4HCZ

PHF1 Tudor in complex with H3K36me3

• PDB DOI:  https://doi.org/10.2210/pdb4HCZ/pdb

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


• Deposited: 2012-10-01 Released: 2012-11-14 
• Deposition Author(s): Musselman, C.A., Roy, S., Nunez, J., Kutateladze, T.G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.244 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 

Literature

Molecular basis for H3K36me3 recognition by the Tudor domain of PHF1.

Musselman, C.A., Avvakumov, N., Watanabe, R., Abraham, C.G., Lalonde, M.E., Hong, Z., Allen, C., Roy, S., Nunez, J.K., Nickoloff, J., Kulesza, C.A., Yasui, A., Cote, J., Kutateladze, T.G.

(2012) Nat Struct Mol Biol 19: 1266-1272

• PubMed: 23142980 
• DOI: https://doi.org/10.1038/nsmb.2435
• Primary Citation of Related Structures:  
  4HCZ


• PubMed Abstract: 
  

The PHD finger protein 1 (PHF1) is essential in epigenetic regulation and genome maintenance. Here we show that the Tudor domain of human PHF1 binds to histone H3 trimethylated at Lys36 (H3K36me3). We report a 1.9-Å resolution crystal structure of the Tudor domain in complex with H3K36me3 and describe the molecular mechanism of H3K36me3 recognition using NMR. Binding of PHF1 to H3K36me3 inhibits the ability of the Polycomb PRC2 complex to methylate Lys27 of histone H3 in vitro and in vivo. Laser microirradiation data show that PHF1 is transiently recruited to DNA double-strand breaks, and PHF1 mutants impaired in the H3K36me3 interaction exhibit reduced retention at double-strand break sites. Together, our findings suggest that PHF1 can mediate deposition of the repressive H3K27me3 mark and acts as a cofactor in early DNA-damage response.

---

Organizational Affiliation: 

Department of Pharmacology, University of Colorado School of Medicine, Aurora, Colorado, USA.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

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

Macromolecule Content

• Total Structure Weight: 15.47 kDa 
• Atom Count: 1,222 
• Modelled Residue Count: 132 
• Deposited Residue Count: 136 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHD finger protein 1	A, B	58	Homo sapiens	Mutation(s): 0  Gene Names: PHF1, PCL1
UniProt & NIH Common Fund Data Resources
Find proteins for O43189 (Homo sapiens) Explore O43189  Go to UniProtKB:  O43189
PHAROS:  O43189

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H3L-like histone	C, D	10	Homo sapiens	Mutation(s): 0
UniProt
Find proteins for Q6TXQ4 (Homo sapiens) Explore Q6TXQ4  Go to UniProtKB:  Q6TXQ4

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.244 
• R-Value Work: 0.204 
• R-Value Observed: 0.206 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.03	α = 90
b = 29.67	β = 116.41
c = 62	γ = 90

Software Package:

Software Name	Purpose
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-14 
Deposition Author(s): Musselman, C.A., Roy, S., Nunez, J., Kutateladze, T.G.

Revision History  

• Version 1.0: 2012-11-14
  Type: Initial release
  
• Version 1.1: 2012-12-19
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description