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- EMDB-7038: RNA Pol II elongation complex bound to Rad26 -

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Basic information

Entry
Database: EMDB / ID: 7038
TitleRNA Pol II elongation complex bound to Rad26
Map dataTernary complex of RNA Pol II, transcription scaffold, and Rad26, filtered according to its local resolution
SampleComplex of RNA Pol II, transcription scaffold, and Rad26:
SourceSaccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Methodsingle particle reconstruction / cryo EM / 5.8 Å resolution
AuthorsLahiri I / Leschziner AE
CitationJournal: Nature / Year: 2017
Title: Structural basis for the initiation of eukaryotic transcription-coupled DNA repair.
Authors: Jun Xu / Indrajit Lahiri / Wei Wang / Adam Wier / Michael A Cianfrocco / Jenny Chong / Alissa A Hare / Peter B Dervan / Frank DiMaio / Andres E Leschziner / Dong Wang
DateDeposition: Sep 21, 2017 / Header (metadata) release: Oct 25, 2017 / Map release: Dec 13, 2017 / Last update: Dec 13, 2017

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0219
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 0.0219
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_7038.map.gz (map file in CCP4 format, 226493 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
384 pix
1.2 Å/pix.
= 460.8 Å
384 pix
1.2 Å/pix.
= 460.8 Å
384 pix
1.2 Å/pix.
= 460.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2 Å
Density
Contour Level:0.0219 (by author), 0.0219 (movie #1):
Minimum - Maximum-0.01931491 - 0.08492859
Average (Standard dev.)4.091753E-6 (0.0028428272)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions384384384
Origin000
Limit383383383
Spacing384384384
CellA=B=C: 460.80002 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.21.21.2
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z460.800460.800460.800
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.0190.0850.000

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Supplemental data

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Sample components

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Entire Complex of RNA Pol II, transcription scaffold, and Rad26

EntireName: Complex of RNA Pol II, transcription scaffold, and Rad26
Details: The map is filtered according to its local resolution.
Number of components: 1

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Component #1: protein, Complex of RNA Pol II, transcription scaffold, and Rad26

ProteinName: Complex of RNA Pol II, transcription scaffold, and Rad26
Details: The map is filtered according to its local resolution.
Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast)
Strain: ATCC 204508 / S288c

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temperature: 277.15 K / Humidity: 90 %

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Electron microscopy imaging

Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company
ImagingMicroscope: FEI TALOS ARCTICA
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 7.7 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: GATAN K2 (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 19331
3D reconstructionSoftware: RELION / Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF
FSC plot
(resolution estimation)

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