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- PDB-1xpx: Structural basis of prospero-DNA interaction; implications for tr... -

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Basic information

Entry
Database: PDB / ID: 1xpx
TitleStructural basis of prospero-DNA interaction; implications for transcription regulation in developing cells
Components
  • 5'-D(*AP*GP*CP*AP*TP*GP*CP*CP*TP*G)-3'
  • 5'-D(*CP*AP*GP*GP*CP*AP*TP*GP*CP*T)-3'
  • Protein prospero
KeywordsTRANSCRIPTION REGULATION/DNA / homeodomain / protein-DNA binding / prospero / neural cell development / TRANSCRIPTION REGULATION-DNA COMPLEX
Function / homology
Function and homology information


regulation of R7 cell differentiation / asymmetric neuroblast division resulting in ganglion mother cell formation / dendrite guidance / ganglion mother cell fate determination / R7 cell fate commitment / cell dedifferentiation / male courtship behavior / basal cortex / regulation of neuroblast proliferation / asymmetric neuroblast division ...regulation of R7 cell differentiation / asymmetric neuroblast division resulting in ganglion mother cell formation / dendrite guidance / ganglion mother cell fate determination / R7 cell fate commitment / cell dedifferentiation / male courtship behavior / basal cortex / regulation of neuroblast proliferation / asymmetric neuroblast division / neuroblast differentiation / negative regulation of axonogenesis / axonogenesis involved in innervation / apical cortex / glial cell differentiation / peripheral nervous system development / regulation of protein localization to nucleus / regulation of DNA-binding transcription factor activity / G1 to G0 transition / regulation of neuron differentiation / dendrite morphogenesis / negative regulation of neuroblast proliferation / positive regulation of neuroblast proliferation / axon development / neuroblast proliferation / cell fate commitment / synapse assembly / axonogenesis / axon guidance / central nervous system development / brain development / DNA-binding transcription repressor activity, RNA polymerase II-specific / intracellular protein localization / sensory perception of taste / regulation of gene expression / cell cortex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / negative regulation of gene expression / positive regulation of gene expression / regulation of transcription by RNA polymerase II / negative regulation of transcription by RNA polymerase II / positive regulation of transcription by RNA polymerase II / DNA binding / nucleus / plasma membrane
Similarity search - Function
Homeo-prospero domain / Homeo-prospero domain / Homeo-prospero domain superfamily / Prospero homeodomain family / Homeo-prospero domain / Homeo-Prospero domain profile. / Homeobox-like domain superfamily / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / Homeobox protein prospero
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsYousef, M.S. / Matthews, B.W.
Citation
Journal: STRUCTURE / Year: 2005
Title: Structural Basis of Prospero-DNA Interaction: Implications for Transcription Regulationin Developing Cells.
Authors: Yousef, M.S. / Matthews, B.W.
#1: Journal: Structure / Year: 2002
Title: Structure of the DNA binding region of prospero reveals a novel homeo-prospero domain.
Authors: Ryter, J.M. / Doe, C.Q. / Matthews, B.W.
History
DepositionOct 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 3, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 650HELIX DETERMINATION METHOD: AUTHOR PROVIDED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
D: 5'-D(*AP*GP*CP*AP*TP*GP*CP*CP*TP*G)-3'
C: 5'-D(*CP*AP*GP*GP*CP*AP*TP*GP*CP*T)-3'
A: Protein prospero


Theoretical massNumber of molelcules
Total (without water)25,6333
Polymers25,6333
Non-polymers00
Water27015
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.708, 44.708, 226.661
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: DNA chain 5'-D(*AP*GP*CP*AP*TP*GP*CP*CP*TP*G)-3'


Mass: 3045.005 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*CP*AP*GP*GP*CP*AP*TP*GP*CP*T)-3'


Mass: 3045.005 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein Protein prospero


Mass: 19543.400 Da / Num. of mol.: 1 / Fragment: HOMEO-PROSPERO DOMAIN (RESIDUES 1245-1401)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: pros / Plasmid: PET15B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P29617
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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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: 2.21 Å3/Da / Density % sol: 44.33 %
Crystal growpH: 5 / Details: pH 5.00

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationMonochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 6354 / % possible obs: 90 % / Observed criterion σ(I): 0 / Net I/σ(I): 33
Reflection shellResolution: 2.8→2.85 Å / % possible all: 90

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.282 317 -RANDOM
Rwork0.217 ---
obs0.217 5532 90 %-
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1240 404 0 15 1659

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