Biological Assembly 1  

 3D View: Structure | Electron Density

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

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

Biological Assembly 2  

 3D View: Structure | Electron Density

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

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

Macromolecule Content

• Total Structure Weight: 72.32 kDa 
• Atom Count: 5092 
• Residue Count: 620 
• Unique protein chains: 3

2CO0

WDR5 and unmodified Histone H3 complex at 2.25 angstrom

• DOI: 10.2210/pdb2CO0/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2006-05-25 Released: 2006-07-03 
• Deposition Author(s): Ruthenburg, A.J., Wang, W., Graybosch, D.M., Li, H., Allis, C.D., Patel, D.J., Verdine, G.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.226 
• R-Value Work: 0.190 
• R-Value Observed: 0.190 

Literature

Histone H3 Recognition and Presentation by the Wdr5 Module of the Mll1 Complex

Ruthenburg, A.J., Wang, W., Graybosch, D.M., Li, H., Allis, C.D., Patel, D.J., Verdine, G.L.

(2006) Nat Struct Mol Biol 13: 704

• PubMed: 16829959 
• DOI: 10.1038/nsmb1119
• Primary Citation of Related Structures:  
  2CO0, 2CNX, 2H68, 2H6Q, 2H6N, 2H6K


• PubMed Abstract: 
  

WDR5 is a core component of SET1-family complexes that achieve transcriptional activation via methylation of histone H3 on Nzeta of Lys4 (H3K4). The role of WDR5 in the MLL1 complex has recently been described as specific recognition of dimethyl-K4 in the context of a histone H3 amino terminus; WDR5 is essential for vertebrate development, Hox gene activation and global H3K4 trimethylation. We report the high-resolution X-ray structures of WDR5 in the unliganded form and complexed with histone H3 peptides having unmodified and mono-, di- and trimethylated K4, which together provide the first comprehensive analysis of methylated histone recognition by the ubiquitous WD40-repeat fold. Contrary to predictions, the structures reveal that WDR5 does not read out the methylation state of K4 directly, but instead serves to present the K4 side chain for further methylation by SET1-family complexes.

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Organizational Affiliation: 

Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, Massachusetts 02138, USA.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WD-REPEAT PROTEIN 5	A	315	Homo sapiens	Mutation(s): 0  Gene Names: WDR5, BIG3
Find proteins for P61964 (Homo sapiens) Explore P61964  Go to UniProtKB:  P61964
NIH Common Fund Data Resources
PHAROS  P61964 GTEx  ENSG00000196363

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HISTONE H3 DIMETHYL-LYSINE 4	B, D	15	Homo sapiens	Mutation(s): 0  Gene Names:  H3C1, H3FA, HIST1H3A, H3C2, H3FL, HIST1H3B, H3C3, H3FC HIST1H3C, H3C4, H3FB, HIST1H3D, H3C6, H3FD, HIST1H3E, H3C7, H3FI, HIST1H3F, H3C8, H3FH, HIST1H3G, H3C10, H3FK, HIST1H3H, H3C11, H3FF, HIST1H3I, H3C12, H3FJ, HIST1H3J
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
NIH Common Fund Data Resources
PHAROS  P68431 GTEx  ENSG00000197409GTEx  ENSG00000197153GTEx  ENSG00000278828GTEx  ENSG00000275714GTEx  ENSG00000273983GTEx  ENSG00000274750GTEx  ENSG00000275379GTEx  ENSG00000277775

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
WD-REPEAT PROTEIN 5	C	315	Homo sapiens	Mutation(s): 0  Gene Names: WDR5, BIG3
Find proteins for P61964 (Homo sapiens) Explore P61964  Go to UniProtKB:  P61964
NIH Common Fund Data Resources
PHAROS  P61964 GTEx  ENSG00000196363

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.226 
• R-Value Work: 0.190 
• R-Value Observed: 0.190 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.916	α = 90
b = 47.03	β = 107.01
c = 101.768	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-05-25 
• Released Date: 2006-07-03 
Deposition Author(s): Ruthenburg, A.J., Wang, W., Graybosch, D.M., Li, H., Allis, C.D., Patel, D.J., Verdine, G.L.

Revision History 

• Version 1.0: 2006-07-03
  Type: Initial release
  
• Version 1.1: 2016-12-21
  Changes: Data collection, Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance
• Version 1.2: 2018-04-04
  Changes: Data collection