3EAE

PWWP domain of human hepatoma-derived growth factor 2 (HDGF2)

• PDB DOI: https://doi.org/10.2210/pdb3EAE/pdb

• Classification: SIGNALING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-08-25 Released: 2008-09-16 
• Deposition Author(s): Amaya, M.F., Zeng, H., Mackenzie, F., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Wu, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 0.260 
• R-Value Work: 0.224 
• R-Value Observed: 0.225 

Literature

Structural and Histone Binding Ability Characterizations of Human PWWP Domains.

Wu, H., Zeng, H., Lam, R., Tempel, W., Amaya, M.F., Xu, C., Dombrovski, L., Qiu, W., Wang, Y., Min, J.

(2011) PLoS One 6: e18919-e18919

• PubMed: 21720545 
• DOI: https://doi.org/10.1371/journal.pone.0018919
• Primary Citation of Related Structures:  
  3EAE, 3L42, 3LLR, 3LYI, 3MO8, 3PFS, 3PMI, 3QBY, 3QJ6, 3QKJ


• PubMed Abstract: 
  

  The PWWP domain was first identified as a structural motif of 100-130 amino acids in the WHSC1 protein and predicted to be a protein-protein interaction domain. It belongs to the Tudor domain 'Royal Family', which consists of Tudor, chromodomain, MBT and PWWP domains. While Tudor, chromodomain and MBT domains have long been known to bind methylated histones, PWWP was shown to exhibit histone binding ability only until recently.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 21.31 kDa 
• Atom Count: 1,367 
• Modelled Residue Count: 167 
• Deposited Residue Count: 186 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatoma-derived growth factor-related protein 2	A, B	93	Homo sapiens	Mutation(s): 0  Gene Names: HDGFRP2, HDGF2, UNQ785/PRO1604
UniProt & NIH Common Fund Data Resources
Find proteins for Q7Z4V5 (Homo sapiens) Explore Q7Z4V5  Go to UniProtKB:  Q7Z4V5
GTEx:  ENSG00000167674

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.24 Å
• R-Value Free: 0.260 
• R-Value Work: 0.224 
• R-Value Observed: 0.225 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.555	α = 90
b = 59.95	β = 90
c = 104.942	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-16 
Deposition Author(s): Amaya, M.F., Zeng, H., Mackenzie, F., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Bochkarev, A., Min, J., Wu, H., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2008-09-16
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2011-07-20
  Changes: Database references
• Version 1.3: 2017-10-25
  Changes: Refinement description
• Version 1.4: 2023-08-30
  Changes: Data collection, Database references, Refinement description