3O70

PHD-type zinc finger of human PHD finger protein 13


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

PHF13 is a molecular reader and transcriptional co-regulator of H3K4me2/3.

Chung, H.R.Xu, C.Fuchs, A.Mund, A.Lange, M.Staege, H.Schubert, T.Bian, C.Dunkel, I.Eberharter, A.Regnard, C.Klinker, H.Meierhofer, D.Cozzuto, L.Winterpacht, A.Di Croce, L.Min, J.Will, H.Kinkley, S.

(2016) Elife 5: --

  • DOI: 10.7554/eLife.10607
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • PHF13 is a chromatin affiliated protein with a functional role in differentiation, cell division, DNA damage response and higher chromatin order. To gain insight into PHF13's ability to modulate these processes, we elucidate the mechanisms targeting ...

    PHF13 is a chromatin affiliated protein with a functional role in differentiation, cell division, DNA damage response and higher chromatin order. To gain insight into PHF13's ability to modulate these processes, we elucidate the mechanisms targeting PHF13 to chromatin, its genome wide localization and its molecular chromatin context. Size exclusion chromatography, mass spectrometry, X-ray crystallography and ChIP sequencing demonstrate that PHF13 binds chromatin in a multivalent fashion via direct interactions with H3K4me2/3 and DNA, and indirectly via interactions with PRC2 and RNA PolII. Furthermore, PHF13 depletion disrupted the interactions between PRC2, RNA PolII S5P, H3K4me3 and H3K27me3 and resulted in the up and down regulation of genes functionally enriched in transcriptional regulation, DNA binding, cell cycle, differentiation and chromatin organization. Together our findings argue that PHF13 is an H3K4me2/3 molecular reader and transcriptional co-regulator, affording it the ability to impact different chromatin processes.


    Organizational Affiliation

    Max Planck Institute for Molecular Genetics, Berlin, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHD finger protein 13
A
68Homo sapiensMutation(s): 0 
Gene Names: PHF13
Find proteins for Q86YI8 (Homo sapiens)
Go to Gene View: PHF13
Go to UniProtKB:  Q86YI8
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.188 
  • R-Value Work: 0.184 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.315α = 90.00
b = 58.315β = 90.00
c = 73.231γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SHARPphasing
SCALEPACKdata scaling
MxDCdata collection
DMphasing
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-09-29
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2016-06-22
    Type: Database references
  • Version 1.3: 2017-11-08
    Type: Refinement description