2WWU | pdb_00002wwu

Crystal structure of the catalytic domain of PHD finger protein 8

• PDB DOI: https://doi.org/10.2210/pdb2WWU/pdb

• Classification: METAL BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2009-10-29 Released: 2009-11-17 
• Deposition Author(s): Yue, W.W., Hozjan, V., Cooper, C., Tumber, A., Krojer, T., Muniz, J., Allerston, C., Salah, E., McDonough, M.A., von Delft, F., Arrowsmith, C., Weigelt, J., Edwards, A., Bountra, C., Schofield, C.J., Kavanagh, K.L., Oppermann, U.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 
  0.211 (Depositor), 0.190 (DCC) 
• R-Value Work: 
  0.175 (Depositor), 0.175 (DCC) 
• R-Value Observed: 
  0.177 (Depositor) 

Starting Model: experimental

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

• PubMed: 20067792 
• DOI: https://doi.org/10.1016/j.febslet.2009.12.055
• Primary Citation Related Structures: 
  2WWU


• 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) 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.

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Organizational Affiliation: 
• Structural Genomics Consortium, University of Oxford, Headington, United Kingdom.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 44.35 kDa 
• Atom Count: 3,159 
• Modeled Residue Count: 363 
• Deposited Residue Count: 371 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHD FINGER PROTEIN 8	A	371	Homo sapiens	Mutation(s): 0  EC: 1.14.11 (UniProt), 1.14.11.65 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UPP1 (Homo sapiens) Explore Q9UPP1  Go to UniProtKB:  Q9UPP1
PHAROS:  Q9UPP1 GTEx:  ENSG00000172943

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BGC	O [auth A], P [auth A]	beta-D-glucopyranose C6 H12 O6 WQZGKKKJIJFFOK-VFUOTHLCSA-N
SO4	B [auth A], C [auth A], D [auth A], E [auth A], F [auth A], G [auth A], H [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	I [auth A], J [auth A], K [auth A], L [auth A], M [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
NI	N [auth A]	NICKEL (II) ION Ni VEQPNABPJHWNSG-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free:  0.211 (Depositor), 0.190 (DCC) 
• R-Value Work:  0.175 (Depositor), 0.175 (DCC) 
• R-Value Observed: 0.177 (Depositor) 

Space Group: I 2₁ 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 150.98	α = 90
b = 150.98	β = 90
c = 150.98	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-11-17 
Deposition Author(s): Yue, W.W., Hozjan, V., Cooper, C., Tumber, A., Krojer, T., Muniz, J., Allerston, C., Salah, E., McDonough, M.A., von Delft, F., Arrowsmith, C., Weigelt, J., Edwards, A., Bountra, C., Schofield, C.J., Kavanagh, K.L., Oppermann, U.

Revision History  

• Version 1.0: 2009-11-17
  Type: Initial release
  
• Version 1.1: 2012-12-05
  Changes: Database references, Derived calculations, Refinement description, Source and taxonomy, Structure summary, Version format compliance
• Version 1.2: 2018-01-24
  Changes: Database references
• Version 1.3: 2018-03-28
  Changes: Database references
• Version 1.4: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary
• Version 1.5: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary