Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (3D View)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22.73 kDa 
• Atom Count: 1681 
• Modelled Residue Count: 176 
• Deposited Residue Count: 188 
• Unique protein chains: 2

4O62

CW-type zinc finger of ZCWPW2 in complex with the amino terminus of histone H3

• PDB DOI: 10.2210/pdb4O62/pdb

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


• Deposited: 2013-12-20 Released: 2014-03-26 
• Deposition Author(s): Liu, Y., Tempel, W., Dong, A., Loppnau, P., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.186 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 

Literature

Family-wide Characterization of Histone Binding Abilities of Human CW Domain-containing Proteins.

Liu, Y., Tempel, W., Zhang, Q., Liang, X., Loppnau, P., Qin, S., Min, J.

(2016) J Biol Chem 291: 9000-9013

• PubMed: 26933034 
• DOI: 10.1074/jbc.M116.718973
• Primary Citation of Related Structures:  
  4O62, 4QQ4


• PubMed Abstract: 
  

Covalent modifications of histone N-terminal tails play a critical role in regulating chromatin structure and controlling gene expression. These modifications are controlled by histone-modifying enzymes and read out by histone-binding proteins. Numerous proteins have been identified as histone modification readers. Here we report the family-wide characterization of histone binding abilities of human CW domain-containing proteins. We demonstrate that the CW domains in ZCWPW2 and MORC3/4 selectively recognize histone H3 trimethylated at Lys-4, similar to ZCWPW1 reported previously, while the MORC1/2 and LSD2 lack histone H3 Lys-4 binding ability. Our crystal structures of the CW domains of ZCWPW2 and MORC3 in complex with the histone H3 trimethylated at Lys-4 peptide reveal the molecular basis of this interaction. In each complex, two tryptophan residues in the CW domain form the "floor" and "right wall," respectively, of the methyllysine recognition cage. Our mutation results based on ZCWPW2 reveal that the right wall tryptophan residue is essential for binding, and the floor tryptophan residue enhances binding affinity. Our structural and mutational analysis highlights the conserved roles of the cage residues of CW domain across the histone methyllysine binders but also suggests why some CW domains lack histone binding ability.

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Organizational Affiliation: 

From the Structural Genomics Consortium, University of Toronto, Toronto, Ontario M5G 1L7, Canada, the Hubei Key Laboratory of Genetic Regulation and Integrative Biology, College of Life Science, Central China Normal University, Wuhan 430079, China, the Department of Physiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Zinc finger CW-type PWWP domain protein 2	A, B, C	59	Homo sapiens	Mutation(s): 0  Gene Names: ZCWPW2
UniProt & NIH Common Fund Data Resources
Find proteins for Q504Y3 (Homo sapiens) Explore Q504Y3  Go to UniProtKB:  Q504Y3
GTEx:  ENSG00000206559

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H3.3	D	11	Homo sapiens	Mutation(s): 0  Gene Names: H3-3A, H3.3A, H3F3, H3F3A, PP781, H3-3B, H3.3B, H3F3B
UniProt & NIH Common Fund Data Resources
Find proteins for P84243 (Homo sapiens) Explore P84243  Go to UniProtKB:  P84243
PHAROS:  P84243 GTEx:  ENSG00000163041

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	E [auth A], Q [auth B], Y [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
UNX	AA [auth C], BA [auth C], CA [auth C], DA [auth C], EA [auth C], F [auth A], FA [auth C], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], N [auth A], O [auth A], P [auth A], R [auth B], S [auth B], T [auth B], U [auth B], V [auth B], W [auth B], X [auth B], Z [auth C]	UNKNOWN ATOM OR ION X

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.78 Å
• R-Value Free: 0.186 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 
• Space Group: H 3
• Diffraction Data DOI: 10.18430/m34o62 Protein Diffraction

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.095	α = 90
b = 127.095	β = 90
c = 63.046	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
SHELX	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-12-20 
• Released Date: 2014-03-26 
Deposition Author(s): Liu, Y., Tempel, W., Dong, A., Loppnau, P., Bountra, C., Weigelt, J., Arrowsmith, C.H., Edwards, A.M., Min, J., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2014-03-26
  Type: Initial release
  
• Version 1.1: 2016-06-08
  Changes: Database references