2G99

Structural basis for the specific recognition of methylated histone H3 lysine 4 by the WD-40 protein WDR5

• PDB DOI: https://doi.org/10.2210/pdb2G99/pdb

• Classification: STRUCTURAL PROTEIN/DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-03-06 Released: 2006-09-06 
• Deposition Author(s): Chai, J., Han, Z., Wang, H., Shen, Y.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.243 
• R-Value Work: 0.212 
• R-Value Observed: 0.212 

Starting Model: experimental

Literature

Structural basis for the specific recognition of methylated histone H3 lysine 4 by the WD-40 protein WDR5

Chai, J., Han, Z., Wang, H., Shen, Y.

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 70.24 kDa 
• Atom Count: 4,800 
• Modelled Residue Count: 618 
• Deposited Residue Count: 636 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
WD-repeat protein 5	A, B	308	Homo sapiens	Mutation(s): 0
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
Histone H3	C, D	10	N/A	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MLY	C, D	L-PEPTIDE LINKING	C8 H18 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.243 
• R-Value Work: 0.212 
• R-Value Observed: 0.212 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 134.19	α = 90
b = 46.89	β = 117.4
c = 112.31	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-09-06 
Deposition Author(s): Chai, J., Han, Z., Wang, H., Shen, Y.

Revision History  

• Version 1.0: 2006-09-06
  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: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description