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- PDB-2jz0: DSX_short -

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Basic information

Entry
Database: PDB / ID: 2jz0
TitleDSX_short
ComponentsProtein doublesex
KeywordsTRANSCRIPTION / double sex / sex determination / development / gene regulation / ubiquitin
Function / homology
Function and homology information


imaginal disc-derived male genitalia development / male analia development / female analia development / female sex differentiation / sex-specific pigmentation / female somatic sex determination / imaginal disc-derived female genitalia development / sex comb development / negative regulation of developmental pigmentation / somatic sex determination ...imaginal disc-derived male genitalia development / male analia development / female analia development / female sex differentiation / sex-specific pigmentation / female somatic sex determination / imaginal disc-derived female genitalia development / sex comb development / negative regulation of developmental pigmentation / somatic sex determination / genital disc development / male sex differentiation / courtship behavior / male courtship behavior, veined wing generated song production / sex determination / male courtship behavior / sex differentiation / axon midline choice point recognition / RNA polymerase II transcription regulatory region sequence-specific DNA binding / DNA-binding transcription repressor activity, RNA polymerase II-specific / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleus
Similarity search - Function
Doublesex dimerisation / Doublesex dimerisation domain / Doublesex dimerisation domain / DM DNA-binding domain / DMRT family / DM DNA-binding domain superfamily / DM DNA binding domain / DM DNA-binding domain signature. / DM DNA-binding domain profile. / Doublesex DNA-binding motif ...Doublesex dimerisation / Doublesex dimerisation domain / Doublesex dimerisation domain / DM DNA-binding domain / DMRT family / DM DNA-binding domain superfamily / DM DNA binding domain / DM DNA-binding domain signature. / DM DNA-binding domain profile. / Doublesex DNA-binding motif / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / DGSA-distance geometry simulated annealing
AuthorsYang, Y. / Zhang, W. / Bayrer, J.R. / Weiss, M.A.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Doublesex and the Regulation of Sexual Dimorphism in Drosophila melanogaster: STRUCTURE, FUNCTION, AND MUTAGENESIS OF A FEMALE-SPECIFIC DOMAIN.
Authors: Yang, Y. / Zhang, W. / Bayrer, J.R. / Weiss, M.A.
History
DepositionDec 21, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 8, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein doublesex
B: Protein doublesex


Theoretical massNumber of molelcules
Total (without water)15,4912
Polymers15,4912
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 100structures with the lowest energy
RepresentativeModel #1closest to the average

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Components

#1: Protein Protein doublesex


Mass: 7745.735 Da / Num. of mol.: 2 / Fragment: UNP residues 350-412
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: dsx / Production host: Escherichia coli (E. coli) / References: UniProt: P23023

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1213D HN(CA)CB
1313D CBCA(CO)NH
1413D C(CO)NH
1513D H(CCO)NH
1613D HNCO
1713D 1H-15N NOESY
1813D 1H-13C NOESY
192Filtered NOESY
11014D 13C/13C edited NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
190 % H2O, 10 % D2O, 1 mM [U-100% 13C; U-100% 15N] protein, H2OH2O
290 % H2O, 10 % D2O, 1.2 mM [U-100% 13C; U-100% 15N] protein, H2OH2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
90 %H2O1
10 %D2O1
1 mMentity 1[U-100% 13C; U-100% 15N]1
1 mMentity 2[U-100% 13C; U-100% 15N]1
90 %H2O2
10 %D2O2
1 mMentity 1[U-100% 13C; U-100% 15N]2
1.2 mMentity 22
Sample conditionsIonic strength: 250 / pH: 6.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE7001
Varian INOVAVarianINOVA6002

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Processing

NMR software
NameDeveloperClassification
NMRPipeDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
PIPPGarrettdata analysis
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
Insight IIAccelrys Software Inc.structure display
TALOSCornilescu, Delaglio and Baxdihedral angles prediction
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: DGSA-distance geometry simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 20

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