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- EMDB-2923: Electron cryo-microscopy of a transcribing Pol IIp complex -

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Basic information

Entry
Database: EMDB / ID: 2923
TitleElectron cryo-microscopy of a transcribing Pol IIp complex
KeywordsTranscription / pre-mRNA capping
Sampletranscribing Pol IIp complex from yeast
SourceSaccharomyces cerevisiae / yeast / Baker's Yeast, Baker's yeast / サッカロミセス・セレビシエ /
Map dataReconstruction of a transcribing Pol IIp complex
Methodsingle particle reconstruction, at 7.2 Å resolution
AuthorsMartinez-Rucobo FW / Kohler R / van de Waterbeemd M / Heck AJR / Hemann M / Herzog F / Stark H / Cramer P
CitationMol. Cell, 2015, 58, 1079-1089

Mol. Cell, 2015, 58, 1079-1089 StrPapers
Molecular Basis of Transcription-Coupled Pre-mRNA Capping.
Fuensanta W Martinez-Rucobo / Rebecca Kohler / Michiel van de Waterbeemd / Albert J R Heck / Matthias Hemann / Franz Herzog / Holger Stark / Patrick Cramer

DateDeposition: Feb 27, 2015 / Header (metadata) release: Apr 1, 2015 / Map release: Sep 23, 2015 / Last update: Sep 23, 2015

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.04
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.04
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_2923.map.gz (map file in CCP4 format, 12665 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
148 pix
2 Å/pix.
= 296. Å
148 pix
2 Å/pix.
= 296. Å
148 pix
2 Å/pix.
= 296. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2 Å
Density
Contour Level:0.04 (by author), 0.04 (movie #1):
Minimum - Maximum-0.31250411 - 0.41651475
Average (Standard dev.)0.00077728 (0.01971558)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions148148148
Origin000
Limit147147147
Spacing148148148
CellA=B=C: 296 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z222
M x/y/z148148148
origin x/y/z0.0000.0000.000
length x/y/z296.000296.000296.000
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS148148148
D min/max/mean-0.3130.4170.001

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Supplemental data

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Sample components

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Entire transcribing Pol IIp complex from yeast

EntireName: transcribing Pol IIp complex from yeast / Number of components: 2
Oligomeric State: One monomer of Pol IIp contains Pol IIp contains 1 DNA/RNA scaffold of 2 DNA and 1 RNA molecules
MassTheoretical: 540 kDa / Experimental: 540 kDa / Measured by: native mass spectroscopy

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Component #1: protein, DNA-directed RNA polymerase II

ProteinName: DNA-directed RNA polymerase II / a.k.a: RNA polymerase II / Oligomeric Details: Monomer / Number of Copies: 1 / Recombinant expression: No
MassTheoretical: 520 kDa / Experimental: 520 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / Baker's Yeast / サッカロミセス・セレビシエ /

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Component #2: nucleic-acid, DNA-RNA Scaffold

Nucleic-acidName: DNA-RNA Scaffold / a.k.a: template DNA, non-template DNA, mRNA / Class: DNA/RNA / Structure: OTHER / Synthetic: Yes
MassTheoretical: 20 kDa / Experimental: 20 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / Baker's yeast / サッカロミセス・セレビシエ /

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.25 mg/ml / Buffer solution: 5mM HEPES, 100mM KCl, 3mM DTT / pH: 7.25
Support film200 mesh grid with thin carbon support
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS / Date: Jan 7, 2014
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 25 e/Å2 / Illumination mode: SPOT SCAN
LensMagnification: 74000 X (calibrated) / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 4500 nm
Specimen HolderModel: FEI TITAN KRIOS AUTOGRID HOLDER
CameraDetector: FEI FALCON II (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 66214
3D reconstructionSoftware: Relion / CTF correction: each particle / Resolution: 7.2 Å / Resolution method: FSC 0.143, gold-standard

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