2H9L

WDR5delta23

• PDB DOI: https://doi.org/10.2210/pdb2H9L/pdb

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


• Deposited: 2006-06-10 Released: 2006-08-01 
• Deposition Author(s): Min, J.R., Schuetz, A., Allali-Hassani, A., Martin, F., Loppnau, P., Vedadi, M., Weigelt, J., Sundstrom, M., Edwards, A.M., Arrowsmith, C.H., Bochkarev, A., Plotnikov, A.N., Structural Genomics Consortium (SGC)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.201 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 

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

• PubMed: 16946699 
• DOI: https://doi.org/10.1038/sj.emboj.7601316
• Primary Citation of Related Structures:  
  2GNQ, 2H9L, 2H9M, 2H9N, 2H9P, 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 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 36.63 kDa 
• Atom Count: 2,966 
• Modelled Residue Count: 321 
• Deposited Residue Count: 329 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WD-repeat protein 5	A	329	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

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.75 Å
• R-Value Free: 0.201 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.094	α = 90
b = 55.535	β = 90
c = 123.934	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-08-01 
Deposition Author(s): Min, J.R., Schuetz, A., Allali-Hassani, A., Martin, F., Loppnau, P., Vedadi, M., Weigelt, J., Sundstrom, M., Edwards, A.M., Arrowsmith, C.H., Bochkarev, A., Plotnikov, A.N., Structural Genomics Consortium (SGC)

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
• Version 1.3: 2024-02-14
  Changes: Data collection, Database references, Derived calculations