2JXJ

NMR structure of the ARID domain from the histone H3K4 demethylase RBP2

• PDB DOI: https://doi.org/10.2210/pdb2JXJ/pdb

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


• Deposited: 2007-11-20 Released: 2008-09-30 
• Deposition Author(s): Tu, S., Yuan, C., Tsai, M.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 

Literature

The ARID domain of the H3K4 demethylase RBP2 binds to a DNA CCGCCC motif

Tu, S., Teng, Y.C., Yuan, C., Wu, Y.T., Chan, M.Y., Cheng, A.N., Lin, P.H., Juan, L.J., Tsai, M.D.

(2008) Nat Struct Mol Biol 15: 419-421

• PubMed: 18270511 
• DOI: https://doi.org/10.1038/nsmb.1400
• Primary Citation of Related Structures:  
  2JXJ


• PubMed Abstract: 
  

  The histone H3 lysine 4 demethylase RBP2 contains a DNA binding domain, the AT-rich interaction domain (ARID). We solved the structure of ARID by NMR, identified its DNA binding motif (CCGCCC) and characterized the binding contacts. Immunofluorescence and luciferase assays indicated that ARID is required for RBP2 demethylase activity in cells and that DNA recognition is essential to regulate transcription.

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Organizational Affiliation: 

Department of Chemistry, Ohio State University, 100 West 18th Ave., Columbus, Ohio 43210, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 10.84 kDa 
• Atom Count: 766 
• Modelled Residue Count: 96 
• Deposited Residue Count: 96 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone demethylase JARID1A	A	96	Homo sapiens	Mutation(s): 0  Gene Names: JARID1A, RBBP2, RBP2 EC: 1.14.11
UniProt & NIH Common Fund Data Resources
Find proteins for P29375 (Homo sapiens) Explore P29375  Go to UniProtKB:  P29375
PHAROS:  P29375 GTEx:  ENSG00000073614

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the least restraint violations 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-30 
Deposition Author(s): Tu, S., Yuan, C., Tsai, M.

Revision History  

• Version 1.0: 2008-09-30
  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