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

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Entry
Database: EMDB / ID: 3727
TitleRNA polymerase I pre-initiation complex
Map data
SampleRNA polymerase I pre-initiation complex with Core Factor, Rrn3 and transcription scaffold
  • RPA1_YEAST DNA-directed RNA polymerase I subunit RPA190
  • RPA2_YEAST DNA-directed RNA polymerase I subunit RPA135
  • RPA49_YEAST DNA-directed RNA polymerase I subunit
  • RPA43_YEAST DNA-directed RNA polymerase I subunit
  • RPAC1_YEAST DNA-directed RNA polymerases I and III subunit RPAC1
  • RPA34_YEAST DNA-directed RNA polymerase I subunit RPA34
  • RPAB1_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC1
  • RPAB2_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC2
  • RPAC2_YEAST DNA-directed RNA polymerases I and III subunit RPAC2
  • RPAB3_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC3
  • RPA14_YEAST DNA-directed RNA polymerase I subunit RPA14
  • RPA12_YEAST DNA-directed RNA polymerase I subunit RPA12
  • RPAB4_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC4
  • RPAB5_YEAST DNA-directed RNA polymerases I, II, and III subunit RPABC5
  • RRN3_YEAST RNA polymerase I-specific transcription initiation factor RRN3
  • RRN6_YEAST RNA polymerase I-specific transcription initiation factor RRN6
  • RRN7_YEAST RNA polymerase I-specific transcription initiation factor RRN7
  • RRN11_YEAST RNA polymerase I-specific transcription initiation factor RRN11
  • (nucleic-acidNucleic acid) x 2
Function / homologyRNA polymerases, subunit N, zinc binding site / DNA-directed RNA polymerase, insert domain superfamily / DNA-directed RNA polymerases I and III subunit AC19 / DNA-directed RNA polymerases I and III subunit AC40 / Pol I subunit A12, C-terminal zinc ribbon / RPB5-like RNA polymerase subunit / RPB6/omega subunit-like superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 ...RNA polymerases, subunit N, zinc binding site / DNA-directed RNA polymerase, insert domain superfamily / DNA-directed RNA polymerases I and III subunit AC19 / DNA-directed RNA polymerases I and III subunit AC40 / Pol I subunit A12, C-terminal zinc ribbon / RPB5-like RNA polymerase subunit / RPB6/omega subunit-like superfamily / RNA polymerase, RBP11-like subunit / RNA polymerase Rpb5, N-terminal domain superfamily / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / RNA polymerase Rpb7-like, N-terminal domain superfamily / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb2, domain 6 / RNA polymerase Rpb1, domain 2 / RNA polymerase I transcription initiation factor TAF1B/Rrn7 / DNA-directed RNA polymerase, subunit RPB6 / Transcription factor S-II (TFIIS) / RNA polymerase I-specific transcription initiation factor Rrn6 / RNA polymerase I, subunit Rpa14, fungi / DNA-directed RNA polymerase I, subunit RPA34.5 / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / RNA polymerase Rpb2, OB-fold / DNA-directed RNA pol I, largest subunit / DNA-directed RNA polymerase, subunit 2 / Transcription initiation factor Rrn11, budding yeast / RNA polymerase subunit RPB10 / RNA polymerase I-specific transcription initiation factor RRN6-like / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerase, subunit H/Rpb5, conserved site / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / Formation of TC-NER Pre-Incision Complex / Transcription initiation factor Rrn7, Zinc-finger / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb5, C-terminal domain / RNA polymerase subunit, RPB6/omega / Zinc finger TFIIS-type signature. / Yeast RNA polymerase I subunit RPA14 / DNA-directed RNA polymerase I subunit RPA34.5 / RNA polymerase I-specific transcription-initiation factor / Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7 / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases D / 30 to 40 Kd subunits signature. / RNA polymerases M / 15 Kd subunits signature. / A49-like RNA polymerase I associated factor / RNA polymerases H / 23 Kd subunits signature. / RNA polymerases K / 14 to 18 Kd subunits signature. / RNA polymerases N / 8 Kd subunits signature. / RNA polymerases L / 13 to 16 Kd subunits signature. / RNA polymerases beta chain signature. / Zinc finger TFIIS-type profile. / RNA polymerase I, Rpa2 specific domain / RNA polymerase I specific transcription initiation factor RRN3 / RNA polymerase Rpb6 / SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 / RNA polymerase Rpb3/Rpb11 dimerisation domain / RNA polymerases N / 8 kDa subunit / RNA polymerases M/15 Kd subunit / DNA directed RNA polymerase, 7 kDa subunit / RNA polymerase Rpb8 / RNA polymerase Rpb5, N-terminal domain / RNA polymerase I specific initiation factor / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb2, domain 7 / RNA polymerase Rpb2, domain 2 / RNA polymerase beta subunit / RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb1, domain 3 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 5 / Nucleic acid-binding, OB-fold / DNA-directed RNA polymerase subunit/transcription factor S / RNA Polymerase II Pre-transcription Events / TP53 Regulates Transcription of DNA Repair Genes / DNA-directed RNA polymerase, M/15kDa subunit / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site / Zinc finger, TFIIS-type / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase, alpha subunit / DNA-directed RNA polymerase, subunit N/Rpb10 / Dual incision in TC-NER / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / RNA polymerase II transcribes snRNA genes / RNA polymerase, Rpb5, N-terminal / mRNA Capping / mRNA Splicing - Minor Pathway / RNA Polymerase I Transcription Initiation / RNA Polymerase II Promoter Escape / RNA Polymerase II Transcription Pre-Initiation And Promoter Opening / RNA Polymerase II Transcription Initiation / RNA Polymerase II Transcription Initiation And Promoter Clearance / RNA Pol II CTD phosphorylation and interaction with CE / Estrogen-dependent gene expression / RNA polymerase, Rpb8 / Gap-filling DNA repair synthesis and ligation in TC-NER / RNA polymerase Rpb7, N-terminal / Transcription initiation factor Rrn11 / DNA-directed RNA polymerase, insert domain
Function and homology information
SourceSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / 4.4 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.
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: Mar 28, 2018

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.01
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  • Surface level: 0.01
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  • Surface view with fitted model
  • Atomic models: : PDB-5oa1
  • Surface level: 0.01
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
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.

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: 90.0 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 (baker's yeast)

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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 (others)

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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 (baker's yeast)

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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 (baker's yeast)

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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 (baker's yeast)

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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 (baker's yeast)

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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 (baker's yeast)

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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 (baker's yeast)

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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 (baker's yeast)

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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 (baker's yeast)

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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 (baker's yeast)

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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 (baker's yeast)

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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 (baker's yeast)

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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 (baker's yeast)

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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 (baker's yeast)

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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 (baker's yeast)

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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 (baker's yeast)

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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 (baker's yeast)

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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 (baker's yeast)

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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 (baker's yeast)

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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

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: 1 %

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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: 750.0 - 4000.0 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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