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- EMDB-3594: RNA polymerase I initially transcribing complex with visible tand... -

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Basic information

Entry
Database: EMDB / ID: 3594
TitleRNA polymerase I initially transcribing complex with visible tandem Winged Helix domain
SampleRNA polymerase I initially transcribing complex
SourceSaccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Map data
Methodsingle particle reconstruction, at 3.4 A resolution
AuthorsEngel C / Gubbey T / Neyer S / Sainsbury S / Oberthuer C / Baejen C / Bernecky C / Cramer P
CitationCell, 2017, 169, 120-131.e22

Cell, 2017, 169, 120-131.e22 StrPapers
Structural Basis of RNA Polymerase I Transcription Initiation.
Christoph Engel / Tobias Gubbey / Simon Neyer / Sarah Sainsbury / Christiane Oberthuer / Carlo Baejen / Carrie Bernecky / Patrick Cramer

DateDeposition: Feb 14, 2017 / Header (metadata) release: Mar 22, 2017 / Map release: Apr 12, 2017 / Last update: Feb 14, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.05
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view with fitted model
  • Atomic models: : PDB-5n61
  • Surface level: 0.05
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_3594.map.gz (map file in CCP4 format, 143749 KB)
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
330 pix
1.13 A/pix
= 372.9 A
330 pix
1.13 A/pix
= 372.9 A
330 pix
1.13 A/pix
= 372.9 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.13 A
Density
Contour Level:0.05 (by author), 0.05 (movie #1):
Minimum - Maximum-0.050090574 - 0.13193528
Average (Standard dev.)0.0006353547 (0.008975409)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions330330330
Origin000
Limit329329329
Spacing330330330
CellA=B=C: 372.9 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.131.131.13
M x/y/z330330330
origin x/y/z0.0000.0000.000
length x/y/z372.900372.900372.900
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS330330330
D min/max/mean-0.0500.1320.001

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Supplemental data

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Sample components

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Entire RNA polymerase I initially transcribing complex

EntireName: RNA polymerase I initially transcribing complex / Number of components: 5

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Component #1: protein, RNA polymerase I initially transcribing complex

ProteinName: RNA polymerase I initially transcribing complex / Recombinant expression: No

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Component #2: protein, RNA polymerase I

ProteinName: RNA polymerase I / Recombinant expression: No
MassTheoretical: 590 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /

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Component #3: protein, Initiation factor Rrn3

ProteinName: Initiation factor Rrn3 / Recombinant expression: No
MassTheoretical: 70 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #4: protein, Core Factor

ProteinName: Core Factor / Recombinant expression: No
MassTheoretical: 220 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Source (engineered)Expression System: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #5: protein, Initial transcription DNA/RNA scaffold

ProteinName: Initial transcription DNA/RNA scaffold / Recombinant expression: No
MassTheoretical: 60 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Source (engineered)Expression System: Synthetic construct

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionpH: 7.8
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 60 e/A2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 345000
3D reconstructionResolution: 3.4 A / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Output model

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