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 1.2 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: https://doi.org/10.1038/s41467-018-07906-3
  • Primary Citation of Related Structures:  
    6MLC

  • 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 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

    Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario, M5G 1L7, Canada.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase 2C
A, B, C, D
92Homo sapiensMutation(s): 0 
Gene Names: KMT2CHALRKIAA1506MLL3
EC: 2.1.1.43
UniProt & NIH Common Fund Data Resources
Find proteins for Q8NEZ4 (Homo sapiens)
Explore Q8NEZ4 
Go to UniProtKB:  Q8NEZ4
PHAROS:  Q8NEZ4
GTEx:  ENSG00000055609 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8NEZ4
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Histone H4
E, F
20Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P62805 (Homo sapiens)
Explore P62805 
Go to UniProtKB:  P62805
PHAROS:  P62805
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62805
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download Ideal Coordinates CCD File 
CA [auth D],
DA [auth D],
K [auth A],
W [auth C],
X [auth C]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN
Query on ZN

Download Ideal Coordinates CCD File 
AA [auth D]
BA [auth D]
G [auth A]
H [auth A]
I [auth A]
AA [auth D],
BA [auth D],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
N [auth A],
O [auth B],
P [auth B],
S [auth C],
T [auth C],
U [auth C],
V [auth C],
Z [auth C]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
UNX
Query on UNX

Download Ideal Coordinates CCD File 
EA [auth D]
FA [auth E]
L [auth A]
M [auth A]
Q [auth B]
EA [auth D],
FA [auth E],
L [auth A],
M [auth A],
Q [auth B],
R [auth B],
Y [auth C]
UNKNOWN ATOM OR ION
X
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  (Full details and data files)

  • Version 1.0: 2018-10-24
    Type: Initial release
  • Version 1.1: 2019-01-16
    Changes: Data collection, Database references
  • Version 1.2: 2024-03-13
    Changes: Data collection, Database references, Derived calculations