4RKG

Structure of the MSL2 CXC domain bound with a non-specific (GC)6 DNA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.231 

wwPDB Validation 3D Report Full Report



Literature

Structural basis of X chromosome DNA recognition by the MSL2 CXC domain during Drosophila dosage compensation.

Zheng, S.Villa, R.Wang, J.Feng, Y.Wang, J.Becker, P.B.Ye, K.

(2014) Genes Dev 28: 2652-2662

  • DOI: 10.1101/gad.250936.114
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • The male-specific lethal dosage compensation complex (MSL-DCC) selectively assembles on the X chromosome in Drosophila males and activates gene transcription by twofold through histone acetylation. An MSL recognition element (MRE) sequence motif nucl ...

    The male-specific lethal dosage compensation complex (MSL-DCC) selectively assembles on the X chromosome in Drosophila males and activates gene transcription by twofold through histone acetylation. An MSL recognition element (MRE) sequence motif nucleates the initial MSL association, but how it is recognized remains unknown. Here, we identified the CXC domain of MSL2 specifically recognizing the MRE motif and determined its crystal structure bound to specific and nonspecific DNAs. The CXC domain primarily contacts one strand of DNA duplex and employs a single arginine to directly read out dinucleotide sequences from the minor groove. The arginine is flexible when bound to nonspecific sequences. The core region of the MRE motif harbors two binding sites on opposite strands that can cooperatively recruit a CXC dimer. Specific DNA-binding mutants of MSL2 are impaired in MRE binding and X chromosome localization in vivo. Our results reveal multiple dynamic DNA-binding modes of the CXC domain that target the MSL-DCC to X chromosomes.


    Organizational Affiliation

    National Institute of Biological Sciences, Beijing 102206, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China yekeqiong@nibs.ac.cn.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
E3 ubiquitin-protein ligase msl-2A, B52Drosophila melanogasterMutation(s): 1 
Gene Names: CG3241msl-2MSL2
EC: 6.3.2 (PDB Primary Data), 2.3.2 (UniProt)
Find proteins for P50534 (Drosophila melanogaster)
Explore P50534 
Go to UniProtKB:  P50534
Protein Feature View
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  • Reference Sequence
  • Find similar nucleic acids by: Sequence   |   Structure
Entity ID: 2
MoleculeChainsLengthOrganism
DNA (5'-D(*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*C)-3')H, I12N/A
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download CCD File 
A, B, H
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.315 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.231 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 40.705α = 90
b = 75.251β = 90
c = 77.436γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
PHASERphasing
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

  • Deposited Date: 2014-10-13 
  • Released Date: 2015-01-21 
  • Deposition Author(s): Zheng, S., Ye, K.

Revision History 

  • Version 1.0: 2015-01-21
    Type: Initial release