2X4W

Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1.

• PDB DOI: https://doi.org/10.2210/pdb2X4W/pdb

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


• Deposited: 2010-02-02 Released: 2010-04-21 
• Deposition Author(s): Vezzoli, A., Bonadies, N., Allen, M.D., Freund, S.M.V., Santiveri, C.M., Kvinlaug, B., Huntly, B.J.P., Gottgens, B., Bycroft, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.216 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 

Literature

Molecular Basis of Histone H3K36Me3 Recognition by the Pwwp Domain of Brpf1.

Vezzoli, A., Bonadies, N., Allen, M.D., Freund, S.M.V., Santiveri, C.M., Kvinlaug, B., Huntly, B.J.P., Gottgens, B., Bycroft, M.

(2010) Nat Struct Mol Biol 17: 617

• PubMed: 20400950 
• DOI: https://doi.org/10.1038/nsmb.1797
• Primary Citation of Related Structures:  
  2X35, 2X4W, 2X4X, 2X4Y


• PubMed Abstract: 
  

  Trimethylation of Lys36 in histone H3 (H3K36me3) coordinates events associated with the elongation phase of transcription and is also emerging as an important epigenetic regulator of cell growth and differentiation. We have identified the PWWP domain of bromo and plant homeodomain (PHD) finger-containing protein 1 (BRPF1) as a H3K36me3 binding module and have determined the structure of this domain in complex with an H3K36me3-derived peptide.

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Organizational Affiliation: 

MRC Centre for Protein Engineering, Cambridge, UK.

Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 17.63 kDa 
• Atom Count: 1,339 
• Modelled Residue Count: 138 
• Deposited Residue Count: 153 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEREGRIN	A	132	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P55201 (Homo sapiens) Explore P55201  Go to UniProtKB:  P55201
PHAROS:  P55201 GTEx:  ENSG00000156983

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HISTONE H3.2	B	21	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q71DI3 (Homo sapiens) Go to UniProtKB:  Q71DI3
PHAROS:  Q71DI3 GTEx:  ENSG00000183598 ENSG00000203811 ENSG00000203852

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FMT	C [auth A]	FORMIC ACID C H2 O2 BDAGIHXWWSANSR-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M3L	B	L-PEPTIDE LINKING	C9 H21 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.216 
• R-Value Work: 0.189 
• R-Value Observed: 0.191 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 43.261	α = 90
b = 71.053	β = 90
c = 113.982	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-04-21 
Deposition Author(s): Vezzoli, A., Bonadies, N., Allen, M.D., Freund, S.M.V., Santiveri, C.M., Kvinlaug, B., Huntly, B.J.P., Gottgens, B., Bycroft, M.

Revision History  

• Version 1.0: 2010-04-21
  Type: Initial release
  
• Version 1.1: 2011-09-21
  Changes: Database references, Derived calculations, Refinement description, Version format compliance
• Version 1.2: 2018-01-24
  Changes: Source and taxonomy