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- PDB-4rkg: Structure of the MSL2 CXC domain bound with a non-specific (GC)6 DNA -

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Basic information

Entry
Database: PDB / ID: 4rkg
TitleStructure of the MSL2 CXC domain bound with a non-specific (GC)6 DNA
Components
  • DNA (5'-D(*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*C)-3')
  • E3 ubiquitin-protein ligase msl-2
KeywordsDNA binding protein/DNA / Zinc cluster / DNA binding domain / Dosage compensation / DNA binding protein-DNA complex
Function / homology
Function and homology information


dosage compensation complex / X chromosome located dosage compensation complex, transcription activating / sex-chromosome dosage compensation / MSL complex / dosage compensation by hyperactivation of X chromosome / nuclear chromosome / X chromosome / transcription factor binding / protein autoubiquitination / RING-type E3 ubiquitin transferase ...dosage compensation complex / X chromosome located dosage compensation complex, transcription activating / sex-chromosome dosage compensation / MSL complex / dosage compensation by hyperactivation of X chromosome / nuclear chromosome / X chromosome / transcription factor binding / protein autoubiquitination / RING-type E3 ubiquitin transferase / protein polyubiquitination / ubiquitin protein ligase activity / chromosome / protein ubiquitination / chromatin binding / DNA binding / metal ion binding
Similarity search - Function
E3 ubiquitin-protein ligase Msl2, zinc RING finger / E3 ubiquitin-protein ligase Msl2, CXC domain / E3 ubiquitin-protein ligase MSL2 / CXC domain of E3 ubiquitin-protein ligase MSL2 / zinc RING finger of MSL2 / Tesmin/TSO1-like CXC domain / Tesmin/TSO1-like CXC domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger RING-type profile. ...E3 ubiquitin-protein ligase Msl2, zinc RING finger / E3 ubiquitin-protein ligase Msl2, CXC domain / E3 ubiquitin-protein ligase MSL2 / CXC domain of E3 ubiquitin-protein ligase MSL2 / zinc RING finger of MSL2 / Tesmin/TSO1-like CXC domain / Tesmin/TSO1-like CXC domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Zinc finger RING-type profile. / Zinc finger, RING-type / Zinc finger, RING/FYVE/PHD-type
Similarity search - Domain/homology
DNA / DNA (> 10) / E3 ubiquitin-protein ligase msl-2
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsZheng, S. / Ye, K.
CitationJournal: Genes Dev. / Year: 2014
Title: Structural basis of X chromosome DNA recognition by the MSL2 CXC domain during Drosophila dosage compensation.
Authors: Zheng, S. / Villa, R. / Wang, J. / Feng, Y. / Wang, J. / Becker, P.B. / Ye, K.
History
DepositionOct 13, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 21, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: E3 ubiquitin-protein ligase msl-2
B: E3 ubiquitin-protein ligase msl-2
H: DNA (5'-D(*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*C)-3')
I: DNA (5'-D(*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,22413
Polymers18,6364
Non-polymers5899
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.705, 75.251, 77.436
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein E3 ubiquitin-protein ligase msl-2 / Protein male-specific lethal-2


Mass: 5652.500 Da / Num. of mol.: 2 / Fragment: CXC domain (UNP RESIDUES 520-570) / Mutation: C560G
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: CG3241, msl-2, MSL2 / Plasmid: pET28a-SMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)
References: UniProt: P50534, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases)
#2: DNA chain DNA (5'-D(*GP*CP*GP*CP*GP*CP*GP*CP*GP*CP*GP*C)-3')


Mass: 3665.368 Da / Num. of mol.: 2 / Source method: obtained synthetically
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.18 Å3/Da / Density % sol: 61.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES-Na (pH 7.5), 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97913 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 12, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97913 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 8732 / Num. obs: 8584 / % possible obs: 98.3 % / Observed criterion σ(I): 6.5
Reflection shellResolution: 2.5→2.55 Å / Redundancy: 12.6 % / Rmerge(I) obs: 0.699 / Num. unique all: 416 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.9_1692)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→18.015 Å / SU ML: 0.38 / σ(F): 1.34 / Phase error: 34.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.3149 406 4.77 %RANDOM
Rwork0.2265 ---
all0.2306 8648 --
obs0.2306 8510 98.42 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→18.015 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms615 486 9 0 1110
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0091170
X-RAY DIFFRACTIONf_angle_d1.0531670
X-RAY DIFFRACTIONf_dihedral_angle_d27.875473
X-RAY DIFFRACTIONf_chiral_restr0.047180
X-RAY DIFFRACTIONf_plane_restr0.006131
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5-2.69240.3854890.3337158799
2.6924-2.96230.3529780.29931611100
2.9623-3.38850.3632820.2569158897
3.3885-4.25980.3672810.22511641100
4.2598-18.01560.26760.1987167796
Refinement TLS params.Method: refined / Origin x: 17.3669 Å / Origin y: 0.2768 Å / Origin z: 18.9614 Å
111213212223313233
T0.5916 Å2-0.0366 Å20.0123 Å2-0.6217 Å2-0.099 Å2--0.5698 Å2
L2.3185 °2-0.0199 °2-1.483 °2-3.7476 °22.0312 °2--4.0102 °2
S0.0033 Å °-0.3163 Å °0.2756 Å °0.3565 Å °-0.2664 Å °0.583 Å °0.1285 Å °0.2669 Å °0.1835 Å °
Refinement TLS groupSelection details: ALL

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