3OA6

Human MSL3 Chromodomain bound to DNA and H4K20me1 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Corecognition of DNA and a methylated histone tail by the MSL3 chromodomain.

Kim, D.Blus, B.J.Chandra, V.Huang, P.Rastinejad, F.Khorasanizadeh, S.

(2010) Nat Struct Mol Biol 17: 1027-1029

  • DOI: https://doi.org/10.1038/nsmb.1856
  • Primary Citation of Related Structures:  
    3M9Q, 3OA6

  • PubMed Abstract: 

    MSL3 resides in the MSL (male-specific lethal) complex, which upregulates transcription by spreading the histone H4 Lys16 (H4K16) acetyl mark. We discovered a DNA-dependent interaction of MSL3 chromodomain with the H4K20 monomethyl mark. The structure of a ternary complex shows that the DNA minor groove accommodates the histone H4 tail, and monomethyllysine inserts in a four-residue aromatic cage in MSL3. H4K16 acetylation antagonizes MSL3 binding, suggesting that MSL function is regulated by a combination of post-translational modifications.


  • Organizational Affiliation

    Department of Biochemistry and Molecular Genetics, University of Virginia Health System, Charlottesville, Virginia, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Male-specific lethal 3 homolog
A, B
110Homo sapiensMutation(s): 0 
Gene Names: MSL3MSL3L1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N5Y2 (Homo sapiens)
Explore Q8N5Y2 
Go to UniProtKB:  Q8N5Y2
PHAROS:  Q8N5Y2
GTEx:  ENSG00000005302 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8N5Y2
Sequence Annotations
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  • Reference Sequence

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
H4 peptide monomethylated at lysine 2024N/AMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations
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  • Reference Sequence

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Entity ID: 2
MoleculeChains LengthOrganismImage
DNA (5'-D(*GP*CP*TP*AP*GP*GP*TP*CP*AP*AP*AP*GP*GP*TP*CP*A)-3')
C, E
16N/A
Sequence Annotations
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
DNA (5'-D(*CP*TP*GP*AP*CP*CP*TP*TP*TP*GP*AP*CP*CP*TP*AP*G)-3')
D, F
16N/A
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
IMD
Query on IMD

Download Ideal Coordinates CCD File 
H [auth B]IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MLZ
Query on MLZ
G
L-PEPTIDE LINKINGC7 H16 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.35 Å
  • R-Value Free: 0.277 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 37.976α = 81.35
b = 44.094β = 89.84
c = 67.5γ = 90.04
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-08-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-08
    Changes: Refinement description