3QBY

Crystal structure of the PWWP domain of human Hepatoma-derived growth factor 2

• PDB DOI: https://doi.org/10.2210/pdb3QBY/pdb

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


• Deposited: 2011-01-14 Released: 2011-02-09 
• Deposition Author(s): Zeng, H., Tempel, W., Amaya, M.F., Adams-Cioaba, M.A., Mackenzie, F., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Min, J., Wu, H., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.253 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 

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: Hetero 4-mer - A3B1 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.78 kDa 
• Atom Count: 2,125 
• Modelled Residue Count: 255 
• Deposited Residue Count: 293 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hepatoma-derived growth factor-related protein 2	A, B, C	94	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
H4K20me3 Histone H4 Peptide	D [auth H]	11	synthetic construct	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens) Explore P62805  Go to UniProtKB:  P62805
PHAROS:  P62805 GTEx:  ENSG00000274618 ENSG00000197238 ENSG00000197837 ENSG00000158406 ENSG00000278705 ENSG00000197061 ENSG00000270882 ENSG00000270276 ENSG00000273542 ENSG00000277157 ENSG00000276966 ENSG00000276180 ENSG00000278637 ENSG00000275126

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	R [auth B], S [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
UNX	E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], T [auth B], U [auth B], V [auth B], W [auth B], X [auth C], Y [auth C], Z [auth C]	UNKNOWN ATOM OR ION X

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
M3L	D [auth H]	L-PEPTIDE LINKING	C9 H21 N2 O2		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.253 
• R-Value Work: 0.216 
• R-Value Observed: 0.218 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.527	α = 90
b = 41.681	β = 90
c = 156.749	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-02-09 
Deposition Author(s): Zeng, H., Tempel, W., Amaya, M.F., Adams-Cioaba, M.A., Mackenzie, F., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Min, J., Wu, H., 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: 2011-07-20
  Changes: Database references
• Version 1.3: 2012-09-05
  Changes: Derived calculations
• Version 1.4: 2017-11-08
  Changes: Refinement description
• Version 1.5: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description