2B2U

Tandem chromodomains of human CHD1 complexed with Histone H3 Tail containing trimethyllysine 4 and dimethylarginine 2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.238 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Double chromodomains cooperate to recognize the methylated histone H3 tail.

Flanagan, J.F.Mi, L.Z.Chruszcz, M.Cymborowski, M.Clines, K.L.Kim, Y.Minor, W.Rastinejad, F.Khorasanizadeh, S.

(2005) Nature 438: 1181-1185

  • DOI: 10.1038/nature04290
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Chromodomains are modules implicated in the recognition of lysine-methylated histone tails and nucleic acids. CHD (for chromo-ATPase/helicase-DNA-binding) proteins regulate ATP-dependent nucleosome assembly and mobilization through their conserved do ...

    Chromodomains are modules implicated in the recognition of lysine-methylated histone tails and nucleic acids. CHD (for chromo-ATPase/helicase-DNA-binding) proteins regulate ATP-dependent nucleosome assembly and mobilization through their conserved double chromodomains and SWI2/SNF2 helicase/ATPase domain. The Drosophila CHD1 localizes to the interbands and puffs of the polytene chromosomes, which are classic sites of transcriptional activity. Other CHD isoforms (CHD3/4 or Mi-2) are important for nucleosome remodelling in histone deacetylase complexes. Deletion of chromodomains impairs nucleosome binding and remodelling by CHD proteins. Here we describe the structure of the tandem arrangement of the human CHD1 chromodomains, and its interactions with histone tails. Unlike HP1 and Polycomb proteins that use single chromodomains to bind to their respective methylated histone H3 tails, the two chromodomains of CHD1 cooperate to interact with one methylated H3 tail. We show that the human CHD1 double chromodomains target the lysine 4-methylated histone H3 tail (H3K4me), a hallmark of active chromatin. Methylammonium recognition involves two aromatic residues, not the three-residue aromatic cage used by chromodomains of HP1 and Polycomb proteins. Furthermore, unique inserts within chromodomain 1 of CHD1 block the expected site of H3 tail binding seen in HP1 and Polycomb, instead directing H3 binding to a groove at the inter-chromodomain junction.


    Organizational Affiliation

    Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia 22908, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Chromodomain-helicase-DNA-binding protein 1
A, B
187Homo sapiensMutation(s): 0 
Gene Names: CHD1
EC: 3.6.4.12
Find proteins for O14646 (Homo sapiens)
Go to Gene View: CHD1
Go to UniProtKB:  O14646
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Chromodomain-helicase-DNA-binding protein 1
C
115Homo sapiensMutation(s): 0 
Gene Names: CHD1
EC: 3.6.4.12
Find proteins for O14646 (Homo sapiens)
Go to Gene View: CHD1
Go to UniProtKB:  O14646
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Histone H3
D
16Homo sapiensMutation(s): 0 
Gene Names: HIST1H3A, HIST1H3B, HIST1H3C, HIST1H3D, HIST1H3E, HIST1H3F, HIST1H3G, HIST1H3H, HIST1H3I, HIST1H3J (H3FA, H3FL, H3FC, H3FB, H3FD, H3FI, H3FH, H3FK, H3FF, H3FJ)
Find proteins for P68431 (Homo sapiens)
Go to UniProtKB:  P68431
Small Molecules
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
D
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
DA2
Query on DA2
D
L-PEPTIDE LINKINGC8 H18 N4 O2ARG
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.95 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.238 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 111.984α = 90.00
b = 54.753β = 112.32
c = 100.274γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-2000data scaling
CNSrefinement
MAR345data collection
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2005-12-27
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-10-11
    Type: Refinement description