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- PDB-6jnx: Cryo-EM structure of a Q-engaged arrested complex -

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Basic information

Entry
Database: PDB / ID: 6jnx
TitleCryo-EM structure of a Q-engaged arrested complex
Components
  • (DNA (63-MER)) x 2
  • (DNA-directed RNA polymerase subunit ...Polymerase) x 4
  • Antiterminator Q protein
  • RNA (5'-R(P*AP*UP*AP*AP*GP*GP*UP*GP*GP*GP*GP*UP*UP*AP*GP*UP*GP*A)-3')
  • RNA polymerase sigma factor RpoD
KeywordsTRANSCRIPTION / DNA / RNA / RNA polymerase / Antitermination
Function / homology
Function and homology information


negative regulation of DNA-templated transcription, termination / RNA polymerase complex / transcription initiation from bacterial-type RNA polymerase promoter / sigma factor activity / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / ec:2.7.7.6: / protein-containing complex assembly / response to heat / protein dimerization activity ...negative regulation of DNA-templated transcription, termination / RNA polymerase complex / transcription initiation from bacterial-type RNA polymerase promoter / sigma factor activity / ribonucleoside binding / DNA-directed 5'-3' RNA polymerase activity / ec:2.7.7.6: / protein-containing complex assembly / response to heat / protein dimerization activity / transcription, DNA-templated / DNA-binding transcription factor activity / DNA binding / zinc ion binding / membrane / cytosol / cytoplasm
RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma-70 like domain / Winged helix-like DNA-binding domain superfamily / RPB6/omega subunit-like superfamily / RNA polymerase sigma factor RpoD / DNA-directed RNA polymerase, beta subunit, external 1 domain / DNA-directed RNA polymerase, subunit 2 / RNA polymerase Rpb2, OB-fold / RNA polymerase sigma factor, region 2 / DNA-directed RNA polymerase, insert domain superfamily ...RNA polymerase sigma factor RpoD, C-terminal / RNA polymerase sigma-70 like domain / Winged helix-like DNA-binding domain superfamily / RPB6/omega subunit-like superfamily / RNA polymerase sigma factor RpoD / DNA-directed RNA polymerase, beta subunit, external 1 domain / DNA-directed RNA polymerase, subunit 2 / RNA polymerase Rpb2, OB-fold / RNA polymerase sigma factor, region 2 / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase sigma factor, region 3/4-like / DNA-directed RNA polymerase, subunit beta-prime / RNA polymerase subunit, RPB6/omega / DNA-directed RNA polymerase, alpha subunit / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / DNA-directed RNA polymerase, insert domain / RNA polymerase, alpha subunit, C-terminal / RNA polymerase, RBP11-like subunit / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase beta subunit / Bacterial RNA polymerase, alpha chain C terminal domain / RNA polymerase Rpb2, domain 7 / Sigma-70, non-essential region / Sigma-70, region 4 / Sigma-70 region 2 / Sigma-70 region 3 / Sigma-70 factor, region 1.1 / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb6 / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb2, domain 6 / Sigma-70 factor, region 1.2 / RNA polymerase Rpb1, domain 3 superfamily / RNA polymerase Rpb1, funnel domain superfamily / Bacteriophage 933W, GpQ / DNA-directed RNA polymerase beta subunit, bacterial-type / RNA polymerase sigma-70 region 1.2 / RNA polymerase, N-terminal / RNA polymerases beta chain signature. / Sigma-70 factors family signature 2. / Sigma-70 factors family signature 1. / RNA polymerase beta subunit external 1 domain / Phage antitermination protein Q / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb2, domain 3 / RNA polymerase, alpha subunit / RNA polymerase sigma-70 / RNA polymerase Rpb2, domain 3 / RNA polymerase, subunit omega/K/RPB6 / DNA-directed RNA polymerase, omega subunit / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb2, domain 2 / RNA polymerase Rpb2, domain 7 / RNA polymerase sigma factor 70, non-essential domain / RNA polymerase sigma-70 region 4 / RNA polymerase sigma-70 region 2 / RNA polymerase sigma-70 region 3 / RNA polymerase Rpb2, domain 2 / RNA polymerase sigma factor 70, region 1.1 / RNA polymerase, beta subunit, conserved site / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 5
Antiterminator Q protein / RNA polymerase sigma factor RpoD / DNA-directed RNA polymerase subunit alpha / DNA-directed RNA polymerase subunit omega / DNA-directed RNA polymerase subunit beta' / DNA-directed RNA polymerase subunit beta
Biological speciesEscherichia coli K-12 (bacteria)
Enterobacteria phage SfI (bacteriophage)
Enterobacteria phage P21 (bacteriophage)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.08 Å
AuthorsFeng, Y. / Shi, J.
CitationJournal: Nat Commun / Year: 2019
Title: Structural basis of Q-dependent transcription antitermination
Authors: Shi, J. / Gao, X. / Tian, T. / Yu, Z. / Gao, B. / Wen, A. / Chang, S. / You, L. / Zhang, Y. / Zhang, X. / Feng, Y.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Mar 18, 2019 / Release: Jun 12, 2019
RevisionDateData content typeProviderType
1.0Jun 12, 2019Structure modelrepositoryInitial release

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Structure visualization

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Assembly

Deposited unit
A: DNA-directed RNA polymerase subunit alpha
B: DNA-directed RNA polymerase subunit alpha
C: DNA-directed RNA polymerase subunit beta
D: DNA-directed RNA polymerase subunit beta'
E: DNA-directed RNA polymerase subunit omega
F: RNA polymerase sigma factor RpoD
N: DNA (63-MER)
R: RNA (5'-R(P*AP*UP*AP*AP*GP*GP*UP*GP*GP*GP*GP*UP*UP*AP*GP*UP*GP*A)-3')
T: DNA (63-MER)
P: Antiterminator Q protein
Q: Antiterminator Q protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)542,22214
Polymers542,06711
Non-polymers1553
Water0
1


TypeNameSymmetry operationNumber
identity operation1_5551
Buried area54020 Å2
ΔGint-275 kcal/mol
Surface area186500 Å2

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Components

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DNA-directed RNA polymerase subunit ... , 4 types, 5 molecules ABCDE

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


Mass: 36558.680 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: rpoA / Production host: Escherichia coli (E. coli) / References: UniProt: P0A7Z4, EC: 2.7.7.6
#2: Protein/peptide DNA-directed RNA polymerase subunit beta / Polymerase / RNAP subunit beta / RNA polymerase subunit beta / Transcriptase subunit beta


Mass: 150820.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: rpoB / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8V2, EC: 2.7.7.6
#3: Protein/peptide DNA-directed RNA polymerase subunit beta' / Polymerase / RNAP subunit beta' / RNA polymerase subunit beta' / Transcriptase subunit beta'


Mass: 155366.781 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: rpoC / Production host: Escherichia coli (E. coli) / References: UniProt: P0A8T7, EC: 2.7.7.6
#4: Protein/peptide DNA-directed RNA polymerase subunit omega / Polymerase / RNAP omega subunit / RNA polymerase omega subunit / Transcriptase subunit omega


Mass: 10249.547 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: rpoZ / Production host: Escherichia coli (E. coli) / References: UniProt: P0A800, EC: 2.7.7.6

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Protein/peptide , 2 types, 3 molecules FPQ

#5: Protein/peptide RNA polymerase sigma factor RpoD / Sigma-70


Mass: 70352.242 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K-12 / Gene: rpoD / Production host: Escherichia coli (E. coli) / References: UniProt: P00579
#9: Protein/peptide Antiterminator Q protein


Mass: 18712.908 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage SfI (bacteriophage)
Gene: Q / Production host: Escherichia coli (E. coli) / References: UniProt: M1FPN0

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DNA chain , 2 types, 2 molecules NT

#6: DNA chain DNA (63-MER)


Mass: 19558.576 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Enterobacteria phage P21 (bacteriophage)
#8: DNA chain DNA (63-MER)


Mass: 19282.377 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Enterobacteria phage P21 (bacteriophage)

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RNA chain , 1 types, 1 molecules R

#7: RNA chain RNA (5'-R(P*AP*UP*AP*AP*GP*GP*UP*GP*GP*GP*GP*UP*UP*AP*GP*UP*GP*A)-3')


Mass: 5893.548 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Enterobacteria phage P21 (bacteriophage)

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Non-polymers , 2 types, 3 molecules

#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Magnesium
#11: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn / Zinc

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: 21Q-engaged arrested complex / Type: COMPLEX / Entity ID: 1, 2, 3, 4, 5, 6, 7, 8, 9 / Source: MULTIPLE SOURCES
Molecular weightExperimental value: NO
Source (natural)

Entity assembly-ID: 1

IDOrganismNcbi tax-ID
1Escherichia coli K-12 (bacteria)83333
2Enterobacteria phage SfI (bacteriophage)1225789
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 8
SpecimenConc.: 8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 95 % / Chamber temperature: 283 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingElectron dose: 56 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 4.08 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 64497 / Symmetry type: POINT

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