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- PDB-1tlh: T4 AsiA bound to sigma70 region 4 -

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Basic information

Entry
Database: PDB / ID: 1tlh
TitleT4 AsiA bound to sigma70 region 4
Components
  • 10 kDa anti-sigma factor
  • RNA polymerase sigma factor rpoD
KeywordsTRANSCRIPTION / anti-sigma / sigma70 / rna polymerase
Function / homology
Function and homology information


sigma factor antagonist complex / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / sigma factor activity / DNA-templated transcription initiation / response to heat / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / DNA binding / cytosol
Similarity search - Function
Anti-sigma factor AsiA / Anti-Sigma Factor A / Anti-Sigma Factor A / Anti-Sigma Factor A superfamily / Anti-Sigma Factor A / RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 ...Anti-sigma factor AsiA / Anti-Sigma Factor A / Anti-Sigma Factor A / Anti-Sigma Factor A superfamily / Anti-Sigma Factor A / RNA polymerase sigma factor 70, non-essential domain / Sigma-70, non-essential region / RNA polymerase sigma factor 70, region 1.1 / Sigma-70 factor, region 1.1 superfamily / Sigma-70 factor, region 1.1 / Sigma-70 factors family signature 1. / RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma factor RpoD / RNA polymerase sigma-70 region 1.2 / Sigma-70 factor, region 1.2 / RNA polymerase sigma-70 region 3 / Sigma-70 region 3 / Sigma-70 factors family signature 2. / RNA polymerase sigma-70 / RNA polymerase sigma-70 region 4 / Sigma-70, region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 like domain / Sigma-70 region 2 / RNA polymerase sigma factor, region 2 / RNA polymerase sigma factor, region 3/4-like / Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain / Arc Repressor Mutant, subunit A / Winged helix-like DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
RNA polymerase sigma factor RpoD / 10 kDa anti-sigma factor
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
Escherichia coli (E. coli)
MethodSOLUTION NMR / dynamical simulated annealing, restrained energy minimization
AuthorsLambert, L.J. / Wei, Y. / Schirf, V. / Demeler, B. / Werner, M.H.
CitationJournal: Embo J. / Year: 2004
Title: T4 AsiA blocks DNA recognition by remodeling sigma(70) region 4
Authors: Lambert, L.J. / Wei, Y. / Schirf, V. / Demeler, B. / Werner, M.H.
History
DepositionJun 9, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_spectrometer
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_spectrometer.model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 10 kDa anti-sigma factor
B: RNA polymerase sigma factor rpoD


Theoretical massNumber of molelcules
Total (without water)19,9252
Polymers19,9252
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 least restraint violations
RepresentativeModel #1fewest violations

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Components

#1: Protein 10 kDa anti-sigma factor / Audrey Stevens' inhibitor / 10 kDa RNA polymerase-associated protein


Mass: 10604.011 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: ASIA / Plasmid: pET-28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-SI / References: UniProt: P32267
#2: Protein RNA polymerase sigma factor rpoD / Sigma-70


Mass: 9320.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: RPOD, ALT, B3067 / Plasmid: pET-28b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P00579

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D 13C-separated NOESY
1213D 15N-separated NOESY
131residual dipolar couplings in Pf1 phage at 9 mg/ml

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Sample preparation

DetailsContents: 0.7 mM protein, phosphate buffered saline, 50 mM sodium azide, 1 mM benzamidine hydrochloride
Solvent system: 97% H2O, 3% D2O
Sample conditionsIonic strength: 150 mM NaCl / pH: 7.0 / Pressure: 1 atm / Temperature: 312 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX5001
Bruker DMXBrukerDMX6002
Bruker AVANCEBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
Xplor-NIH2.9.3Clore and Schweitersrefinement
NMRPipe2.2Delagliodata analysis
RefinementMethod: dynamical simulated annealing, restrained energy minimization
Software ordinal: 1
NMR representativeSelection criteria: fewest violations
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 100 / Conformers submitted total number: 20

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