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- EMDB-9852: Cryo-EM structure of a Q-engaged arrested complex -

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Basic information

Entry
Database: EMDB / ID: EMD-9852
TitleCryo-EM structure of a Q-engaged arrested complex
Map data
Sample21Q-engaged arrested complex
  • (DNA-directed RNA polymerase subunit ...Polymerase) x 4
  • RNA polymerase sigma factor RpoD
  • (nucleic-acidNucleic acid) x 3
  • Antiterminator Q protein
  • (ligand) x 2
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 P21 (bacteriophage) / Enterobacteria phage SfI (bacteriophage)
Methodsingle 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 ReportPDB-ID: 6jnx

SummaryFull reportAbout validation report
DateDeposition: Mar 18, 2019 / Header (metadata) release: Jun 12, 2019 / Map release: Jun 12, 2019 / Update: Jun 12, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.026
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.026
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-6jnx
  • Surface level: 0.026
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_9852.map.gz / Format: CCP4 / Size: 30.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.31 Å/pix.
x 200 pix.
= 261.4 Å
1.31 Å/pix.
x 200 pix.
= 261.4 Å
1.31 Å/pix.
x 200 pix.
= 261.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.307 Å
Density
Contour LevelBy AUTHOR: 0.026 / Movie #1: 0.026
Minimum - Maximum-0.093437344 - 0.15141062
Average (Standard dev.)0.000053063934 (±0.006916749)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions200200200
Spacing200200200
CellA=B=C: 261.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.3071.3071.307
M x/y/z200200200
origin x/y/z0.0000.0000.000
length x/y/z261.400261.400261.400
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ192192192
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS200200200
D min/max/mean-0.0930.1510.000

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Supplemental data

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Sample components

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Entire 21Q-engaged arrested complex

EntireName: 21Q-engaged arrested complex / Number of components: 12

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Component #1: protein, 21Q-engaged arrested complex

ProteinName: 21Q-engaged arrested complex / Recombinant expression: No
SourceSpecies: Escherichia coli K-12 (bacteria)

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Component #2: protein, DNA-directed RNA polymerase subunit alpha

ProteinName: DNA-directed RNA polymerase subunit alphaPolymerase / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 36.55868 kDa
SourceSpecies: Escherichia coli K-12 (bacteria) / Strain: K-12
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, DNA-directed RNA polymerase subunit beta

ProteinName: DNA-directed RNA polymerase subunit betaPolymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 150.820875 kDa
SourceSpecies: Escherichia coli K-12 (bacteria) / Strain: K-12
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, DNA-directed RNA polymerase subunit beta'

ProteinName: DNA-directed RNA polymerase subunit beta'Polymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 155.366781 kDa
SourceSpecies: Escherichia coli K-12 (bacteria) / Strain: K-12
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #5: protein, DNA-directed RNA polymerase subunit omega

ProteinName: DNA-directed RNA polymerase subunit omegaPolymerase / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 10.249547 kDa
SourceSpecies: Escherichia coli K-12 (bacteria) / Strain: K-12
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #6: protein, RNA polymerase sigma factor RpoD

ProteinName: RNA polymerase sigma factor RpoD / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 70.352242 kDa
SourceSpecies: Escherichia coli K-12 (bacteria) / Strain: K-12
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #7: nucleic-acid, DNA (63-MER)

nucleic acidName: DNA (63-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DC)(DA)(DT)(DC)(DA)(DT)(DT)(DG)(DA)(DG) (DC)(DA)(DA)(DA)(DT)(DG)(DA)(DG)(DC)(DA) (DA)(DC)(DA)(DC)(DT)(DA)(DT)(DT)(DC)(DG) (DC)(DA)(DT)(DA)(DA)(DG)(DG)(DT)(DG)(DG) (DG)(DA)(DG)(DT)(DA)(DG)(DT)(DG)(DA)(DG) (DT)(DC)(DT)(DT)(DA)(DA)(DG)(DT)(DT)(DG) (DC)(DA)(DA)
MassTheoretical: 19.558576 kDa
SourceSpecies: Enterobacteria phage P21 (bacteriophage)

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Component #8: nucleic-acid, RNA (5'-R(P*AP*UP*AP*AP*GP*GP*UP*GP*GP*GP*GP*UP*UP*...

nucleic acidName: RNA (5'-R(P*AP*UP*AP*AP*GP*GP*UP*GP*GP*GP*GP*UP*UP*AP*GP*UP*GP*A)-3')
Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AUAAGGUGGG GUUAGUGA
MassTheoretical: 5.893548 kDa
SourceSpecies: Enterobacteria phage P21 (bacteriophage)

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Component #9: nucleic-acid, DNA (63-MER)

nucleic acidName: DNA (63-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DT)(DT)(DG)(DC)(DA)(DA)(DC)(DT)(DT)(DA) (DA)(DG)(DA)(DC)(DT)(DC)(DA)(DC)(DT)(DA) (DA)(DC)(DC)(DC)(DC)(DA)(DC)(DC)(DT)(DT) (DA)(DT)(DG)(DC)(DG)(DA)(DA)(DT)(DA)(DG) (DT)(DG)(DT)(DT)(DG)(DC)(DT)(DC)(DA)(DT) (DT)(DT)(DG)(DC)(DT)(DC)(DA)(DA)(DT)(DG) (DA)(DT)(DG)
MassTheoretical: 19.282377 kDa
SourceSpecies: Enterobacteria phage P21 (bacteriophage)

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Component #10: protein, Antiterminator Q protein

ProteinName: Antiterminator Q protein / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 18.712908 kDa
SourceSpecies: Enterobacteria phage SfI (bacteriophage)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #11: ligand, MAGNESIUM ION

LigandName: MAGNESIUM ION / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 2.430505 MDa

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Component #12: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 2 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionSpecimen conc.: 8 mg/mL / pH: 8
VitrificationCryogen name: ETHANE / Temperature: 283 K / Humidity: 95 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 56 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 64497
3D reconstructionResolution: 4.08 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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