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- PDB-2jvv: Solution Structure of E. coli NusG carboxyterminal domain -

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Basic information

Entry
Database: PDB / ID: 2jvv
TitleSolution Structure of E. coli NusG carboxyterminal domain
ComponentsTranscription antitermination protein nusG
KeywordsTRANSCRIPTION / NusG / transcription factor / Transcription antitermination / Transcription regulation / Transcription termination
Function / homology
Function and homology information


transcription elongation-coupled chromatin remodeling / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription termination / ribosome biogenesis / cytosol
Similarity search - Function
: / Transcription antitermination protein, NusG / Transcription antitermination protein, NusG, bacteria, conserved site / Transcription termination factor nusG signature. / SH3 type barrels. - #30 / NusG-like / Transcription termination factor nusG / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily ...: / Transcription antitermination protein, NusG / Transcription antitermination protein, NusG, bacteria, conserved site / Transcription termination factor nusG signature. / SH3 type barrels. - #30 / NusG-like / Transcription termination factor nusG / NusG, N-terminal / In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. / NusG, N-terminal domain superfamily / SH3 type barrels. / KOW (Kyprides, Ouzounis, Woese) motif. / Translation protein SH3-like domain superfamily / KOW motif / KOW / Ribosomal protein L2, domain 2 / Roll / Mainly Beta
Similarity search - Domain/homology
Transcription termination/antitermination protein NusG
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsSchweimer, K. / Scheckenhofer, U. / Roesch, P.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Two structurally independent domains of E. coli NusG create regulatory plasticity via distinct interactions with RNA polymerase and regulators.
Authors: Mooney, R.A. / Schweimer, K. / Rosch, P. / Gottesman, M. / Landick, R.
History
DepositionSep 26, 2007Deposition site: BMRB / Processing site: RCSB
Revision 1.0Oct 14, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 30, 2013Group: Data collection
Revision 1.3Aug 13, 2014Group: Database references
Revision 1.4May 1, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_nmr_software / pdbx_nmr_spectrometer
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

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Transcription antitermination protein nusG


Theoretical massNumber of molelcules
Total (without water)20,5611
Polymers20,5611
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 / 120structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Transcription antitermination protein nusG


Mass: 20560.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nusG / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0AFG0

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1313D HNCO
1413D HNCA
1513D CBCA(CO)NH
1613D HN(CA)CB
1713D HBHA(CO)NH
1813D (H)CCH-TOCSY
1913D 1H-15N NOESY
11013D 1H-13C NOESY
NMR detailsText: The protein shows aggregation via the aminoterminal domain, and the resulting line broading of the signals of the aminoterminal domain did not allow a structure determination of the ...Text: The protein shows aggregation via the aminoterminal domain, and the resulting line broading of the signals of the aminoterminal domain did not allow a structure determination of the aminoterminal domain using the full length protein. Becuase of flexible linked domains the carboxyterminal domain showed sufficient signals to determine the structure of this domain using the full length protein. Only the carboxyterminal domain (res. 124-181) gave interpretable NMR data for assignment and structure determination.

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Sample preparation

DetailsContents: 0.45 mM [U-95% 13C; U-95% 15N] NusG, 10 mM potassium phosphate, 50 mM sodium chloride, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.45 mMNusG[U-95% 13C; U-95% 15N]1
10 mMpotassium phosphate1
50 mMsodium chloride1
Sample conditionspH: 6.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE8001
Bruker AvanceBrukerAVANCE9002

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Processing

NMR software
NameVersionDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
X-PLOR NIH1.2.1Schwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIH1.2.1Schwieters, Kuszewski, Tjandra and Clorerefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 120 / Conformers submitted total number: 20

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