3M9Q

Drosophila MSL3 chromodomain

• PDB DOI: https://doi.org/10.2210/pdb3M9Q/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-03-22 Released: 2010-07-21 
• Deposition Author(s): Kim, D., Huang, P., Rastinejad, F., Khorasanizadeh, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free: 
  0.192 (Depositor), 0.200 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

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

• PubMed: 20657587 
• 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.

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Organizational Affiliation: 

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 24.56 kDa 
• Atom Count: 2,087 
• Modelled Residue Count: 176 
• Deposited Residue Count: 202 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein male-specific lethal-3	A, B	101	Drosophila melanogaster	Mutation(s): 1  Gene Names: msl-3, CG8631
UniProt
Find proteins for P50536 (Drosophila melanogaster) Explore P50536  Go to UniProtKB:  P50536

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.29 Å
• R-Value Free:  0.192 (Depositor), 0.200 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.407	α = 90
b = 60.407	β = 90
c = 113.805	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction
HKL-2000	data scaling
PHASES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-07-21 
Deposition Author(s): Kim, D., Huang, P., Rastinejad, F., Khorasanizadeh, S.

Revision History  

• Version 1.0: 2010-07-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Advisory, Refinement description
• Version 1.3: 2023-09-06
  Changes: Advisory, Data collection, Database references, Refinement description