3QII

Crystal structure of tudor domain 2 of human PHD finger protein 20

• PDB DOI: https://doi.org/10.2210/pdb3QII/pdb

• Classification: TRANSCRIPTION REGULATOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2011-01-27 Released: 2011-02-09 
• Deposition Author(s): Li, Z., Tempel, W., Wernimont, A.K., Chao, X., Bian, C., Lam, R., Crombet, L., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.268 
• R-Value Work: 0.235 
• R-Value Observed: 0.237 

Literature

Crystal structures of the Tudor domains of human PHF20 reveal novel structural variations on the Royal Family of proteins.

Adams-Cioaba, M.A., Li, Z., Tempel, W., Guo, Y., Bian, C., Li, Y., Lam, R., Min, J.

(2012) FEBS Lett 586: 859-865

• PubMed: 22449972 
• DOI: https://doi.org/10.1016/j.febslet.2012.02.012
• Primary Citation of Related Structures:  
  3Q1J, 3QII


• PubMed Abstract: 
  

  The human PHD finger protein 20 (PHF20) is a putative transcription factor. While little is known about its cognate cellular role, antibodies against PHF20 are present in sera from patients with hepatocellular carcinoma, glioblastoma and childhood medulloblastula. PHF20 comprises two N-terminal Tudor domains, a central C2H2-link zinc finger domain and a C-terminal zinc-binding PHD domain, and is a component of some MLL methyltransferase complexes. Here, we report the crystal structures of the N-terminal Tudor domains of PHF20 and highlight the novel structural features of each domain. We also confirm previous studies suggesting that the second Tudor domain of PHF20 exhibits preference for dimethylated histone substrates.

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Organizational Affiliation: 

Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 9.82 kDa 
• Atom Count: 432 
• Modelled Residue Count: 52 
• Deposited Residue Count: 85 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PHD finger protein 20	A	85	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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
UNX	B [auth A]	UNKNOWN ATOM OR ION X

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.268 
• R-Value Work: 0.235 
• R-Value Observed: 0.237 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.683	α = 90
b = 48.683	β = 90
c = 96.273	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-09 
Deposition Author(s): Li, Z., Tempel, W., Wernimont, A.K., Chao, X., Bian, C., Lam, R., Crombet, L., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2011-02-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2012-03-07
  Changes: Database references
• Version 1.3: 2012-04-11
  Changes: Database references
• Version 1.4: 2017-11-08
  Changes: Refinement description
• Version 1.5: 2023-09-13
  Changes: Data collection, Database references, Refinement description