6BPH

Crystal structure of the chromodomain of RBBP1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.206 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of chromo barrel domain of RBBP1.

Lei, M.Feng, Y.Zhou, M.Yang, Y.Loppnau, P.Li, Y.Yang, Y.Liu, Y.

(2018) Biochem. Biophys. Res. Commun. 496: 1344-1348

  • DOI: 10.1016/j.bbrc.2018.02.016

  • PubMed Abstract: 
  • RBBP1 is a retinoblastoma protein (pRb) binding protein acting as a repressor of gene transcription. RBBP1 is a multidomain protein including a chromo barrel domain, and its chromo barrel domain has been reported to recognize histone H4K20me3 weakly, ...

    RBBP1 is a retinoblastoma protein (pRb) binding protein acting as a repressor of gene transcription. RBBP1 is a multidomain protein including a chromo barrel domain, and its chromo barrel domain has been reported to recognize histone H4K20me3 weakly, and this binding is enhanced by the simultaneous binding of DNA. However, the molecular basis of this DNA-mediated histone binding by the chromo barrel domain of RBBP1 is unclear. Here we attempted to co-crystallize the chromo barrel domain of RBBP1 with either a histone H4K20me3 peptide alone or with both a histone H4K20me3 peptide and DNA, but only solved the peptide/DNA unbound crystal structure. Our structural analysis indicates that RBBP1 could interact with histone H4K20me3 similar to other histone binding chromo barrel domains, and the surface charge representation analysis of the chromo barrel domain of RBBP1 suggests that the chromo barrel domain of RBBP1 does not have a typical DNA binding surface, indicating that it might not bind to DNA. Consistently, our ITC assays also showed that DNA does not significantly enhance the histone binding ability of the chromo barrel domain of RBBP1.


    Organizational Affiliation

    Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China.,College of Health Science, Wuhan Sports University, Wuhan 430079, PR China. Electronic address: yangyi999999@yahoo.com.,Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada.,Graduate School, Wuhan Sports University, Wuhan 430079, PR China.,Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada.,Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, PR China; Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario M5G 1L7, Canada. Electronic address: yanliliu@mail.ccnu.edu.cn.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
AT-rich interactive domain-containing protein 4A
A
69Homo sapiensMutation(s): 0 
Gene Names: ARID4A (RBBP1, RBP1)
Find proteins for P29374 (Homo sapiens)
Go to Gene View: ARID4A
Go to UniProtKB:  P29374
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
UNX
Query on UNX

Download SDF File 
Download CCD File 
A
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 41.493α = 90.00
b = 41.493β = 90.00
c = 81.349γ = 90.00
Software Package:
Software NamePurpose
Aimlessdata scaling
PHASERphasing
XDSdata reduction
BUSTERrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-12-20
    Type: Initial release
  • Version 1.1: 2018-02-21
    Type: Database references
  • Version 1.2: 2018-02-28
    Type: Database references