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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: 8777
TitlePol I Initial Transcribing Complex with a truncated scaffold at 6.9 angstrom
SampleRNA Polymerase I Initial Transcribing Complex with a truncated scaffold
SourceSaccharomyces cerevisiae s288c / yeast / image: Saccharomyces cerevisiae
Map dataRNA polymerase I Initial Transcribing Complex with a truncated scaffold
Methodsingle particle reconstruction, at 6.9 Å resolution
AuthorsHan Y / He Y
CitationElife, 2017, 6

Elife, 2017, 6 Yorodumi Papers
Structural mechanism of ATP-independent transcription initiation by RNA polymerase I.
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 5, 2017

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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
3D viewer


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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 package.

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
Origin000
Limit127127127
Spacing128128128
CellA=B=C: 302.08 Å
α=β=γ: 90 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
NX/NY/NZ
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
MassTheoretical: 900 kDa

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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 / image: Saccharomyces cerevisiae
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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

ProteinName: DNA-directed RNA polymerase I subunit RPA190 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae s288c / yeast / image: Saccharomyces cerevisiae

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

ProteinName: DNA-directed RNA polymerase I subunit RPA135 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae s288c / yeast / image: Saccharomyces cerevisiae

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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 / image: Saccharomyces cerevisiae

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

ProteinName: DNA-directed RNA polymerase I subunit RPA14 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae s288c / yeast / image: Saccharomyces cerevisiae

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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 RPABC1
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae s288c / yeast / image: Saccharomyces cerevisiae

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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 RPABC2
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae s288c / yeast / image: Saccharomyces cerevisiae

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

ProteinName: DNA-directed RNA polymerase I subunit RPA43 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae s288c / yeast / image: Saccharomyces cerevisiae

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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 RPABC3
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae s288c / yeast / image: Saccharomyces cerevisiae

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

ProteinName: DNA-directed RNA polymerase I subunit RPA12 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae s288c / yeast / image: Saccharomyces cerevisiae

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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 RPABC5
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae s288c / yeast / image: Saccharomyces cerevisiae

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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 / image: Saccharomyces cerevisiae

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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 RPABC4
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae s288c / yeast / image: Saccharomyces cerevisiae

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

ProteinName: DNA-directed RNA polymerase I subunit RPA49 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae s288c / yeast / image: Saccharomyces cerevisiae

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

ProteinName: DNA-directed RNA polymerase I subunit RPA34 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae s288c / yeast / image: Saccharomyces cerevisiae

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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
Source (engineered)Expression System: Saccharomyces cerevisiae s288c / yeast / image: Saccharomyces cerevisiae

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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
Source (engineered)Expression System: Saccharomyces cerevisiae s288c / yeast / image: Saccharomyces cerevisiae

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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
Source (engineered)Expression System: Saccharomyces cerevisiae s288c / yeast / image: Saccharomyces cerevisiae

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Component #19: nucleic-acid, RNA

Nucleic-acidName: RNA / Class: RNA / Structure: OTHER / Synthetic: No
Sequence:
AUGCGA

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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

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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

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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

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Experimental details

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Sample preparation

Specimen stateparticle
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 (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 assessment)

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