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- EMDB-3727: RNA polymerase I pre-initiation complex -

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Basic information

Entry
Database: EMDB / ID: 3727
TitleRNA polymerase I pre-initiation complex
SampleRNA polymerase I pre-initiation complex with Core Factor, Rrn3 and transcription scaffold
SourceSaccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Map data
Methodsingle particle reconstruction, at 4.4 Å resolution
AuthorsSadian Y / Tafur L / Kosinski J / Jakobi AJ / Wetzel R / Buczak K / Hagen WJH / Beck M / Sachse C / Muller CW
CitationEMBO J., 2017, 36, 2698-2709

EMBO J., 2017, 36, 2698-2709 Yorodumi Papers
Structural insights into transcription initiation by yeast RNA polymerase I.
Yashar Sadian / Lucas Tafur / Jan Kosinski / Arjen J Jakobi / Rene Wetzel / Katarzyna Buczak / Wim Jh Hagen / Martin Beck / Carsten Sachse / Christoph W Müller

Validation ReportPDB-ID: 5oa1

SummaryFull reportAbout validation report
DateDeposition: May 17, 2017 / Header (metadata) release: May 31, 2017 / Map release: Jul 26, 2017 / Last update: Sep 27, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.01
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-5oa1
  • Surface level: 0.01
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_3727.map.gz (map file in CCP4 format, 95552 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
288 pix
1.35 Å/pix.
= 388.8 Å
288 pix
1.35 Å/pix.
= 388.8 Å
288 pix
1.35 Å/pix.
= 388.8 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:0.01 (by author), 0.01 (movie #1):
Minimum - Maximum-0.037984867 - 0.06979046
Average (Standard dev.)0.00024136012 (0.0025315944)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions288288288
Origin000
Limit287287287
Spacing288288288
CellA=B=C: 388.80002 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z288288288
origin x/y/z0.0000.0000.000
length x/y/z388.800388.800388.800
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS288288288
D min/max/mean-0.0380.0700.000

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Supplemental data

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Sample components

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Entire RNA polymerase I pre-initiation complex with Core Factor, Rrn3 an...

EntireName: RNA polymerase I pre-initiation complex with Core Factor, Rrn3 and transcription scaffold
Number of components: 23
MassTheoretical: 875 MDa

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Component #1: protein, RNA polymerase I pre-initiation complex with Core Factor...

ProteinName: RNA polymerase I pre-initiation complex with Core Factor, Rrn3 and transcription scaffold
Recombinant expression: No
MassTheoretical: 875 MDa

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Component #2: protein, RNA polymerase I pre-initiation complex with Core Factor...

ProteinName: RNA polymerase I pre-initiation complex with Core Factor, Rrn3 and transcription scaffold
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #3: protein, RNA polymerase I pre-initiation complex with Core Factor...

ProteinName: RNA polymerase I pre-initiation complex with Core Factor, Rrn3 and transcription scaffold
Recombinant expression: No
Source (engineered)Expression System: Synthetic construct

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Component #4: protein, RPA1_YEAST DNA-directed RNA polymerase I subunit RPA190

ProteinName: RPA1_YEAST DNA-directed RNA polymerase I subunit RPA190
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #5: protein, RPA2_YEAST DNA-directed RNA polymerase I subunit RPA135

ProteinName: RPA2_YEAST DNA-directed RNA polymerase I subunit RPA135
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #6: protein, RPA49_YEAST DNA-directed RNA polymerase I subunit

ProteinName: RPA49_YEAST DNA-directed RNA polymerase I subunit / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #7: protein, RPA43_YEAST DNA-directed RNA polymerase I subunit

ProteinName: RPA43_YEAST DNA-directed RNA polymerase I subunit / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #8: protein, RPAC1_YEAST DNA-directed RNA polymerases I and III subun...

ProteinName: RPAC1_YEAST DNA-directed RNA polymerases I and III subunit RPAC1
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #9: protein, RPA34_YEAST DNA-directed RNA polymerase I subunit RPA34

ProteinName: RPA34_YEAST DNA-directed RNA polymerase I subunit RPA34
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #10: protein, RPAB1_YEAST DNA-directed RNA polymerases I, II, and III ...

ProteinName: RPAB1_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC1
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #11: protein, RPAB2_YEAST DNA-directed RNA polymerases I, II, and III ...

ProteinName: RPAB2_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC2
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #12: protein, RPAC2_YEAST DNA-directed RNA polymerases I and III subun...

ProteinName: RPAC2_YEAST DNA-directed RNA polymerases I and III subunit RPAC2
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #13: protein, RPAB3_YEAST DNA-directed RNA polymerases I, II, and III ...

ProteinName: RPAB3_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC3
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #14: protein, RPA14_YEAST DNA-directed RNA polymerase I subunit RPA14

ProteinName: RPA14_YEAST DNA-directed RNA polymerase I subunit RPA14
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #15: protein, RPA12_YEAST DNA-directed RNA polymerase I subunit RPA12

ProteinName: RPA12_YEAST DNA-directed RNA polymerase I subunit RPA12
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #16: protein, RPAB4_YEAST DNA-directed RNA polymerases I, II, and III ...

ProteinName: RPAB4_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC4
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #17: protein, RPAB5_YEAST DNA-directed RNA polymerases I, II, and III ...

ProteinName: RPAB5_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC5
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #18: protein, RRN3_YEAST RNA polymerase I-specific transcription initi...

ProteinName: RRN3_YEAST RNA polymerase I-specific transcription initiation factor RRN3
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #19: protein, RRN6_YEAST RNA polymerase I-specific transcription initi...

ProteinName: RRN6_YEAST RNA polymerase I-specific transcription initiation factor RRN6
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #20: protein, RRN7_YEAST RNA polymerase I-specific transcription initi...

ProteinName: RRN7_YEAST RNA polymerase I-specific transcription initiation factor RRN7
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #21: protein, RRN11_YEAST RNA polymerase I-specific transcription init...

ProteinName: RRN11_YEAST RNA polymerase I-specific transcription initiation factor RRN11
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #22: nucleic-acid, non-template DNA strand

Nucleic-acidName: non-template DNA strand / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
GGTTTAGTCA TGGAGTACAA GTGTGAGGAA AAGTAGTTGG CGTAGCAGGA GAAGTAAAGC AGTTGAAGAC

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Component #23: nucleic-acid, template DNA strand

Nucleic-acidName: template DNA strand / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
CCAAATCAGT ACCTCATGTT CACACTCCTT TTCATCAACC CTCCATGAAG TACGCTTTCG TCAACTTCTG

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.2 mg/ml / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / 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: 2 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 105000 X (nominal) / Imaging mode: BRIGHT FIELD / Defocus: 750 - 4000 nm
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 4235

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 38589
3D reconstructionSoftware: RELION / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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