2H14 | pdb_00002h14

Crystal of WDR5 (apo-form)

• PDB DOI: https://doi.org/10.2210/pdb2H14/pdb

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


• Deposited: 2006-05-15 Released: 2006-07-11 
• Deposition Author(s): Couture, J.F., Collazo, E., Trievel, R.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 
  0.197 (Depositor), 0.196 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Literature

Molecular recognition of histone H3 by the WD40 protein WDR5.

Couture, J.F., Collazo, E., Trievel, R.C.

(2006) Nat Struct Mol Biol 13: 698-703

• PubMed: 16829960 
• DOI: https://doi.org/10.1038/nsmb1116
• Primary Citation Related Structures: 
  2H13, 2H14


• PubMed Abstract: 
  

  The WD40-repeat protein WDR5 is a conserved subunit of Trithorax (TRX) histone methyltransferase complexes. WDR5 has been reported to selectively bind dimethylated Lys4 (K4me2) in histone H3 to promote K4 trimethylation by TRX. To elucidate the basis of this binding specificity, we have determined the crystal structure of WDR5 bound to a histone H3 peptide bearing K4me2. The structure reveals that the N terminus of histone H3 binds as a 3(10)-helix in the central depression formed by the WD40 repeats. R2 in histone H3 is bound in the acidic channel in the protein's core, whereas K4me2 is solvent exposed and does not engage in direct interactions with WDR5. Functional studies confirm that WDR5 recognizes A1, R2 and T3 in histone H3 but has virtually identical affinities for the unmodified and mono-, di- and trimethylated forms of K4, demonstrating that it does not discriminate among different degrees of methylation of this residue.

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Organizational Affiliation: 
• Department of Biological Chemistry, University of Michigan, 1301 Catherine Road, Ann Arbor, Michigan 48109-0606, USA.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 34.71 kDa 
• Atom Count: 2,873 
• Modeled Residue Count: 303 
• Deposited Residue Count: 317 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WD-repeat protein 5	A	317	Homo sapiens	Mutation(s): 0  Gene Names: WDR5
UniProt & NIH Common Fund Data Resources
Find proteins for P61964 (Homo sapiens) Explore P61964  Go to UniProtKB:  P61964
PHAROS:  P61964 GTEx:  ENSG00000196363

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free:  0.197 (Depositor), 0.196 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.76	α = 90
b = 98.06	β = 90
c = 80.79	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
ADSC	data collection
d*TREK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-07-11 
Deposition Author(s): Couture, J.F., Collazo, E., Trievel, R.C.

Revision History  

• Version 1.0: 2006-07-11
  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: 2018-02-14
  Changes: Experimental preparation
• Version 1.4: 2024-02-14
  Changes: Data collection, Database references