Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22725.95 
• Atom Count: 1510 
• Residue Count: 188 
• Unique protein chains: 2

4O62

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

• DOI: 10.2210/pdb4O62/pdb

• Classification: METAL/DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• 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 

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:  
  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.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Zinc finger CW-type PWWP domain protein 2	A, B, C	59	Homo sapiens	Mutation(s): 0  Gene Names: ZCWPW2
Find proteins for Q504Y3 (Homo sapiens) Go to Gene View: ZCWPW2 Go to UniProtKB:  Q504Y3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Histone H3.3	D	11	Homo sapiens	Mutation(s): 0  Gene Names: H3F3A, H3F3B (H3.3A, H3F3, H3.3B)
Find proteins for P84243 (Homo sapiens) Go to Gene View: H3F3A H3F3B Go to UniProtKB:  P84243

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A, B, C	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
UNX	A, B, 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 
• Space Group: H 3

Unit Cell:

Length (Å)	Angle (°)
a = 127.095	α = 90.00
b = 127.095	β = 90.00
c = 63.046	γ = 120.00

Software Package:

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

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
  Type: Database references