5TBN | pdb_00005tbn

Solution NMR structure of PHF20 PHD domain in complex with a histone H3K4me2 peptide

• PDB DOI: https://doi.org/10.2210/pdb5TBN/pdb
• BMRB: 30177

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


• Deposited: 2016-09-12 Released: 2016-10-12 
• Deposition Author(s): Cui, G., Botuyan, M.V., Mer, G.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

---

Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

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.

---

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: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 8.24 kDa 
• Atom Count: 561 
• Modeled Residue Count: 69 
• Deposited Residue Count: 69 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHD finger protein 20	A	57	Homo sapiens	Mutation(s): 0  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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.1	B [auth C]	12	Homo sapiens	Mutation(s): 1
UniProt & NIH Common Fund Data Resources
Find proteins for P68431 (Homo sapiens) Explore P68431  Go to UniProtKB:  P68431
PHAROS:  P68431 GTEx:  ENSG00000197409 ENSG00000197153 ENSG00000278828 ENSG00000275714 ENSG00000273983 ENSG00000274750 ENSG00000275379 ENSG00000277775

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A], D [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 20 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-10-12 
Deposition Author(s): Cui, G., Botuyan, M.V., Mer, G.

---

Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	CA132878

Revision History  

• Version 1.0: 2016-10-12
  Type: Initial release
  
• Version 1.1: 2016-11-02
  Changes: Database references
• Version 1.2: 2017-09-20
  Changes: Author supporting evidence, Structure summary
• Version 1.3: 2019-12-04
  Changes: Author supporting evidence, Data collection
• Version 1.4: 2025-04-02
  Changes: Data collection, Database references, Derived calculations, Structure summary