2H9P

WDR5 in complex with trimethylated H3K4 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structural basis for molecular recognition and presentation of histone H3 By WDR5.

Schuetz, A.Allali-Hassani, A.Loppnau, P.Vedadi, M.Bochkarev, A.Plotnikov, A.N.Arrowsmith, C.H.Min, J.

(2006) EMBO J 25: 4245-4252

  • DOI: 10.1038/sj.emboj.7601316
  • Primary Citation of Related Structures:  
    2H9P, 2H9N, 2H9M, 2H9L, 2GNQ, 2O9K

  • PubMed Abstract: 
  • Histone methylation at specific lysine residues brings about various downstream events that are mediated by different effector proteins. The WD40 domain of WDR5 represents a new class of histone methyl-lysine recognition domains that is important for ...

    Histone methylation at specific lysine residues brings about various downstream events that are mediated by different effector proteins. The WD40 domain of WDR5 represents a new class of histone methyl-lysine recognition domains that is important for recruiting H3K4 methyltransferases to K4-dimethylated histone H3 tail as well as for global and gene-specific K4 trimethylation. Here we report the crystal structures of full-length WDR5, WDR5Delta23 and its complexes with unmodified, mono-, di- and trimethylated histone H3K4 peptides. The structures reveal that WDR5 is able to bind all of these histone H3 peptides, but only H3K4me2 peptide forms extra interactions with WDR5 by use of both water-mediated hydrogen bonding and the altered hydrophilicity of the modified lysine 4. We propose a mechanism for the involvement of WDR5 in binding and presenting histone H3K4 for further methylation as a component of MLL complexes.


    Organizational Affiliation

    Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
WD-repeat protein 5A329Homo sapiensMutation(s): 0 
Gene Names: WDR5BIG3
Find proteins for P61964 (Homo sapiens)
Explore P61964 
Go to UniProtKB:  P61964
NIH Common Fund Data Resources
PHAROS  P61964
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
H3 histoneB11N/AMutation(s): 1 
Find proteins for Q6P823 (Xenopus tropicalis)
Explore Q6P823 
Go to UniProtKB:  Q6P823
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
BL-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.164 
  • R-Value Observed: 0.166 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.794α = 90
b = 98.727β = 90
c = 80.205γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
CrystalCleardata reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Revision History 

  • Version 1.0: 2006-08-01
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance