4O62

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


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 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • 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 ...

    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.


    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 jr.min@utoronto.ca.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Zinc finger CW-type PWWP domain protein 2 ABC59Homo sapiensMutation(s): 0 
Gene Names: ZCWPW2
Find proteins for Q504Y3 (Homo sapiens)
Explore Q504Y3 
Go to UniProtKB:  Q504Y3
NIH Common Fund Data Resources
PHAROS:  Q504Y3
Protein Feature View
Expand
  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3.3 D11Homo sapiensMutation(s): 0 
Gene Names: H3-3AH3.3AH3F3H3F3APP781H3-3BH3.3BH3F3B
Find proteins for P84243 (Homo sapiens)
Explore P84243 
Go to UniProtKB:  P84243
NIH Common Fund Data Resources
PHAROS:  P84243
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

Download Ideal Coordinates CCD File 
A, B, C
UNKNOWN ATOM OR ION
X
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
DL-PEPTIDE LINKINGC9 H21 N2 O2LYS
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 = 127.095α = 90
b = 127.095β = 90
c = 63.046γ = 120
Software Package:
Software NamePurpose
Aimlessdata scaling
SHELXphasing
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

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