Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 78824.70 
• Atom Count: 4924 
• Residue Count: 714 
• Unique protein chains: 3

2XL3

WDR5 IN COMPLEX WITH AN RBBP5 PEPTIDE AND HISTONE H3 PEPTIDE

• DOI: 10.2210/pdb2XL3/pdb

• Classification: TRANSCRIPTION
• Organism(s): Mus musculus
• Expression System: Escherichia coli


• Deposited: 2010-07-19 Released: 2010-08-04 
• Deposition Author(s): Odho, Z., Southall, S.M., Wilson, J.R.

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Experimental Data Snapshot

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

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

• PubMed: 20716525 
• DOI: 10.1074/jbc.M110.159921
• Primary Citation of Related Structures:  
  2XL2


• 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 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.

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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
Molecule	Chains	Sequence Length	Organism	Details
WD REPEAT-CONTAINING PROTEIN 5	A, B	334	Mus musculus	Mutation(s): 0  Gene Names: Wdr5 (Big, Big3)
Find proteins for P61965 (Mus musculus) Go to UniProtKB:  P61965

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
RETINOBLASTOMA-BINDING PROTEIN 5	C, E	14	Mus musculus	Mutation(s): 0  Gene Names: Rbbp5
Find proteins for Q8BX09 (Mus musculus) Go to UniProtKB:  Q8BX09

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
HISTONE H3.1	D, F	9	Mus musculus	Mutation(s): 0  Gene Names: H3c1, H3c8, H3c10, H3c11 (H3a, Hist1h3a, H3.1-221, H3g, Hist1h3g, H3.1-291, H3h, Hist1h3h, H3.1-I, H3i, Hist1h3i)
Find proteins for P68433 (Mus musculus) Go to UniProtKB:  P68433

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GOL	A, B	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

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 = 47.100	α = 90.00
b = 81.320	β = 91.13
c = 86.350	γ = 90.00

Software Package:

Software Name	Purpose
SCALA	data scaling
iMOSFLM	data reduction
PHENIX	refinement
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2010-07-19 
• Released Date: 2010-08-04 
• Deposition Author(s): Odho, Z., Southall, S.M., Wilson, J.R.

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