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 

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:  

  • 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. Numer ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Zinc finger CW-type PWWP domain protein 2
A, B, C
59Homo sapiensMutation(s): 0 
Gene Names: ZCWPW2
Find proteins for Q504Y3 (Homo sapiens)
Go to Gene View: ZCWPW2
Go to UniProtKB:  Q504Y3
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H3.3
D
11Homo sapiensMutation(s): 0 
Gene Names: H3-3A, H3-3B (H3.3A, H3F3, H3F3A, H3.3B, H3F3B)
Find proteins for P84243 (Homo sapiens)
Go to UniProtKB:  P84243
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A, B, C
UNKNOWN ATOM OR ION
X
*
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
D
L-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 
  • Space Group: H 3
Unit Cell:
Length (Å)Angle (°)
a = 127.095α = 90.00
b = 127.095β = 90.00
c = 63.046γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
Aimlessdata scaling
REFMACrefinement
SHELXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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