2G99 | pdb_00002g99

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.

Experimental Data Snapshot

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

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2G99

This is version 1.3 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P61964
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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 Query on 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 (Depositor)
R-Value Work: 0.212 (Depositor)
R-Value Observed: 0.212 (Depositor)

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

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Entry History

Deposition Data

Released Date: 2006-09-06

Deposition Author(s):

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.