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- EMDB-8777: Pol I Initial Transcribing Complex with a truncated scaffold at 6... -

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Basic information

Entry
Database: EMDB / ID: EMD-8777
TitlePol I Initial Transcribing Complex with a truncated scaffold at 6.9 angstrom
Map data
SampleRNA Polymerase I Initial Transcribing Complex with a truncated scaffold
  • (DNA-directed RNA polymerase I subunit ...Polymerase) x 7
  • (DNA-directed RNA polymerases I and III subunit ...) x 2
  • (DNA-directed RNA polymerases I, II, and III subunit ...RNA polymerase) x 5
  • (RNA polymerase I-specific transcription initiation factor ...) x 3
  • (nucleic-acidNucleic acid) x 4
Function / homology
Function and homology information


RNA polymerase transcription factor SL1 complex / RNA polymerase I core factor complex / RNA polymerase I transcription regulatory region sequence-specific DNA binding / RNA polymerase I general transcription initiation factor activity / RNA polymerase I core promoter sequence-specific DNA binding / RNA polymerase I general transcription initiation factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / RNA polymerase I preinitiation complex assembly / nucleolar large rRNA transcription by RNA polymerase I / transposon integration ...RNA polymerase transcription factor SL1 complex / RNA polymerase I core factor complex / RNA polymerase I transcription regulatory region sequence-specific DNA binding / RNA polymerase I general transcription initiation factor activity / RNA polymerase I core promoter sequence-specific DNA binding / RNA polymerase I general transcription initiation factor binding / RNA polymerase II-specific DNA-binding transcription factor binding / RNA polymerase I preinitiation complex assembly / nucleolar large rRNA transcription by RNA polymerase I / transposon integration / transcription elongation from RNA polymerase I promoter / termination of RNA polymerase I transcription / termination of RNA polymerase III transcription / RNA polymerase I activity / regulation of cell size / tRNA transcription by RNA polymerase III / RNA polymerase I complex / RNA polymerase III complex / mRNA cleavage / transcription by RNA polymerase III / transcription by RNA polymerase I / RNA polymerase II, core complex / TBP-class protein binding / ribonucleoside binding / promoter-specific chromatin binding / DNA-directed RNA polymerase / transcription by RNA polymerase II / transcription, RNA-templated / ribosome biogenesis / nucleic acid binding / protein dimerization activity / nucleolus / negative regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / metal ion binding / nucleus / cytoplasm
RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, domain 2 / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase I subunit RPA2, domain 4 / RNA polymerase I associated factor, A49-like / DNA-directed RNA polymerase, RBP11-like dimerisation domain / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / RPB6/omega subunit-like superfamily / RNA polymerase, beta subunit, protrusion ...RNA polymerase Rpb2, domain 3 / RNA polymerase Rpb2, domain 2 / DNA-directed RNA polymerase, RpoA/D/Rpb3-type / DNA-directed RNA polymerase, insert domain / DNA-directed RNA polymerase I subunit RPA2, domain 4 / RNA polymerase I associated factor, A49-like / DNA-directed RNA polymerase, RBP11-like dimerisation domain / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / RPB6/omega subunit-like superfamily / RNA polymerase, beta subunit, protrusion / RNA polymerase Rpb2, domain 7 / RNA polymerase subunit, RPB6/omega / Transcription initiation factor Rrn11 / RNA polymerase, beta subunit, conserved site / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain / RNA polymerase Rpb1, domain 4 / RNA polymerase Rpb1, domain 5 / RNA polymerase Rpb1, domain 1 / RNA polymerase Rpb1, domain 3 / RNA polymerase, N-terminal / RNA polymerase archaeal subunit P/eukaryotic subunit RPABC4 / DNA-directed RNA polymerase subunit/transcription factor S / Nucleic acid-binding, OB-fold / RNA polymerase, subunit omega/K/RPB6 / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / DNA-directed RNA polymerases I and III subunit AC40 / DNA-directed RNA polymerases I and III subunit AC19 / RNA polymerase I transcription initiation factor TAF1B/Rrn7 / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / DNA-directed RNA polymerase, subunit RPB6 / RNA polymerase subunit RPB10 / Transcription initiation factor Rrn7, Zinc-finger / RNA polymerases, subunit N, zinc binding site / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerase, subunit H/Rpb5, conserved site / RNA polymerase I, subunit Rpa14, fungi / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / RNA polymerase I-specific transcription initiation factor RRN6-like / Transcription initiation factor Rrn11, budding yeast / RNA polymerase I-specific transcription initiation factor Rrn6 / DNA-directed RNA polymerase, subunit 2 / DNA-directed RNA pol I, largest subunit / RNA polymerase Rpb2, OB-fold / DNA-directed RNA polymerase RPB5 subunit, eukaryote/virus / DNA-directed RNA polymerase I, subunit RPA34.5 / Archaeal RpoK/eukaryotic RPB6 RNA polymerase subunit / RNA polymerase Rpb7-like , N-terminal / RPB5-like RNA polymerase subunit superfamily / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase Rpb1, domain 3 superfamily / Rpa43, N-terminal ribonucleoprotein (RNP) domain / RPA43, OB domain / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerase subunit Rpb5-like / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase, Rpb5, N-terminal / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain superfamily / Pol I subunit A12, C-terminal zinc ribbon / RNA polymerase, RBP11-like subunit / RNA polymerase, Rpb8 / Zinc finger, TFIIS-type / RNA polymerase, subunit H/Rpb5 C-terminal / RNA polymerase, alpha subunit / DNA-directed RNA polymerase, subunit N/Rpb10 / DNA-directed RNA polymerase, M/15kDa subunit / DNA-directed RNA polymerase, 30-40kDa subunit, conserved site
RNA polymerase I-specific transcription initiation factor RRN6 / DNA-directed RNA polymerase I subunit RPA49 / DNA-directed RNA polymerase I subunit RPA14 / DNA-directed RNA polymerase I subunit RPA34 / DNA-directed RNA polymerase I subunit RPA43 / RNA polymerase I-specific transcription initiation factor RRN7 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase I subunit RPA12 / DNA-directed RNA polymerases I and III subunit RPAC2 ...RNA polymerase I-specific transcription initiation factor RRN6 / DNA-directed RNA polymerase I subunit RPA49 / DNA-directed RNA polymerase I subunit RPA14 / DNA-directed RNA polymerase I subunit RPA34 / DNA-directed RNA polymerase I subunit RPA43 / RNA polymerase I-specific transcription initiation factor RRN7 / DNA-directed RNA polymerases I, II, and III subunit RPABC4 / DNA-directed RNA polymerases I, II, and III subunit RPABC1 / DNA-directed RNA polymerase I subunit RPA12 / DNA-directed RNA polymerases I and III subunit RPAC2 / DNA-directed RNA polymerases I, II, and III subunit RPABC5 / DNA-directed RNA polymerase I subunit RPA135 / DNA-directed RNA polymerases I, II, and III subunit RPABC3 / DNA-directed RNA polymerases I, II, and III subunit RPABC2 / DNA-directed RNA polymerase I subunit RPA190 / DNA-directed RNA polymerases I and III subunit RPAC1 / RNA polymerase I-specific transcription initiation factor RRN11
Biological speciesSaccharomyces cerevisiae S288c (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.9 Å
AuthorsHan Y / He Y
Funding support United States, 5 items
OrganizationGrant numberCountry
Northwestern UniversityCornew Innovation Award United States
National Institutes of Health/National Cancer Institute (NIH/NCI)NCI 5K22CA184235 United States
American Cancer SocietyIRG-15-173-21 United States
National Science Foundation (NSF, United States)MCB-1149521 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)NIGMS GM110387 United States
CitationJournal: Elife / Year: 2017
Title: Structural mechanism of ATP-independent transcription initiation by RNA polymerase I.
Authors: Yan Han / Chunli Yan / Thi Hoang Duong Nguyen / Ashleigh J Jackobel / Ivaylo Ivanov / Bruce A Knutson / Yuan He /
Abstract: Transcription initiation by RNA Polymerase I (Pol I) depends on the Core Factor (CF) complex to recognize the upstream promoter and assemble into a Pre-Initiation Complex (PIC). Here, we solve a ...Transcription initiation by RNA Polymerase I (Pol I) depends on the Core Factor (CF) complex to recognize the upstream promoter and assemble into a Pre-Initiation Complex (PIC). Here, we solve a structure of Pol I-CF-DNA to 3.8 Å resolution using single-particle cryo-electron microscopy. The structure reveals a bipartite architecture of Core Factor and its recognition of the promoter from -27 to -16. Core Factor's intrinsic mobility correlates well with different conformational states of the Pol I cleft, in addition to the stabilization of either Rrn7 N-terminal domain near Pol I wall or the tandem winged helix domain of A49 at a partially overlapping location. Comparison of the three states in this study with the Pol II system suggests that a ratchet motion of the Core Factor-DNA sub-complex at upstream facilitates promoter melting in an ATP-independent manner, distinct from a DNA translocase actively threading the downstream DNA in the Pol II PIC.
Validation ReportSummary, Full report, XML, About validation report
History
DepositionJun 16, 2017-
Header (metadata) releaseJul 5, 2017-
Map releaseJul 5, 2017-
UpdateDec 25, 2019-
Current statusDec 25, 2019Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8777.png

Downloads & links

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Map

FileDownload / File: emd_8777.map.gz / Format: CCP4 / Size: 8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.36 Å/pix.
x 128 pix.
= 302.08 Å		2.36 Å/pix.
x 128 pix.
= 302.08 Å		2.36 Å/pix.
x 128 pix.
= 302.08 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.36 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.10179037 - 0.23072258
Average (Standard dev.)0.0028788708 (±0.015079218)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions128128128
Spacing128128128
CellA=B=C: 302.08 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.362.362.36
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z302.080302.080302.080
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS128128128
D min/max/mean-0.1020.2310.003

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Supplemental data

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Sample components

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Entire RNA Polymerase I Initial Transcribing Complex with a truncated sc...

EntireName: RNA Polymerase I Initial Transcribing Complex with a truncated scaffold
Number of components: 22

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Component #1: protein, RNA Polymerase I Initial Transcribing Complex with a tru...

ProteinName: RNA Polymerase I Initial Transcribing Complex with a truncated scaffold
Recombinant expression: No
MassTheoretical: 900 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

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Component #2: protein, DNA-directed RNA polymerase I subunit RPA190

ProteinName: DNA-directed RNA polymerase I subunit RPA190Polymerase
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

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Component #3: protein, DNA-directed RNA polymerase I subunit RPA135

ProteinName: DNA-directed RNA polymerase I subunit RPA135Polymerase
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

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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
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

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Component #5: protein, DNA-directed RNA polymerase I subunit RPA14

ProteinName: DNA-directed RNA polymerase I subunit RPA14Polymerase / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

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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 RPABC1RNA polymerase
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

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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 RPABC2RNA polymerase
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

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Component #8: protein, DNA-directed RNA polymerase I subunit RPA43

ProteinName: DNA-directed RNA polymerase I subunit RPA43Polymerase / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

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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 RPABC3RNA polymerase
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

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Component #10: protein, DNA-directed RNA polymerase I subunit RPA12

ProteinName: DNA-directed RNA polymerase I subunit RPA12Polymerase / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

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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 RPABC5RNA polymerase
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

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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
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

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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 RPABC4RNA polymerase
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

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Component #14: protein, DNA-directed RNA polymerase I subunit RPA49

ProteinName: DNA-directed RNA polymerase I subunit RPA49Polymerase / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

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Component #15: protein, DNA-directed RNA polymerase I subunit RPA34

ProteinName: DNA-directed RNA polymerase I subunit RPA34Polymerase / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

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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
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

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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
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

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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
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #19: nucleic-acid, RNA

nucleic acidName: RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AUGCGA
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

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Component #20: nucleic-acid, template strand DNA

nucleic acidName: template strand DNA / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
TGTCTTCAAC TGCTTTCGCA TGAAGTACCT CCCAACTACT TTTCCTCACA CTTG
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

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Component #21: nucleic-acid, upstream non-template strand DNA

nucleic acidName: upstream non-template strand DNA / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
TGAGGAAAAG TAGTTGGG
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

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

nucleic acidName: downstream non-template strand DNA / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
GCAGTTGAAG ACA
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.6
VitrificationCryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %

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Electron microscopy imaging

ImagingMicroscope: JEOL 3200FS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 17.2 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 15000.0 X (nominal) / Cs: 2 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: GATAN LIQUID NITROGEN
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 43843
3D reconstructionSoftware: RELION
CTF correction: CTF amplitude correction was performed following 3D auto refinement in relion.
Resolution: 6.9 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible / Refinement space: REAL

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