6MLC

PHD6 domain of MLL3 in complex with histone H4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural insights into trans-histone regulation of H3K4 methylation by unique histone H4 binding of MLL3/4.

Liu, Y.Qin, S.Chen, T.Y.Lei, M.Dhar, S.S.Ho, J.C.Dong, A.Loppnau, P.Li, Y.Lee, M.G.Min, J.

(2019) Nat Commun 10: 36-36

  • DOI: 10.1038/s41467-018-07906-3
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • MLL3 and MLL4 are two closely related members of the SET1/MLL family of histone H3K4 methyltransferases and are responsible for monomethylating histone H3K4 on enhancers, which are essential in regulating cell-type-specific gene expression. Mutations ...

    MLL3 and MLL4 are two closely related members of the SET1/MLL family of histone H3K4 methyltransferases and are responsible for monomethylating histone H3K4 on enhancers, which are essential in regulating cell-type-specific gene expression. Mutations of MLL3 or MLL4 have been reported in different types of cancer. Recently, the PHD domains of MLL3/4 have been reported to recruit the MLL3/4 complexes to their target genes by binding to histone H4 during the NT2/D1 stem cell differentiation. Here we show that an extended PHD domain (ePHD 6 ) involving the sixth PHD domain and its preceding zinc finger in MLL3 and MLL4 specifically recognizes an H4H18-containing histone H4 fragment and that modifications of residues surrounding H4H18 modulate H4 binding to MLL3/4. Our in vitro methyltransferase assays and cellular experiments further reveal that the interaction between ePHD 6 of MLL3/4 and histone H4 is required for their nucleosomal methylation activity and MLL4-mediated neuronal differentiation of NT2/D1 cells.


    Organizational Affiliation

    Department of Physiology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada. jr.min@utoronto.ca.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Histone-lysine N-methyltransferase 2C
A, B, C, D
92Homo sapiensMutation(s): 0 
Gene Names: KMT2CHALRKIAA1506MLL3
EC: 2.1.1.43 (PDB Primary Data), 2.1.1.354 (UniProt)
Find proteins for Q8NEZ4 (Homo sapiens)
Go to UniProtKB:  Q8NEZ4
NIH Common Fund Data Resources
PHAROS  Q8NEZ4
Protein Feature View
  • Reference Sequence
  • Find similar proteins by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
E, F
20Homo sapiensMutation(s): 0 
Gene Names: 
Find proteins for P62805 (Homo sapiens)
Go to UniProtKB:  P62805
NIH Common Fund Data Resources
PHAROS  P62805
Protein Feature View
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download CCD File 
A, C, D
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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

Download CCD File 
A, B, C, D, E
UNKNOWN ATOM OR ION
X
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 6
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 85.939α = 90
b = 85.939β = 90
c = 98.733γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing
HKL-3000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2019-01-16
    Changes: Data collection, Database references