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- EMDB-3728: RNA polymerase I pre-initiation complex (CF focused refinement) -

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Basic information

Entry
Database: EMDB / ID: 3728
TitleRNA polymerase I pre-initiation complex (CF focused refinement)
Map data
SampleRNA polymerase I pre-initiation complex with Core Factor, Rrn3 and transcription scaffold
  • RRN11_YEAST RNA polymerase I-specific transcription initiation factor RRN11
  • RRN7_YEAST RNA polymerase I-specific transcription initiation factor RRN7
  • RRN6_YEAST RNA polymerase I-specific transcription initiation factor RRN6
  • (nucleic-acidNucleic acid) x 2
SourceSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / 4 Å resolution
AuthorsSadian Y / Tafur L / Kosinski J / Jakobi AJ / Wetzel R / Buczak K / Hagen WJH / Beck M / Sachse C / Muller CW
CitationJournal: EMBO J. / Year: 2017
Title: Structural insights into transcription initiation by yeast RNA polymerase I.
Authors: Yashar Sadian / Lucas Tafur / Jan Kosinski / Arjen J Jakobi / Rene Wetzel / Katarzyna Buczak / Wim Jh Hagen / Martin Beck / Carsten Sachse / Christoph W Müller
Abstract: In eukaryotic cells, RNA polymerase I (Pol I) synthesizes precursor ribosomal RNA (pre-rRNA) that is subsequently processed into mature rRNA. To initiate transcription, Pol I requires the assembly of ...In eukaryotic cells, RNA polymerase I (Pol I) synthesizes precursor ribosomal RNA (pre-rRNA) that is subsequently processed into mature rRNA. To initiate transcription, Pol I requires the assembly of a multi-subunit pre-initiation complex (PIC) at the ribosomal RNA promoter. In yeast, the minimal PIC includes Pol I, the transcription factor Rrn3, and Core Factor (CF) composed of subunits Rrn6, Rrn7, and Rrn11. Here, we present the cryo-EM structure of the 18-subunit yeast Pol I PIC bound to a transcription scaffold. The cryo-EM map reveals an unexpected arrangement of the DNA and CF subunits relative to Pol I. The upstream DNA is positioned differently than in any previous structures of the Pol II PIC. Furthermore, the TFIIB-related subunit Rrn7 also occupies a different location compared to the Pol II PIC although it uses similar interfaces as TFIIB to contact DNA. Our results show that although general features of eukaryotic transcription initiation are conserved, Pol I and Pol II use them differently in their respective transcription initiation complexes.
DateDeposition: May 17, 2017 / Header (metadata) release: Jun 7, 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: 0.0079
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.0079
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: : PDB-5oa1
  • Surface level: 0.0079
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3728.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.

Voxel sizeX=Y=Z: 1.35 Å
Density
Contour Level:0.0079 (by author), 0.0079 (movie #1):
Minimum - Maximum-0.06729799 - 0.10905698
Average (Standard dev.)7.751664E-5 (0.0017210566)
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-0.0670.1090.000

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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: 6

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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
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #2: protein, RRN11_YEAST RNA polymerase I-specific transcription init...

ProteinName: RRN11_YEAST RNA polymerase I-specific transcription initiation factor RRN11
Recombinant expression: No

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Component #3: protein, RRN7_YEAST RNA polymerase I-specific transcription initi...

ProteinName: RRN7_YEAST RNA polymerase I-specific transcription initiation factor RRN7
Recombinant expression: No

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Component #4: protein, RRN6_YEAST RNA polymerase I-specific transcription initi...

ProteinName: RRN6_YEAST RNA polymerase I-specific transcription initiation factor RRN6
Recombinant expression: No

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Component #5: nucleic-acid, non-template strand DNA

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

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Component #6: nucleic-acid, template strand DNA

Nucleic-acidName: template strand DNA / 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

SpecimenSpecimen state: particle / Method: cryo EM
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 / Number of projections: 38589
3D reconstructionSoftware: RELION / Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF

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