6MLC

PHD6 domain of MLL3 in complex with histone H4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.194 

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

  • 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

    Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario, M5G 1L7, Canada.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas, 77030, USA. mglee@mdanderson.org.,Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas, 77030, USA.,Department of Physiology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada. jr.min@utoronto.ca.,Structural Genomics Consortium, University of Toronto, 101 College Street, Toronto, Ontario, M5G 1L7, 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: KMT2C (HALR, KIAA1506, MLL3)
EC: 2.1.1.43
Find proteins for Q8NEZ4 (Homo sapiens)
Go to Gene View: KMT2C
Go to UniProtKB:  Q8NEZ4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Histone H4
E, F
20Homo sapiensMutation(s): 0 
Gene Names: H4C1, H4C2, H4C3, H4C4, H4C5, H4C6, H4C8, H4C9, H4C11, H4C12, H4C13, H4C14, H4C15, H4-16 (H4/A, H4FA, HIST1H4A, H4/I, H4FI, HIST1H4B, H4/G, H4FG, HIST1H4C, H4/B, H4FB, HIST1H4D, H4/J, H4FJ, HIST1H4E, H4/C, H4FC, HIST1H4F, H4/H, H4FH, HIST1H4H, H4/M, H4FM, HIST1H4I, H4/E, H4FE, HIST1H4J, H4/D, H4FD, HIST1H4K, H4/K, H4FK, HIST1H4L, H4/N, H4F2, H4FN, HIST2H4, HIST2H4A, H4/O, H4FO, HIST2H4B, HIST4H4)
Find proteins for P62805 (Homo sapiens)
Go to UniProtKB:  P62805
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
A, C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
UNX
Query on UNX

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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: 1.8 Å
  • R-Value Free: 0.216 
  • R-Value Work: 0.194 
  • Space Group: P 6
Unit Cell:
Length (Å)Angle (°)
a = 85.939α = 90.00
b = 85.939β = 90.00
c = 98.733γ = 120.00
Software Package:
Software NamePurpose
REFMACrefinement
Aimlessdata scaling
HKL-3000data reduction
PDB_EXTRACTdata extraction
MOLREPphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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