3EMH

Structural basis of WDR5-MLL interaction

• PDB DOI: https://doi.org/10.2210/pdb3EMH/pdb

• Classification: GENE REGULATION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-09-24 Released: 2008-10-07 
• Deposition Author(s): Song, J.J., Kingston, R.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 0.200 
• R-Value Work: 0.190 
• R-Value Observed: 0.190 

Starting Model: experimental

Literature

WDR5 Interacts with Mixed Lineage Leukemia (MLL) Protein via the Histone H3-binding Pocket.

Song, J.J., Kingston, R.E.

(2008) J Biol Chem 283: 35258-35264

• PubMed: 18840606 
• DOI: https://doi.org/10.1074/jbc.M806900200
• Primary Citation of Related Structures:  
  3EMH


• PubMed Abstract: 
  

  WDR5 is a component of the mixed lineage leukemia (MLL) complex, which methylates lysine 4 of histone H3, and was identified as a methylated Lys-4 histone H3-binding protein. Here, we present a crystal structure of WDR5 bound to an MLL peptide. Surprisingly, we find that WDR5 utilizes the same pocket shown to bind histone H3 for this MLL interaction. Furthermore, the WDR5-MLL interaction is disrupted preferentially by mono- and di-methylated Lys-4 histone H3 over unmodified and tri-methylated Lys-4 histone H3. These data implicate a delicate interplay between the effector, WDR5, the catalytic subunit, MLL, and the substrate, histone H3, of the MLL complex. We suggest that the activity of the MLL complex might be regulated through this interplay.

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Organizational Affiliation: 

Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts 02114, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 36.61 kDa 
• Atom Count: 2,676 
• Modelled Residue Count: 306 
• Deposited Residue Count: 331 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WD repeat-containing protein 5	A	318	Homo sapiens	Mutation(s): 0  Gene Names: WDR5, BIG3
UniProt & NIH Common Fund Data Resources
Find proteins for P61964 (Homo sapiens) Explore P61964  Go to UniProtKB:  P61964
PHAROS:  P61964 GTEx:  ENSG00000196363

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mixed-lineage leukemia protein 1	B	13	N/A	Mutation(s): 0  EC: 2.1.1.364 (UniProt), 2.1.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q03164 (Homo sapiens) Explore Q03164  Go to UniProtKB:  Q03164
PHAROS:  Q03164 GTEx:  ENSG00000118058

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.37 Å
• R-Value Free: 0.200 
• R-Value Work: 0.190 
• R-Value Observed: 0.190 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.44	α = 90
b = 98.29	β = 90
c = 80.03	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-10-07 
Deposition Author(s): Song, J.J., Kingston, R.E.

Revision History  

• Version 1.0: 2008-10-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description