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- EMDB-8772: Core Factor local refinement from Pol I Initial Transcribing Comp... -

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Basic information

Entry
Database: EMDB / ID: EMD-8772
TitleCore Factor local refinement from Pol I Initial Transcribing Complex at 4.2 angstrom
Map data
SampleYeast Core Factor:
Rrn7 / Rrn11 / Rrn6 / (nucleic-acidNucleic acid) x 2
Function / homology
Function and homology information


RNA polymerase I core factor complex / RNA polymerase transcription factor SL1 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 / nucleolar large rRNA transcription by RNA polymerase I / TBP-class protein binding / nucleolus / metal ion binding / cytoplasm
Transcription initiation factor Rrn11 / RNA polymerase I transcription initiation factor TAF1B/Rrn7 / Transcription initiation factor Rrn7, Zinc-finger / RNA polymerase I-specific transcription initiation factor RRN6-like / Transcription initiation factor Rrn11, budding yeast / RNA polymerase I-specific transcription initiation factor Rrn6
RNA polymerase I-specific transcription initiation factor RRN6 / RNA polymerase I-specific transcription initiation factor RRN7 / RNA polymerase I-specific transcription initiation factor RRN11
Biological speciesSaccharomyces cerevisiae S288c (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.2 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.
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
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8772.png

Downloads & links

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Map

FileDownload / File: emd_8772.map.gz / Format: CCP4 / Size: 27 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.3 Å/pix.
x 192 pix.
= 249.6 Å		1.3 Å/pix.
x 192 pix.
= 249.6 Å		1.3 Å/pix.
x 192 pix.
= 249.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.3 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.27590472 - 0.39845526
Average (Standard dev.)0.0007010981 (±0.010016483)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions192192192
Spacing192192192
CellA=B=C: 249.59999 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.31.31.3
M x/y/z192192192
origin x/y/z0.0000.0000.000
length x/y/z249.600249.600249.600
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS192192192
D min/max/mean-0.2760.3980.001

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Supplemental data

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Sample components

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Entire Yeast Core Factor

EntireName: Yeast Core Factor / Number of components: 6

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Component #1: protein, Yeast Core Factor

ProteinName: Yeast Core Factor / Recombinant expression: No
MassTheoretical: 250 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

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Component #2: protein, Rrn7

ProteinName: Rrn7 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #3: protein, Rrn11

ProteinName: Rrn11 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

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Component #4: protein, Rrn6

ProteinName: Rrn6 / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)
Source (engineered)Expression System: Escherichia coli (E. coli)

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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:
CAAGTGTGAG GAAAAGTAGT TGGGTTTTTT TTTTTTTTTT TGCAGTTGAA GACA
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)

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Component #6: nucleic-acid, template DNA

nucleic acidName: template DNA / Class: DNA / Structure: OTHER / Synthetic: No
Sequence:
TGTCTTCAAC TGCTTTCGCA TGAAGTACCT CCCAACTACT TTTCCTCACA CTTG
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

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: 56.8 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 22500.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 124112
3D reconstructionSoftware: RELION
CTF correction: CTF amplitude correction was performed following 3D auto refinement in relion.
Resolution: 4.2 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot (resolution estimation)

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Atomic model buiding

Modeling #1Refinement protocol: flexible

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