4L58

Crystal structure of the MLL5 PHD finger in complex with H3K4me3

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.126 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Molecular basis for chromatin binding and regulation of MLL5.

Ali, M., Rincon-Arano, H., Zhao, W., Rothbart, S.B., Tong, Q., Parkhurst, S.M., Strahl, B.D., Deng, L.W., Groudine, M., Kutateladze, T.G.

(2013) Proc Natl Acad Sci U S A 110: 11296-11301

  • DOI: 10.1073/pnas.1310156110
  • Primary Citation of Related Structures:  
    4L58

  • PubMed Abstract: 

    • The human mixed-lineage leukemia 5 (MLL5) protein mediates hematopoietic cell homeostasis, cell cycle, and survival; however, the molecular basis underlying MLL5 activities remains unknown. Here, we show that MLL5 is recruited to gene-rich euchromatic regions via the interaction of its plant homeodomain finger with the histone mark H3K4me3 ...

    The human mixed-lineage leukemia 5 (MLL5) protein mediates hematopoietic cell homeostasis, cell cycle, and survival; however, the molecular basis underlying MLL5 activities remains unknown. Here, we show that MLL5 is recruited to gene-rich euchromatic regions via the interaction of its plant homeodomain finger with the histone mark H3K4me3. The 1.48-Å resolution crystal structure of MLL5 plant homeodomain in complex with the H3K4me3 peptide reveals a noncanonical binding mechanism, whereby K4me3 is recognized through a single aromatic residue and an aspartate. The binding induces a unique His-Asp swapping rearrangement mediated by a C-terminal α-helix. Phosphorylation of H3T3 and H3T6 abrogates the association with H3K4me3 in vitro and in vivo, releasing MLL5 from chromatin in mitosis. This regulatory switch is conserved in the Drosophila ortholog of MLL5, UpSET, and suggests the developmental control for targeting of H3K4me3. Together, our findings provide first insights into the molecular basis for the recruitment, exclusion, and regulation of MLL5 at chromatin.

    Organizational Affiliation: 

    Department of Pharmacology, University of Colorado School of Medicine, Aurora, CO 80045, USA.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Histone-lysine N-methyltransferase MLL5A69Homo sapiensMutation(s): 0 
Gene Names: MLL5, KMT2E
EC: 2.1.1.43
Find proteins for Q8IZD2 (Homo sapiens)
Explore Q8IZD2 
Go to UniProtKB:  Q8IZD2
NIH Common Fund Data Resources
PHAROS  Q8IZD2
GTEx  ENSG00000005483
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H3 peptideB12Homo sapiensMutation(s): 0 
Gene Names: H3-3A, H3.3A, H3F3, H3F3A, PP781, H3-3B, H3.3B, H3F3B
Find proteins for P84243 (Homo sapiens)
Explore P84243 
Go to UniProtKB:  P84243
NIH Common Fund Data Resources
PHAROS  P84243
GTEx  ENSG00000163041
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L		BL-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.48 Å
  • R-Value Free: 0.140 
  • R-Value Work: 0.125 
  • R-Value Observed: 0.126 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 31.286α = 90
b = 43.638β = 90
c = 52.856γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHENIXmodel building
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-26
    Type: Initial release
  • Version 1.1: 2013-07-17
    Changes: Database references
  • Version 1.2: 2013-07-24
    Changes: Database references