5TAB | pdb_00005tab

Crystal Structure of the PHD Finger of PHF20

• PDB DOI: https://doi.org/10.2210/pdb5TAB/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2016-09-09 Released: 2016-10-26 
• Deposition Author(s): Klein, B.J., Kutateladze, T.G.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 
  0.143 (Depositor), 0.145 (DCC) 
• R-Value Work: 
  0.118 (Depositor), 0.121 (DCC) 
• R-Value Observed: 
  0.121 (Depositor) 

Literature

PHF20 Readers Link Methylation of Histone H3K4 and p53 with H4K16 Acetylation.

Klein, B.J., Wang, X., Cui, G., Yuan, C., Botuyan, M.V., Lin, K., Lu, Y., Wang, X., Zhao, Y., Bruns, C.J., Mer, G., Shi, X., Kutateladze, T.G.

(2016) Cell Rep 17: 1158-1170

• PubMed: 27760318 
• DOI: https://doi.org/10.1016/j.celrep.2016.09.056
• Primary Citation Related Structures: 
  5TAB, 5TBN


• PubMed Abstract: 
  

  PHF20 is a core component of the lysine acetyltransferase complex MOF (male absent on the first)-NSL (non-specific lethal) that generates the major epigenetic mark H4K16ac and is necessary for transcriptional regulation and DNA repair. The role of PHF20 in the complex remains elusive. Here, we report on functional coupling between methylation readers in PHF20. We show that the plant homeodomain (PHD) finger of PHF20 recognizes dimethylated lysine 4 of histone H3 (H3K4me2) and represents an example of a native reader that selects for this modification. Biochemical and structural analyses help to explain this selectivity and the preference of Tudor2, another reader in PHF20, for dimethylated p53. Binding of the PHD finger to H3K4me2 is required for histone acetylation, accumulation of PHF20 at target genes, and transcriptional activation. Together, our findings establish a unique PHF20-mediated link between MOF histone acetyltransferase (HAT), p53, and H3K4me2, and suggest a model for rapid spreading of H4K16ac-enriched open chromatin.

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Organizational Affiliation: 
• Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.
Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Faculty of Medicine, Ludwig Maximilian University of Munich, Munich 80336, Germany.
Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA.
Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
Department of General, Visceral and Tumor Surgery, University Clinic Cologne, Cologne 50931, Germany.
Faculty of Medicine, Ludwig Maximilian University of Munich, Munich 80336, Germany; Department of General, Visceral and Tumor Surgery, University Clinic Cologne, Cologne 50931, Germany.
Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN 55905, USA. Electronic address: [e-mail].
Department of Epigenetics and Molecular Carcinogenesis, Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA. Electronic address: [e-mail].
Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 6.31 kDa 
• Atom Count: 510 
• Modeled Residue Count: 53 
• Deposited Residue Count: 53 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHD finger protein 20	A	53	Homo sapiens	Mutation(s): 1  Gene Names: PHF20, C20orf104, GLEA2, HCA58, NZF, TZP
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BVI0 (Homo sapiens) Explore Q9BVI0  Go to UniProtKB:  Q9BVI0
PHAROS:  Q9BVI0 GTEx:  ENSG00000025293

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A], C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free:  0.143 (Depositor), 0.145 (DCC) 
• R-Value Work:  0.118 (Depositor), 0.121 (DCC) 
• R-Value Observed: 0.121 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.739	α = 90
b = 46.739	β = 90
c = 50.928	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-10-26 
Deposition Author(s): Klein, B.J., Kutateladze, T.G.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM100907, GM106416, GM101664

Revision History  

• Version 1.0: 2016-10-26
  Type: Initial release
  
• Version 1.1: 2017-09-20
  Changes: Author supporting evidence, Derived calculations
• Version 1.2: 2018-05-16
  Changes: Data collection, Database references
• Version 1.3: 2019-12-25
  Changes: Author supporting evidence
• Version 1.4: 2024-03-06
  Changes: Data collection, Database references