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- EMDB-8585: CryoEM structure of crosslinked E.coli RNA polymerase elongation ... -

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Basic information

Entry
Database: EMDB / ID: 8585
TitleCryoEM structure of crosslinked E.coli RNA polymerase elongation complex
SampleCrosslinked E.coli RNA polymerase ternary elongation complex
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataCryoEM structure of crosslinked E.coli RNA polymerase elongation complex
Methodsingle particle reconstruction, at 4.05 Å resolution
AuthorsKang JY / Darst SA
CitationElife, 2017, 6

Elife, 2017, 6 Yorodumi Papers
Structural basis of transcription arrest by coliphage HK022 Nun in an Escherichia coli RNA polymerase elongation complex.
Jin Young Kang / Paul Dominic B Olinares / James Chen / Elizabeth A Campbell / Arkady Mustaev / Brian T Chait / Max E Gottesman / Seth A Darst

Validation ReportPDB-ID: 6alf

SummaryFull reportAbout validation report
DateDeposition: Feb 2, 2017 / Header (metadata) release: Apr 5, 2017 / Map release: Apr 5, 2017 / Last update: Apr 5, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.015
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-6alf
  • Surface level: 0.015
  • Imaged by UCSF CHIMERA
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3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_8585.map.gz (map file in CCP4 format, 67109 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
256 pix
1.3 Å/pix.
= 332.8 Å
256 pix
1.3 Å/pix.
= 332.8 Å
256 pix
1.3 Å/pix.
= 332.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.3 Å
Density
Contour Level:0.015 (by emdb), 0.015 (movie #1):
Minimum - Maximum-0.03737607 - 0.09016131
Average (Standard dev.)0.00014599922 (0.0035888213)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions256256256
Origin000
Limit255255255
Spacing256256256
CellA=B=C: 332.8 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z332.800332.800332.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-152-37
NX/NY/NZ998271
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS256256256
D min/max/mean-0.0370.0900.000

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Supplemental data

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Sample components

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Entire Crosslinked E.coli RNA polymerase ternary elongation complex

EntireName: Crosslinked E.coli RNA polymerase ternary elongation complex
Number of components: 10
MassTheoretical: 393.145 kDa

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Component #1: protein, Crosslinked E.coli RNA polymerase ternary elongation complex

ProteinName: Crosslinked E.coli RNA polymerase ternary elongation complex
Recombinant expression: No
MassTheoretical: 393.145 kDa
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #2: nucleic-acid, DNA (29-MER)

Nucleic-acidName: DNA (29-MER) / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DG)(DG)(DG)(DC)(DT)(DA)(DC)(DC)(DT)(DC) (DT)(DC)(DC)(DA)(DT)(DG)(DA)(DC)(DG)(DG) (DC)(DG)(DA)(DA)(DT)(DA)(DC)(DC)(DC)
MassTheoretical: 8.840689 kDa

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Component #3: nucleic-acid, DNA (29-MER)

Nucleic-acidName: DNA (29-MER) / Class: DNA / Details: Template DNA / Structure: OTHER / Synthetic: No
Sequence:
(DG)(DG)(DG)(DT)(DA)(DT)(DT)(DC)(DG)(DC) (DC)(DG)(DT)(DG)(DT)(DA)(DC)(DC)(DT)(DC) (DT)(DC)(DC)(DT)(DA)(DG)(DC)(DC)(DC)
MassTheoretical: 8.813646 kDa

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Component #4: nucleic-acid, RNA (5'-R(*GP*CP*A*UP*UP*CP*AP*AP*AP*GP*CP*GP*GP*AP...

Nucleic-acidName: RNA (5'-R(*GP*CP*A*UP*UP*CP*AP*AP*AP*GP*CP*GP*GP*AP*GP*AP*GP*GP*UP*A)-3')
Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
GCAUUCAAAG CGGAGAGGUA
MassTheoretical: 6.509968 kDa

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

ProteinName: DNA-directed RNA polymerase subunit alpha / Recombinant expression: No
MassTheoretical: 26.459125 kDa
Source (engineered)Expression System: Escherichia coli o157:h7 / bacteria / image: Escherichia coli

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Component #6: protein, DNA-directed RNA polymerase subunit beta

ProteinName: DNA-directed RNA polymerase subunit beta / Recombinant expression: No
MassTheoretical: 150.820875 kDa
Source (engineered)Expression System: Escherichia coli o45:k1 (strain s88 / expec) / bacteria / image: Escherichia coli
Strain: S88 / ExPEC

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Component #7: protein, DNA-directed RNA polymerase subunit beta'

ProteinName: DNA-directed RNA polymerase subunit beta' / Recombinant expression: No
MassTheoretical: 155.366781 kDa
Source (engineered)Expression System: Escherichia coli o157:h7 / bacteria / image: Escherichia coli

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Component #8: protein, DNA-directed RNA polymerase subunit omega

ProteinName: DNA-directed RNA polymerase subunit omega / Recombinant expression: No
MassTheoretical: 9.094239 kDa
Source (engineered)Expression System: Escherichia coli o45:k1 (strain s88 / expec) / bacteria / image: Escherichia coli
Strain: S88 / ExPEC

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Component #9: ligand, MAGNESIUM ION

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

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Component #10: 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

Specimen stateparticle
Sample solutionSpecimen conc.: 3 mg/ml / pH: 8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 295 K / Humidity: 100 %

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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: 85.2 e/Å2 / Illumination mode: FLOOD BEAM
LensCs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 800 - 2400 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 2000

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 83800
3D reconstructionSoftware: RELION / CTF correction: CTF parameters were estimated by CTFFIND4 / Resolution: 4.05 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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