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- PDB-8f36: Ubx Homeodomain NMR solution structure -

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Basic information

Entry
Database: PDB / ID: 8f36
TitleUbx Homeodomain NMR solution structure
ComponentsHomeotic protein ultrabithoraxHomeosis
KeywordsDNA BINDING PROTEIN / Homeodomain Ubx / Transcription factor
Function / homology
Function and homology information


dorsal vessel aortic cell fate commitment / positive regulation of muscle organ development / anterior Malpighian tubule development / specification of animal organ identity / regulation of imaginal disc growth / haltere development / mesodermal cell fate specification / specification of segmental identity, thorax / open tracheal system development / imaginal disc-derived leg morphogenesis ...dorsal vessel aortic cell fate commitment / positive regulation of muscle organ development / anterior Malpighian tubule development / specification of animal organ identity / regulation of imaginal disc growth / haltere development / mesodermal cell fate specification / specification of segmental identity, thorax / open tracheal system development / imaginal disc-derived leg morphogenesis / somatic muscle development / muscle cell fate specification / polytene chromosome band / endoderm formation / regulation of cell fate specification / cell fate determination / anterior/posterior pattern specification / midgut development / cis-regulatory region sequence-specific DNA binding / transcription repressor complex / transcription coregulator binding / protein-DNA complex / heart development / transcription regulator complex / sequence-specific DNA binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / DNA binding / nucleus
Similarity search - Function
Homeobox protein, antennapedia type, conserved site / 'Homeobox' antennapedia-type protein signature. / Homeobox domain, metazoa / Homeobox, conserved site / 'Homeobox' domain signature. / Homeodomain / 'Homeobox' domain profile. / Homeodomain / Homeobox domain / Homeobox-like domain superfamily
Similarity search - Domain/homology
Homeotic protein ultrabithorax
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
MethodSOLUTION NMR / simulated annealing
AuthorsBeasley, S.A. / Loss, J.W. / Mekkaoui, F. / Advocate, M.R. / Spratt, D.E.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)2R15GM126432 United States
CitationJournal: To Be Published
Title: Ubx Homeodomain NMR solution structure
Authors: Beasley, S.A. / Loss, J.W. / Mekkaoui, F. / Advocate, M.R. / Spratt, D.E.
History
DepositionNov 9, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 19, 2023Provider: repository / Type: Initial release
Revision 1.1May 15, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2 / Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Homeotic protein ultrabithorax


Theoretical massNumber of molelcules
Total (without water)7,9111
Polymers7,9111
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, elutes as a monomer at expected MW
TypeNameSymmetry operationNumber
identity operation1_5551
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 Homeotic protein ultrabithorax / Homeosis


Mass: 7911.260 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Ubx, CG10388 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P83949

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDSample stateSpectrometer-IDType
111isotropic12D 1H-15N HSQC
121isotropic12D 1H-13C HSQC aliphatic
131isotropic12D 1H-13C HSQC aromatic
141isotropic13D HNCA
151isotropic13D HNCO
161isotropic13D HN(CO)CA
171isotropic13D (H)CCH-TOCSY aromatic
181isotropic13D (H)CCH-TOCSY aliphatic
191isotropic13D HN(CA)CO
1101isotropic13D C(CO)NH
1111isotropic13D CBCA(CO)NH
1121isotropic13D HN(CA)CB
1131isotropic13D 1H-15N NOESY
1141isotropic13D 1H-13C NOESY aromatic
1151isotropic13D 1H-13C NOESY aliphatic
1161isotropic13D H(CCO)NH

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Sample preparation

DetailsType: solution
Contents: 0.76 mM [U-100% 13C; U-100% 15N] UbxHD, 20 mM MES, 100 mM NaCl, 2 mM TCEP, 5 mM MgCl2, 90% H2O/10% D2O
Label: UbxHD / Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.76 mMUbxHD[U-100% 13C; U-100% 15N]1
20 mMMESnatural abundance1
100 mMNaClnatural abundance1
2 mMTCEPnatural abundance1
5 mMMgCl2natural abundance1
Sample conditionsIonic strength: 128 mM / Label: standard / pH: 6.0 Not defined / Pressure: 1 atm / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Varian INOVA AVANCE / Manufacturer: Varian / Model: INOVA AVANCE / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
CYANAGuntertrefinement
NMRViewJ9.1.0-b63One Moon Scientificchemical shift assignment
NMRViewJ9.1.0-b63One Moon Scientificpeak picking
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
CYANAGuntertstructure calculation
RefinementMethod: simulated annealing / Software ordinal: 2
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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