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- EMDB-3590: Cryo-EM structure of RNA polymerase I in complex with Rrn3 and Co... -

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Basic information

Entry
Database: EMDB / ID: 3590
TitleCryo-EM structure of RNA polymerase I in complex with Rrn3 and Core Factor (Orientation III)
SampleRNA polymerase I in complex with Rrn3 and Core Factor
SourceSaccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Map dataNone
Methodsingle particle reconstruction, at 7.7 Å resolution
AuthorsEngel C / Gubbey T / Neyer S / Sainsbury S / Oberthuer C / Baejen C / Bernecky C / Cramer P
CitationCell, 2017, 169, 120-131.e22

Cell, 2017, 169, 120-131.e22 StrPapers
Structural Basis of RNA Polymerase I Transcription Initiation.
Christoph Engel / Tobias Gubbey / Simon Neyer / Sarah Sainsbury / Christiane Oberthuer / Carlo Baejen / Carrie Bernecky / Patrick Cramer

DateDeposition: Feb 14, 2017 / Header (metadata) release: Mar 22, 2017 / Map release: Apr 5, 2017 / Last update: Feb 14, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0205
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.0205
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5n5y
  • Surface level: 0.0205
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_3590.map.gz (map file in CCP4 format, 55297 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
240 pix
1.35 Å/pix.
= 324. Å
240 pix
1.35 Å/pix.
= 324. Å
240 pix
1.35 Å/pix.
= 324. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.35 Å
Density
Contour Level:0.0205 (by author), 0.0205 (movie #1):
Minimum - Maximum-0.029996127 - 0.06755038
Average (Standard dev.)-6.4416134E-5 (0.004714947)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions240240240
Origin000
Limit239239239
Spacing240240240
CellA=B=C: 324 Å
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.351.351.35
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z324.000324.000324.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0300.068-0.000

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Supplemental data

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Sample components

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Entire RNA polymerase I in complex with Rrn3 and Core Factor

EntireName: RNA polymerase I in complex with Rrn3 and Core Factor / Number of components: 25

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Component #1: protein, RNA polymerase I in complex with Rrn3 and Core Factor

ProteinName: RNA polymerase I in complex with Rrn3 and Core Factor / Recombinant expression: No

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Component #2: protein, RNA polymerase I

ProteinName: RNA polymerase I / Recombinant expression: No
MassTheoretical: 590 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #3: protein, Initiation factor Rrn3

ProteinName: Initiation factor Rrn3 / Recombinant expression: No
MassTheoretical: 70 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Source (engineered)Expression System: Escherichia coli bl21(de3) / bacteria / image: Escherichia coli

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Component #4: protein, Core Factor

ProteinName: Core Factor / Recombinant expression: No
MassTheoretical: 220 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Source (engineered)Expression System: Escherichia coli bl21(de3) / bacteria / image: Escherichia coli

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Component #5: protein, DNA-directed RNA polymerase I subunit RPA190

ProteinName: DNA-directed RNA polymerase I subunit RPA190 / Recombinant expression: No
MassTheoretical: 186.676969 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #6: protein, DNA-directed RNA polymerase I subunit RPA135

ProteinName: DNA-directed RNA polymerase I subunit RPA135 / Recombinant expression: No
MassTheoretical: 135.910328 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #7: protein, DNA-directed RNA polymerases I and III subunit RPAC1

ProteinName: DNA-directed RNA polymerases I and III subunit RPAC1 / Recombinant expression: No
MassTheoretical: 37.732613 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #8: protein, DNA-directed RNA polymerase I subunit RPA14

ProteinName: DNA-directed RNA polymerase I subunit RPA14 / Recombinant expression: No
MassTheoretical: 14.599128 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #9: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC1

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC1
Recombinant expression: No
MassTheoretical: 25.117094 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #10: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC2

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC2
Recombinant expression: No
MassTheoretical: 17.931834 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #11: protein, DNA-directed RNA polymerase I subunit RPA43

ProteinName: DNA-directed RNA polymerase I subunit RPA43 / Recombinant expression: No
MassTheoretical: 36.264852 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #12: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC3

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC3
Recombinant expression: No
MassTheoretical: 16.525363 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #13: protein, DNA-directed RNA polymerase I subunit RPA12

ProteinName: DNA-directed RNA polymerase I subunit RPA12 / Recombinant expression: No
MassTheoretical: 13.676566 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #14: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC5

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC5
Recombinant expression: No
MassTheoretical: 8.290732 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #15: protein, DNA-directed RNA polymerases I and III subunit RPAC2

ProteinName: DNA-directed RNA polymerases I and III subunit RPAC2 / Recombinant expression: No
MassTheoretical: 16.16786 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #16: protein, DNA-directed RNA polymerases I, II, and III subunit RPABC4

ProteinName: DNA-directed RNA polymerases I, II, and III subunit RPABC4
Recombinant expression: No
MassTheoretical: 7.729969 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #17: protein, DNA-directed RNA polymerase I subunit RPA49

ProteinName: DNA-directed RNA polymerase I subunit RPA49 / Recombinant expression: No
MassTheoretical: 46.721707 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #18: protein, DNA-directed RNA polymerase I subunit RPA34

ProteinName: DNA-directed RNA polymerase I subunit RPA34 / Recombinant expression: No
MassTheoretical: 26.933518 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #19: protein, RNA polymerase I-specific transcription initiation facto...

ProteinName: RNA polymerase I-specific transcription initiation factor RRN3
Recombinant expression: No
MassTheoretical: 72.458258 kDa
Source (engineered)Expression System: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #20: protein, RNA polymerase I-specific transcription initiation facto...

ProteinName: RNA polymerase I-specific transcription initiation factor RRN6
Recombinant expression: No
MassTheoretical: 102.163227 kDa
Source (engineered)Expression System: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #21: protein, RNA polymerase I-specific transcription initiation facto...

ProteinName: RNA polymerase I-specific transcription initiation factor RRN7
Recombinant expression: No
MassTheoretical: 60.435195 kDa
Source (engineered)Expression System: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #22: protein, RNA polymerase I-specific transcription initiation facto...

ProteinName: RNA polymerase I-specific transcription initiation factor RRN11
Recombinant expression: No
MassTheoretical: 59.334262 kDa
Source (engineered)Expression System: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #23: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 8 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Component #24: ligand, SULFATE ION

LigandName: SULFATE ION / Number of Copies: 5 / Recombinant expression: No
MassTheoretical: 9.606305 MDa

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Component #25: ligand, MAGNESIUM ION

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

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.1 mg/ml / pH: 7.8
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 298 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: 40 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 8317
3D reconstructionResolution: 7.7 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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