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- EMDB-8771: RNA polymerase I Initial Transcribing Complex -

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Entry
Database: EMDB / ID: 8771
TitleRNA polymerase I Initial Transcribing Complex
SampleRNA Polymerase I Initial Transcribing Complex
SourceSaccharomyces cerevisiae s288c / yeast / image: Saccharomyces cerevisiae
Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Map dataRNA Polymerase I Initial Transcribing Complex
Methodsingle particle reconstruction, at 3.8 Å resolution
AuthorsHan Y / He Y
CitationElife, 2017, 6

Elife, 2017, 6 Yorodumi Papers
Structural mechanism of ATP-independent transcription initiation by RNA polymerase I.
Yan Han / Chunli Yan / Thi Hoang Duong Nguyen / Ashleigh J Jackobel / Ivaylo Ivanov / Bruce A Knutson / Yuan He

Validation ReportPDB-ID: 5w5y

SummaryFull reportAbout validation report
DateDeposition: Jun 16, 2017 / Header (metadata) release: Jul 26, 2017 / Map release: Jul 26, 2017 / Last update: Sep 20, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5w5y
  • Surface level: 0.04
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_8771.map.gz (map file in CCP4 format, 28312 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
192 pix
1.3 Å/pix.
= 249.6 Å
192 pix
1.3 Å/pix.
= 249.6 Å
192 pix
1.3 Å/pix.
= 249.6 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:0.04 (by author), 0.04 (movie #1):
Minimum - Maximum-0.14364254 - 0.2684227
Average (Standard dev.)0.0003082453 (0.013421878)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions192192192
Origin000
Limit191191191
Spacing192192192
CellA=B=C: 249.59999 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z249.600249.600249.600
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.1440.2680.000

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Supplemental data

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Sample components

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Entire RNA Polymerase I Initial Transcribing Complex

EntireName: RNA Polymerase I Initial Transcribing Complex / Number of components: 22
MassTheoretical: 900 kDa

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Component #1: protein, RNA Polymerase I Initial Transcribing Complex

ProteinName: RNA Polymerase I Initial Transcribing Complex / Recombinant expression: No
MassTheoretical: 900 kDa
SourceSpecies: Saccharomyces cerevisiae s288c / yeast / image: Saccharomyces cerevisiae
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #2: 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 (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #3: 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 (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #4: 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 (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #5: 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 (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #6: 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 (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #7: 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 (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #8: 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 (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #9: 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 (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #10: 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 (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #11: 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 (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #12: 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 (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #13: 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 (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #14: 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 (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #15: 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 (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #16: protein, RNA polymerase I-specific transcription initiation facto...

ProteinName: RNA polymerase I-specific transcription initiation factor RRN6
Recombinant expression: No
MassTheoretical: 100.721156 kDa
Source (engineered)Expression System: Saccharomyces cerevisiae (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #17: 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 (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #18: 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 (strain atcc 204508 / s288c) / yeast /
Strain: ATCC 204508 / S288c

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Component #19: nucleic-acid, RNA

Nucleic-acidName: RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AUGCGA
MassTheoretical: 1.915213 kDa

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Component #20: nucleic-acid, non-template strand DNA

Nucleic-acidName: non-template strand DNA / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DC)(DA)(DA)(DG)(DT)(DG)(DT)(DG)(DA)(DG) (DG)(DA)(DA)(DA)(DA)(DG)(DT)(DA)(DG)(DT) (DT)(DG)(DG)(DG)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT)(DT) (DT)(DG)(DC)(DA)(DG)(DT)(DT)(DG)(DA)(DA) (DG)(DA)(DC)(DA)
MassTheoretical: 16.803787 kDa

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Component #21: nucleic-acid, template strand DNA

Nucleic-acidName: template strand DNA / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
(DT)(DG)(DT)(DC)(DT)(DT)(DC)(DA)(DA)(DC) (DT)(DG)(DC)(DT)(DT)(DT)(DC)(DG)(DC)(DA) (DT)(DG)(DA)(DA)(DG)(DT)(DA)(DC)(DC)(DT) (DC)(DC)(DC)(DA)(DA)(DC)(DT)(DA)(DC)(DT) (DT)(DT)(DT)(DC)(DC)(DT)(DC)(DA)(DC)(DA) (DC)(DT)(DT)(DG)
MassTheoretical: 16.360488 kDa

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Component #22: ligand, ZINC ION

LigandName: ZINC ION / Number of Copies: 6 / Recombinant expression: No
MassTheoretical: 6.540905 MDa

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.6
VitrificationCryogen name: ETHANE / Temperature: 277 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: 56.8 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 22500 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 124112
3D reconstructionSoftware: RELION
CTF correction: CTF amplitude correction was performed following 3D auto refinement in relion.
Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution assessment)

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Atomic model buiding

Output model

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