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- PDB-2lmc: Structure of T7 transcription factor Gp2-E. coli RNAp jaw domain ... -

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Basic information

Entry
Database: PDB / ID: 2lmc
TitleStructure of T7 transcription factor Gp2-E. coli RNAp jaw domain complex
Components
  • Bacterial RNA polymerase inhibitor
  • DNA-directed RNA polymerase subunit betaPolymerase
KeywordsTRANSCRIPTION / TRANSFERASE
Function / homology
Function and homology information


symbiont-mediated suppression of host transcription / 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 ...symbiont-mediated suppression of host transcription / 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 / cell motility / DNA-templated transcription initiation / DNA-directed 5'-3' RNA polymerase activity / DNA-directed RNA polymerase / response to heat / intracellular iron ion homeostasis / response to antibiotic / magnesium ion binding / DNA binding / zinc ion binding / membrane / cytosol / cytoplasm
Similarity search - Function
RNA polymerase inhibitor / RNA polymerase inhibitor / RNA polymerase inhibitor superfamily / RNA polymerase inhibitor / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 ...RNA polymerase inhibitor / RNA polymerase inhibitor / RNA polymerase inhibitor superfamily / RNA polymerase inhibitor / RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain / DNA-directed RNA polymerase, subunit beta-prime, bacterial type / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, clamp domain superfamily / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 1 / RNA polymerase, alpha subunit / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb1, domain 4 / RNA polymerase, N-terminal / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase I subunit A N-terminus / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 5 / Ubiquitin-like (UB roll) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Bacterial RNA polymerase inhibitor / DNA-directed RNA polymerase subunit beta'
Similarity search - Component
Biological speciesEnterobacteria phage T7 (virus)
Escherichia coli K-12 (bacteria)
MethodSOLUTION NMR / simulated annealing
Model detailsminimized average structure, model 1
Model type detailsminimized average
AuthorsLiu, M.
CitationJournal: Mol.Cell / Year: 2012
Title: Structural and Mechanistic Basis for the Inhibition of Escherichia coli RNA Polymerase by T7 Gp2.
Authors: James, E. / Liu, M. / Sheppard, C. / Mekler, V. / Camara, B. / Liu, B. / Simpson, P. / Cota, E. / Severinov, K. / Matthews, S. / Wigneshweraraj, S.
History
DepositionNov 29, 2011Deposition site: BMRB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Database references
Revision 1.2Oct 3, 2012Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Bacterial RNA polymerase inhibitor
B: DNA-directed RNA polymerase subunit beta


Theoretical massNumber of molelcules
Total (without water)18,7092
Polymers18,7092
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)10 / 100structures with the lowest energy
RepresentativeModel #1minimized average structure

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Components

#1: Protein Bacterial RNA polymerase inhibitor


Mass: 9352.351 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T7 (virus) / Gene: 2, Gp2 / Production host: Escherichia coli (E. coli) / References: UniProt: P03704
#2: Protein DNA-directed RNA polymerase subunit beta / Polymerase / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 9356.563 Da / Num. of mol.: 1 / Fragment: UNP residues 1151-1213
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: b3988, JW3951, RNAP, rpoC, tabB / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8T7, DNA-directed RNA polymerase

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: 2D 1H-15N HSQC

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Sample preparation

DetailsContents: 300 mM [U-100% 13C; U-100% 15N] Gp2-Jaw complex, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
SampleConc.: 300 mM / Component: Gp2-Jaw complex-1 / Isotopic labeling: [U-100% 13C; U-100% 15N]
Sample conditionsIonic strength: 0.05 / pH: 6.5 / Pressure: ambient / Temperature: 303 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DRXBrukerDRX6001
Bruker DPXBrukerDPX8002

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Processing

NMR software
NameDeveloperClassification
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
RefinementMethod: simulated annealing / Software ordinal: 1
NMR representativeSelection criteria: minimized average structure
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 100 / Conformers submitted total number: 10

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