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

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Entry
Database: EMDB / ID: 8777
TitlePol I Initial Transcribing Complex with a truncated scaffold at 6.9 angstrom
Map dataRNA polymerase I Initial Transcribing Complex with a truncated scaffold
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 / homologyRNA polymerase subunit RPB10 / RNA polymerase I transcription initiation factor TAF1B/Rrn7 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb2, domain 6 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain superfamily / DNA-directed RNA polymerase, insert domain superfamily ...RNA polymerase subunit RPB10 / RNA polymerase I transcription initiation factor TAF1B/Rrn7 / RNA polymerase Rpb1, domain 2 / RNA polymerase Rpb2, domain 6 / RNA polymerase Rpb1, funnel domain superfamily / RNA polymerase Rpb2, domain 2 superfamily / DNA-directed RNA polymerase, subunit 2, hybrid-binding domain superfamily / RNA polymerase Rpb7-like, N-terminal domain superfamily / RNA polymerase Rpb5, N-terminal domain superfamily / DNA-directed RNA polymerase, insert domain superfamily / RNA polymerase, RBP11-like subunit / RPB6/omega subunit-like superfamily / RPB5-like RNA polymerase subunit superfamily / Pol I subunit A12, C-terminal zinc ribbon / DNA-directed RNA polymerases I and III subunit AC40 / DNA-directed RNA polymerases I and III subunit AC19 / RNA polymerase subunit RPABC4/transcription elongation factor Spt4 / Transcription factor S-II (TFIIS) / RNA polymerase I-specific transcription initiation factor RRN6-like / 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 / RNA polymerase I-specific transcription initiation factor Rrn6 / Transcription initiation factor Rrn11, budding yeast / DNA-directed RNA polymerase M, 15kDa subunit, conserved site / DNA-directed RNA polymerase, subunit RPB6 / RNA polymerase, subunit H/Rpb5, conserved site / Archaeal RpoH /eukaryotic RPB5 RNA polymerase subunit / DNA-directed RNA polymerase, 14-18kDa subunit, conserved site / RNA polymerases, subunit N, zinc binding site / Transcription initiation factor Rrn7, Zinc-finger / Formation of TC-NER Pre-Incision Complex / RNA polymerase Rpb3/RpoA insert domain / RNA polymerase Rpb5, C-terminal domain / RNA polymerase I, subunit Rpa14, fungi / 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 Rpb1, domain 4 / 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 5 / 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 / DNA-directed RNA polymerase I, subunit RPA34.5 / Nucleic acid-binding, OB-fold / 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 / RNA polymerase subunit, RPB6/omega / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / 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 / Formation of the Early Elongation Complex / RNA polymerase Rpb7, N-terminal / RNA polymerase Rpb2, domain 3 / DNA-directed RNA polymerase Rpb11, 13-16kDa subunit, conserved site / DNA-directed RNA polymerase, RBP11-like dimerisation domain / RNA polymerase, beta subunit, protrusion
Function and homology information
SourceSaccharomyces cerevisiae S288c (yeast)
Methodsingle particle reconstruction / cryo EM / 6.9 Å resolution
AuthorsHan Y / He Y
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
DateDeposition: Jun 16, 2017 / Header (metadata) release: Jul 5, 2017 / Map release: Jul 5, 2017 / Last update: Jul 18, 2018

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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

Downloads & links

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Map

Fileemd_8777.map.gz (map file in CCP4 format, 8389 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
128 pix
2.36 Å/pix.
= 302.08 Å
128 pix
2.36 Å/pix.
= 302.08 Å
128 pix
2.36 Å/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
Contour Level:0.07 (by author), 0.07 (movie #1):
Minimum - Maximum-0.10179037 - 0.23072258
Average (Standard dev.)0.0028788708 (0.015079218)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions128128128
Origin0.0.0.
Limit127.127.127.
Spacing128128128
CellA=B=C: 302.08 Å
α=β=γ: 90.0 deg.

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/NZ-152-37
NX/NY/NZ998271
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. 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 reconstructionCTF 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 space: REAL

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