5TAB

Crystal Structure of the PHD Finger of PHF20


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.143 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.121 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


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

  • DOI: 10.1016/j.celrep.2016.09.056
  • Primary Citation of 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 ...

    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. Electronic address: tatiana.kutateladze@ucdenver.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PHD finger protein 20A53Homo sapiensMutation(s): 1 
Gene Names: PHF20C20orf104GLEA2HCA58NZFTZP
UniProt & NIH Common Fund Data Resources
Find proteins for Q9BVI0 (Homo sapiens)
Explore Q9BVI0 
Go to UniProtKB:  Q9BVI0
PHAROS:  Q9BVI0
GTEx:  ENSG00000025293 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9BVI0
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
D [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
B [auth A],
C [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.143 
  • R-Value Work: 0.118 
  • R-Value Observed: 0.121 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 46.739α = 90
b = 46.739β = 90
c = 50.928γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXmodel building

Structure Validation

View Full Validation Report




Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM100907, GM106416, GM101664

Revision History  (Full details and data files)

  • 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