2WWU

Crystal structure of the catalytic domain of PHD finger protein 8


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.175 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structure of the PHF8 Jumonji domain, an Nepsilon-methyl lysine demethylase.

Yue, W.W.Hozjan, V.Ge, W.Loenarz, C.Cooper, C.D.Schofield, C.J.Kavanagh, K.L.Oppermann, U.McDonough, M.A.

(2010) FEBS Lett. 584: 825-830

  • DOI: 10.1016/j.febslet.2009.12.055

  • PubMed Abstract: 
  • Crystallographic analysis of the catalytic domain of PHD finger protein 8 (PHF8), an N(epsilon)-methyl lysine histone demethylase associated with mental retardation and cleft lip/palate, reveals a double-stranded beta-helix fold with conserved Fe(II) ...

    Crystallographic analysis of the catalytic domain of PHD finger protein 8 (PHF8), an N(epsilon)-methyl lysine histone demethylase associated with mental retardation and cleft lip/palate, reveals a double-stranded beta-helix fold with conserved Fe(II) and cosubstrate binding sites typical of the 2-oxoglutarate dependent oxygenases. The PHF8 active site is highly conserved with those of the FBXL10/11demethylases, which are also selective for the di-/mono-methylated lysine states, but differs from that of the JMJD2 demethylases which are selective for tri-/di-methylated states. The results rationalize the lack of activity for the clinically observed F279S PHF8 variant and they will help to identify inhibitors selective for specific N(epsilon)-methyl lysine demethylase subfamilies.


    Organizational Affiliation

    Structural Genomics Consortium, University of Oxford, Headington, United Kingdom.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PHD FINGER PROTEIN 8
A
371Homo sapiensMutation(s): 0 
Gene Names: PHF8 (KIAA1111, ZNF422)
EC: 1.14.11.27
Find proteins for Q9UPP1 (Homo sapiens)
Go to Gene View: PHF8
Go to UniProtKB:  Q9UPP1
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ACT
Query on ACT

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Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
BGC
Query on BGC

Download SDF File 
Download CCD File 
A
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
NI
Query on NI

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Download CCD File 
A
NICKEL (II) ION
Ni
VEQPNABPJHWNSG-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.175 
  • Space Group: I 21 3
Unit Cell:
Length (Å)Angle (°)
a = 150.980α = 90.00
b = 150.980β = 90.00
c = 150.980γ = 90.00
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
MOSFLMdata reduction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2009-11-17
    Type: Initial release
  • Version 1.1: 2012-12-05
    Type: Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary, Version format compliance
  • Version 1.2: 2018-01-24
    Type: Database references
  • Version 1.3: 2018-03-28
    Type: Database references