3AAD | pdb_00003aad

Structure of the histone chaperone CIA/ASF1-double bromodomain complex linking histone modifications and site-specific histone eviction


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free: 
    0.293 (Depositor), 0.379 (DCC) 
  • R-Value Work: 
    0.237 (Depositor), 0.328 (DCC) 
  • R-Value Observed: 
    0.240 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 3AAD

This is version 1.4 of the entry. See complete history

Literature

Structure of the histone chaperone CIA/ASF1-double bromodomain complex linking histone modifications and site-specific histone eviction

Akai, Y.Adachi, N.Hayashi, Y.Eitoku, M.Sano, N.Natsume, R.Kudo, N.Tanokura, M.Senda, T.Horikoshi, M.

(2010) Proc Natl Acad Sci U S A 107: 8153-8158

  • DOI: https://doi.org/10.1073/pnas.0912509107
  • Primary Citation Related Structures: 
    3AAD

  • PubMed Abstract: 

    Nucleosomes around the promoter region are disassembled for transcription in response to various signals, such as acetylation and methylation of histones. Although the interactions between histone-acetylation-recognizing bromodomains and factors involved in nucleosome disassembly have been reported, no structural basis connecting histone modifications and nucleosome disassembly has been obtained. Here, we determined at 3.3 A resolution the crystal structure of histone chaperone cell cycle gene 1 (CCG1) interacting factor A/antisilencing function 1 (CIA/ASF1) in complex with the double bromodomain in the CCG1/TAF1/TAF(II)250 subunit of transcription factor IID. Structural, biochemical, and biological studies suggested that interaction between double bromodomain and CIA/ASF1 is required for their colocalization, histone eviction, and pol II entry at active promoter regions. Furthermore, the present crystal structure has characteristics that can connect histone acetylation and CIA/ASF1-mediated histone eviction. These findings suggest that the molecular complex between CIA/ASF1 and the double bromodomain plays a key role in site-specific histone eviction at active promoter regions. The model we propose here is the initial structure-based model of the biological signaling from histone modifications to structural change of the nucleosome (hi-MOST model).


  • Organizational Affiliation
    • Biomedicinal Information Research Center, National Institute of Advanced Industrial Science and Technology, 2-4-7 Aomi, Koto-ku, Tokyo 135-0064, Japan.

Macromolecule Content 

  • Total Structure Weight: 70.22 kDa 
  • Atom Count: 4,617 
  • Modeled Residue Count: 569 
  • Deposited Residue Count: 608 
  • Unique protein chains: 2

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Transcription initiation factor TFIID subunit 1292Homo sapiensMutation(s): 0 
Gene Names: CCG1TAF1TAFII250
EC: 2.7.11.1 (PDB Primary Data), 2.3.1.48 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P21675 (Homo sapiens)
Explore P21675 
Go to UniProtKB:  P21675
PHAROS:  P21675
GTEx:  ENSG00000147133 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP21675
Sequence Annotations
Expand
Reference Sequence
Find similar proteins by:|  3D Structure
Entity ID: 2
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone chaperone ASF1AB,
C [auth D]
158Homo sapiensMutation(s): 0 
Gene Names: ASF1ACIA-I
UniProt & NIH Common Fund Data Resources
Find proteins for Q9Y294 (Homo sapiens)
Explore Q9Y294 
Go to UniProtKB:  Q9Y294
PHAROS:  Q9Y294
GTEx:  ENSG00000111875 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9Y294
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
SO4

Query on SO4



Download:Ideal Coordinates CCD File
D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.30 Å
  • R-Value Free:  0.293 (Depositor), 0.379 (DCC) 
  • R-Value Work:  0.237 (Depositor), 0.328 (DCC) 
  • R-Value Observed: 0.240 (Depositor) 
Space Group: P 61 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.12α = 90
b = 102.12β = 90
c = 271.92γ = 120
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-04-28
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Advisory, Version format compliance
  • Version 1.2: 2014-01-29
    Changes: Database references
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2024-11-20
    Changes: Data collection, Database references, Derived calculations, Structure summary