2XL3

WDR5 IN COMPLEX WITH AN RBBP5 PEPTIDE AND HISTONE H3 PEPTIDE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.176 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Characterisation of a Novel Wdr5 Binding Site that Recruits Rbbp5 Through a Conserved Motif and Enhances Methylation of H3K4 by Mll1.

Odho, Z., Southall, S.M., Wilson, J.R.

(2010) J.Biol.Chem. 285: 32967

  • DOI: 10.1074/jbc.M110.159921
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • Histone modification is well established as a fundamental mechanism driving the regulation of transcription, replication, and DNA repair through the control of chromatin structure. Likewise, it is apparent that incorrect targeting of histone modifica ...

    Histone modification is well established as a fundamental mechanism driving the regulation of transcription, replication, and DNA repair through the control of chromatin structure. Likewise, it is apparent that incorrect targeting of histone modifications contributes to misregulated gene expression and hence to developmental disorders and diseases of genomic instability such as cancer. The KMT2 family of SET domain methyltransferases, typified by mixed lineage leukemia protein-1 (MLL1), is responsible for histone H3 lysine 4 methylation, a marker of active genes. To ensure that this modification is correctly targeted, a multiprotein complex associates with the methyltransferase and directs activity. We have identified a novel interaction site on the core complex protein WD repeat protein-5 (WDR5), and we mapped the complementary site on its partner retinoblastoma-binding protein-5 (RbBP5). We have characterized this interaction by x-ray crystallography and show how it is fundamental to the assembly of the complex and to the regulation of methyltransferase activity. We show which region of RbBP5 contributes directly to mixed lineage leukemia activation, and we combine our structural and biochemical data to produce a model to show how WDR5 and RbBP5 act cooperatively to stimulate activity.

    Organizational Affiliation: 

    Section of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, London SW3 6JB, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
WD REPEAT-CONTAINING PROTEIN 5
A, B
334Mus musculusMutation(s): 0 
Gene Names: Wdr5 (Big, Big3)
Find proteins for P61965 (Mus musculus)
Go to UniProtKB:  P61965
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RETINOBLASTOMA-BINDING PROTEIN 5
C, E
14Mus musculusMutation(s): 0 
Gene Names: Rbbp5
Find proteins for Q8BX09 (Mus musculus)
Go to UniProtKB:  Q8BX09
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
HISTONE H3.1
D, F
9Mus musculusMutation(s): 0 
Gene Names: Hist1h3a, Hist1h3g, Hist1h3h, Hist1h3i (H3a, H3.1-221, H3g, H3.1-291, H3h, H3.1-I, H3i)
Find proteins for P68433 (Mus musculus)
Go to UniProtKB:  P68433
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL
Download SDF File 
Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.176 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 47.100α = 90.00
b = 81.320β = 91.13
c = 86.350γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
iMOSFLMdata reduction
PHENIXrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-08-04
    Type: Initial release
  • Version 1.1: 2011-06-23
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance