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- PDB-2o8k: NMR Structure of the Sigma-54 RpoN Domain Bound to the-24 Promote... -

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Basic information

Entry
Database: PDB / ID: 2o8k
TitleNMR Structure of the Sigma-54 RpoN Domain Bound to the-24 Promoter Element
Components
  • 5'-D(*GP*AP*AP*AP*CP*GP*TP*GP*CP*CP*AP*AP*AP*A)-3'
  • 5'-D(*TP*TP*TP*TP*GP*GP*CP*AP*CP*GP*TP*TP*TP*C)-3'
  • RNA polymerase sigma factor RpoN
KeywordsTRANSCRIPTION/DNA / PROTEIN-DNA COMPLEX / HELIX-TURN-HELIX / TRANSCRIPTION FACTOR / SIGMA-54 / RNA POLYMERASE / TRANSCRIPTION-DNA COMPLEX
Function / homology
Function and homology information


DNA-binding transcription activator activity / sigma factor activity / nucleotidyltransferase activity / DNA-directed RNA polymerase complex / DNA-templated transcription initiation / DNA binding
Similarity search - Function
RNA polymerase sigma factor 54, core-binding domain / RNA polymerase sigma factor 54, DNA-binding / RNA polymerase sigma-54 factor, core-binding domain superfamily / Sigma-54 factor, Activator interacting domain (AID) / Sigma-54, DNA binding domain / Sigma-54 factor, core binding domain / Sigma-54 factors family signature 2. / Sigma-54 factors family profile. / RNA polymerase sigma factor 54 / Homeodomain-like ...RNA polymerase sigma factor 54, core-binding domain / RNA polymerase sigma factor 54, DNA-binding / RNA polymerase sigma-54 factor, core-binding domain superfamily / Sigma-54 factor, Activator interacting domain (AID) / Sigma-54, DNA binding domain / Sigma-54 factor, core binding domain / Sigma-54 factors family signature 2. / Sigma-54 factors family profile. / RNA polymerase sigma factor 54 / Homeodomain-like / Arc Repressor Mutant, subunit A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA / DNA (> 10) / RNA polymerase sigma factor RpoN
Similarity search - Component
Biological speciesAquifex aeolicus (bacteria)
MethodSOLUTION NMR / docking, rigid-body minimization, simulated annealing
AuthorsDoucleff, M. / Pelton, J.G. / Lee, P.S. / Wemmer, D.E.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Structural basis of DNA recognition by the alternative sigma-factor, sigma54.
Authors: Doucleff, M. / Pelton, J.G. / Lee, P.S. / Nixon, B.T. / Wemmer, D.E.
History
DepositionDec 12, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_spectrometer ...database_2 / 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_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.4Dec 27, 2023Group: 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
B: 5'-D(*TP*TP*TP*TP*GP*GP*CP*AP*CP*GP*TP*TP*TP*C)-3'
C: 5'-D(*GP*AP*AP*AP*CP*GP*TP*GP*CP*CP*AP*AP*AP*A)-3'
A: RNA polymerase sigma factor RpoN


Theoretical massNumber of molelcules
Total (without water)16,0483
Polymers16,0483
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 / 5020 structures with lowest energy and no restraint violations greater than 0.5 A and 5 degrees for distance and dihedral restraints, respectively
RepresentativeModel #1lowest energy

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Components

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


Mass: 4252.761 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: DNA chain 5'-D(*GP*AP*AP*AP*CP*GP*TP*GP*CP*CP*AP*AP*AP*A)-3'


Mass: 4306.846 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Protein RNA polymerase sigma factor RpoN


Mass: 7488.800 Da / Num. of mol.: 1 / Fragment: C-TERMINAL RPON DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aquifex aeolicus (bacteria) / Gene: rpoN / Plasmid: pSKB3 / Production host: Escherichia coli (E. coli)
Strain (production host): BL21(DE3) with Rosetta.pLysS plasmid
References: UniProt: O66858

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1113D C13-seperated[F1], C12-filtered[F2] NOESY
2223D C13-seperated NOESY
3333D 15N-seperated NOESY
1412D C12-filtered[F1,F2] NOESY
1512D C12-filtered[F1] NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
11 mM Sigma-54-DNA (U-15N U-13C) complex; 250 mM NaCl; 10 mM deuterated-HEPES, pH 6.9; 1 mM EDTA; 100% D2O100% D2O
21 mM Sigma-54-DNA (U-15N U-13C) complex; 250 mM NaCl; 10 mM HEPES, pH 6.9; 1 mM EDTA; 90% H2O; 10% D2O90% H2O/10% D2O
31 mM Sigma-54-DNA (U-15N) complex; 250 mM NaCl; 10 mM HEPES, pH 6.9; 1 mM EDTA; 90% H2O; 10% D2O90% H2O/10% D2O
Sample conditions
Conditions-IDIonic strengthpHPressure (kPa)Temperature (K)
1250 mM NaCl 6.9ambient 303 K
2250 mM NaCl 6.9ambient 303 K
3250 mM NaCl 6.9ambient 303 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMXBrukerDMX6001
Bruker AVANCEBrukerAVANCE6002
Bruker AVANCEBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipe2.3Delaglio et al. 1995processing
NMRView5.0.4Johnson et al. 1994data analysis
CYANA2.1Guntert 2004structure solution
X-PLOR2.14Schwieters et al. 2003refinement
RefinementMethod: docking, rigid-body minimization, simulated annealing
Software ordinal: 1
Details: protein and DNA structures determined individually via simulated annealing; the two structures were docked using rigid body minimization; the whole structure was refined by simulated annealing
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: 20 structures with lowest energy and no restraint violations greater than 0.5 A and 5 degrees for distance and dihedral restraints, respectively
Conformers calculated total number: 50 / Conformers submitted total number: 20

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