Structure of the N-terminal Domain of DC-UbP/UBTD2

• PDB DOI: https://doi.org/10.2210/pdb2KSN/pdb

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


• Deposited: 2010-01-08 Released: 2010-05-19 
• Deposition Author(s): Song, A., Zhou, C., Guan, X., Sze, K., Hu, H.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Solution structure of the N-terminal domain of DC-UbP/UBTD2 and its interaction with ubiquitin

Song, A., Zhou, C., Guan, X., Sze, K., Hu, H.

(2010) Protein Sci 19: 1104-1109

• PubMed: 20440844 
• DOI: https://doi.org/10.1002/pro.386
• Primary Citation of Related Structures:  
  2KSN


• PubMed Abstract: 
  

  DC-UbP/UBTD2 is a ubiquitin (Ub) domain-containing protein first identified from dendritic cells, and is implicated in ubiquitination pathway. The solution structure and backbone dynamics of the C-terminal Ub-like (UbL) domain were elucidated in our previous work. To further understand the biological function of DC-UbP, we then solved the solution structure of the N-terminal domain of DC-UbP (DC-UbP_N) and studied its Ub binding properties by NMR techniques. The results show that DC-UbP_N holds a novel structural fold and acts as a Ub-binding domain (UBD) but with low affinity. This implies that the DC-UbP protein, composing of a combination of both UbL and UBD domains, might play an important role in regulating protein ubiquitination and delivery of ubiquitinated substrates in eukaryotic cells.

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Organizational Affiliation: 
• State Key Laboratory of Molecular Biology, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 15.59 kDa 
• Atom Count: 1,011 
• Modeled Residue Count: 128 
• Deposited Residue Count: 137 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin domain-containing protein 2	A	137	Homo sapiens	Mutation(s): 0  Gene Names: UBTD2, DCUBP, SB72
UniProt & NIH Common Fund Data Resources
Find proteins for Q8WUN7 (Homo sapiens) Explore Q8WUN7  Go to UniProtKB:  Q8WUN7
PHAROS:  Q8WUN7 GTEx:  ENSG00000168246

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 200 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-05-19 
Deposition Author(s): Song, A., Zhou, C., Guan, X., Sze, K., Hu, H.

Revision History  

• Version 1.0: 2010-05-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2022-03-16
  Changes: Data collection, Database references, Derived calculations
• Version 1.3: 2024-05-29
  Changes: Data collection