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- PDB-2jzb: Solution structure of the complex between E.coli NusA-AR2 and RNA... -

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Basic information

Entry
Database: PDB / ID: 2jzb
TitleSolution structure of the complex between E.coli NusA-AR2 and RNAP-aCTD
Components
  • DNA-directed RNA polymerase subunit alpha
  • Transcription elongation protein nusA
KeywordsTRANSFERASE/transcription / transcription / NusA / RNAP / helix-hairpin-helix / DNA-directed RNA polymerase / Nucleotidyltransferase / Transferase / RNA-binding / Stress response / Transcription antitermination / Transcription regulation / Transcription termination / TRANSFERASE-transcription COMPLEX
Function / homology
Function and homology information


bacterial-type RNA polymerase core enzyme binding / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / regulation of DNA-templated transcription elongation ...bacterial-type RNA polymerase core enzyme binding / submerged biofilm formation / cellular response to cell envelope stress / cytosolic DNA-directed RNA polymerase complex / regulation of DNA-templated transcription initiation / bacterial-type flagellum assembly / bacterial-type flagellum-dependent cell motility / nitrate assimilation / transcription elongation factor complex / regulation of DNA-templated transcription elongation / transcription antitermination / DNA-templated transcription initiation / cell motility / DNA-templated transcription termination / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / ribosome biogenesis / protein complex oligomerization / response to heat / intracellular iron ion homeostasis / protein dimerization activity / DNA-binding transcription factor activity / protein domain specific binding / nucleotide binding / DNA-templated transcription / DNA binding / RNA binding / membrane / cytoplasm / cytosol
Similarity search - Function
Transcription termination factor NusA, C-terminal duplication / Transcription termination factor NusA / Transcription factor NusA, N-terminal / KH domain, NusA-like / NusA, N-terminal domain superfamily / NusA N-terminal domain / NusA-like KH domain / Transcription termination/antitermination protein NusA, bacterial / Type-1 KH domain profile. / DNA repair Rad51/transcription factor NusA, alpha-helical ...Transcription termination factor NusA, C-terminal duplication / Transcription termination factor NusA / Transcription factor NusA, N-terminal / KH domain, NusA-like / NusA, N-terminal domain superfamily / NusA N-terminal domain / NusA-like KH domain / Transcription termination/antitermination protein NusA, bacterial / Type-1 KH domain profile. / DNA repair Rad51/transcription factor NusA, alpha-helical / Helix-hairpin-helix domain / S1 domain profile. / RNA polymerase, alpha subunit, C-terminal / Bacterial RNA polymerase, alpha chain C terminal domain / DNA-directed RNA polymerase, alpha subunit / Ribosomal protein S1-like RNA-binding domain / S1 RNA binding domain / S1 domain / 5' to 3' exonuclease, C-terminal subdomain / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / DNA polymerase; domain 1 / K homology domain superfamily, prokaryotic type / K homology domain-like, alpha/beta / Nucleic acid-binding, OB-fold / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
DNA-directed RNA polymerase subunit alpha / Transcription termination/antitermination protein NusA / DNA-directed RNA polymerase subunit alpha
Similarity search - Component
Biological speciesYersinia pseudotuberculosis (bacteria)
Escherichia coli (E. coli)
MethodSOLUTION NMR / simulated annealing
AuthorsPrasch, S. / Schweimer, K. / Roesch, P.
CitationJournal: To be Published
Title: structural basis of transcription elongation control: the NusA-aCTD complex
Authors: Prasch, S. / Schweimer, K. / Roesch, P.
History
DepositionJan 2, 2008Deposition site: BMRB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_nmr_spectrometer / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name ..._pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.3May 1, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit alpha
B: Transcription elongation protein nusA


Theoretical massNumber of molelcules
Total (without water)18,9402
Polymers18,9402
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 240structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein DNA-directed RNA polymerase subunit alpha / RNAP subunit alpha / Transcriptase subunit alpha / RNA polymerase subunit alpha


Mass: 11116.710 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Yersinia pseudotuberculosis (bacteria) / Gene: rpoA / Species (production host): coli / Production host: Escherichia coli (E. coli)
References: UniProt: P0A7Z4, UniProt: Q664U6*PLUS, DNA-directed RNA polymerase
#2: Protein Transcription elongation protein nusA / N utilization substance protein A / L factor


Mass: 7823.672 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: nusA / Species (production host): coli / Production host: Escherichia coli (E. coli) / References: UniProt: P0AFF6

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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 CBCA(CO)NH
1413D HN(CA)CB
1513D HNCA
1613D 1H-15N NOESY
1713D 1H-13C NOESY
1813D (H)CCH-TOCSY
1922D 1H-15N HSQC
11022D 1H-13C HSQC
11123D CBCA(CO)NH
11223D HN(CA)CB
11323D HNCA
11423D (H)CCH-TOCSY
11523D 1H-15N NOESY
11623D 1H-13C NOESY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.7 mM [U-98% 13C; U-98% 15N] actd, 2.1 mM ar2, 10 mM potassium phosphate, 50 mM sodium chloride, 1 mM beta-mercaptoethanol, 90% H2O/10% D2O90% H2O/10% D2O
20.7 mM [U-98% 13C; U-98% 15N] ar2, 2.1 mM actd, 10 mM potassium phosphate, 50 mM sodium chloride, 1 mM beta-mercaptoethanol, 90% H2O/10% D2O90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.7 mMactd[U-98% 13C; U-98% 15N]1
2.1 mMar21
10 mMpotassium phosphate1
50 mMsodium chloride1
1 mMbeta-mercaptoethanol1
0.7 mMar2[U-98% 13C; U-98% 15N]2
2.1 mMactd2
10 mMpotassium phosphate2
50 mMsodium chloride2
1 mMbeta-mercaptoethanol2
Sample conditionspH: 6.4 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometerType: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz

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Processing

NMR software
NameDeveloperClassification
NMRViewJohnson, One Moon Scientificchemical shift assignment
NMRViewJohnson, One Moon Scientificpeak picking
X-PLOR NIHSchwieters, Kuszewski, Tjandra and Clorestructure solution
X-PLOR NIHSchwieters, 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: 240 / Conformers submitted total number: 20

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