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- EMDB-3628: RNA polymerase II-Paf1C-TFIIS-B -

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Basic information

Entry
Database: EMDB / ID: 3628
TitleRNA polymerase II-Paf1C-TFIIS-B
Map dataNon-B factor sharpened, locally filtered map
SampleRNA polymerase II-Paf1C-TFIIS-B:
Paf1C / RNA polymerase II / TFIIS
SourceSaccharomyces cerevisiae (baker's yeast) / Saccharomyces cerevisiae S288c (yeast)
Methodsingle particle reconstruction / cryo EM / 5.9 Å resolution
AuthorsXu Y / Cramer P
CitationJournal: Nat Commun / Year: 2017
Title: Architecture of the RNA polymerase II-Paf1C-TFIIS transcription elongation complex.
Authors: Youwei Xu / Carrie Bernecky / Chung-Tien Lee / Kerstin C Maier / Björn Schwalb / Dimitry Tegunov / Jürgen M Plitzko / Henning Urlaub / Patrick Cramer
DateDeposition: Mar 9, 2017 / Header (metadata) release: Apr 19, 2017 / Map release: Jun 7, 2017 / Last update: Aug 30, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.015
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_3628.map.gz (map file in CCP4 format, 55297 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
240 pix
1.35 Å/pix.
= 324. Å
240 pix
1.35 Å/pix.
= 324. Å
240 pix
1.35 Å/pix.
= 324. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.35 Å
Density
Contour Level:0.01 (by author), 0.015 (movie #1):
Minimum - Maximum-0.03488018 - 0.09223701
Average (Standard dev.)-0.000075158816 (0.0043981983)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions240240240
Origin0.00.00.0
Limit239.0239.0239.0
Spacing240240240
CellA=B=C: 324.0 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.351.351.35
M x/y/z240240240
origin x/y/z0.0000.0000.000
length x/y/z324.000324.000324.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS240240240
D min/max/mean-0.0350.092-0.000

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Supplemental data

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Mask #1

Fileemd_3628_msk_1.map
Projections & Slices
AxesZYX
Projections
Slices (1/2)
Density Histograms

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Sample components

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Entire RNA polymerase II-Paf1C-TFIIS-B

EntireName: RNA polymerase II-Paf1C-TFIIS-B / Details: Elongation complex / Number of components: 4

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Component #1: protein, RNA polymerase II-Paf1C-TFIIS-B

ProteinName: RNA polymerase II-Paf1C-TFIIS-B / Details: Elongation complex / Recombinant expression: No
MassTheoretical: 900 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Component #2: protein, Paf1C

ProteinName: Paf1C / Details: Ctr9 C-terminal truncation / Recombinant expression: No
MassTheoretical: 340 kDa
SourceSpecies: Saccharomyces cerevisiae S288c (yeast)
Source (engineered)Expression System: Escherichia coli (E. coli) / Strain: BL21 CodonPlus(DE3)RIL

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Component #3: protein, RNA polymerase II

ProteinName: RNA polymerase II / Details: 12 subunits / Recombinant expression: No
MassExperimental: 500 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast) / Strain: BJ5464

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Component #4: protein, TFIIS

ProteinName: TFIIS / Details: TFIIS (D290A, E291A) inactive mutant / Recombinant expression: No
MassExperimental: 35 kDa
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)
Source (engineered)Expression System: Escherichia coli (E. coli) / Strain: BL21 CodonPlus(DE3)RIL

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionSpecimen conc.: 0.3 mg/ml / pH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277 K / Humidity: 100 %
Details: 4 micro-L of sample was placed onto Quantifoil Cu R3.5/1 and Cu R2/1 glow-discharged 200 mesh holey carbon grids, which were then blotted for 8.5 s with blot force 13 to remove the excess solution before they were flash-frozen in liquid ethane..

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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: 0.93 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 37000.0 X (nominal) / Cs: 2.7 mm / Imaging mode: BRIGHT FIELD / Defocus: 600.0 - 4200.0 nm / Energy filter: GIF Quantum
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: GATAN K2 SUMMIT (4k x 4k)

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Image acquisition

Image acquisition #1Number of digital images: 595
Image acquisition #2Number of digital images: 2146

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 54722
3D reconstructionAlgorithm: FOURIER SPACE / Software: RELION / Resolution: 5.9 Å / Resolution method: FSC 0.143 CUT-OFF / Euler angles: RELION 1.4
FSC plot
(resolution estimation)

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