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- EMDB-1753: YEAST RNA POLYMERASE III -

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Basic information

Entry
Database: EMDB / ID: 1753
TitleYEAST RNA POLYMERASE III
KeywordsTranscription / RNA polymerase / tRNA
SampleRNA polymerase III
SourceSaccharomyces cerevisiae / yeast / Baker's Yeast / サッカロミセス・セレビシエ /
Map dataRNA-Polymerase III in its free form
Methodsingle particle reconstruction, at 21 A resolution
AuthorsVannini A / Ringel R / Kusser AG / Berninghausen O / Kassavetis GA / Cramer P
CitationCell, 2010, 143, 59-70

Cell, 2010, 143, 59-70 StrPapers
Molecular basis of RNA polymerase III transcription repression by Maf1.
Alessandro Vannini / Rieke Ringel / Anselm G Kusser / Otto Berninghausen / George A Kassavetis / Patrick Cramer

DateDeposition: Jun 30, 2010 / Header (metadata) release: Jul 23, 2010 / Map release: Oct 8, 2010 / Last update: Jun 30, 2010

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0035
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.0035
  • Imaged by UCSF CHIMERA
  • Download
3D viewer


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Supplemental images

Downloads & links

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Map

Fileemd_1753.map.gz (map file in CCP4 format, 2849 KB)
Projections & slicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
90 pix
3.31 A/pix
= 297.9 A
90 pix
3.31 A/pix
= 297.9 A
90 pix
3.31 A/pix
= 297.9 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 3.31 A
Density
Contour Level:0.0035 (by author), 0.0035 (movie #1):
Minimum - Maximum-0.00569051 - 0.253301
Average (Standard dev.)0.00280515 (0.0138798)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions909090
Origin000
Limit898989
Spacing909090
CellA=B=C: 297.9 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z3.313.313.31
M x/y/z909090
origin x/y/z0.0000.0000.000
length x/y/z297.900297.900297.900
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-100-100-100
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS909090
D min/max/mean-0.0060.2530.003

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Supplemental data

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Sample components

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Entire RNA polymerase III

EntireName: RNA polymerase III / Details: The sample was monodisperse / Number of components: 1 / Oligomeric State: Monomeric
MassTheoretical: 700 kDa / Experimental: 700 kDa / Measured by: Native Mass Spectrometry

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Component #1: protein, RNA polymerase III

ProteinName: RNA polymerase III / a.k.a: RNA polymerase III / Oligomeric Details: Monomeric / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 700 kDa / Experimental: 700 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / Baker's Yeast / サッカロミセス・セレビシエ /
Strain: NZ-16
Source (engineered)Expression System: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Source (natural)Location in cell: Nucleus

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.1 mg/ml
Buffer solution: 20mM Hepes pH 7.8, 50 mM Ammonium Sulfate, 0.1 mM MgCl2, 0.01 mM ZnCl2, 5mM DTT
pH: 7.8
Support filmQuantifoil R3/3 2nm carbon pre-coated holey grids
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Temperature: 184 K / Humidity: 95 % / Details: Vitrification instrument: Vitrobot, FEI

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: LAB6 / Accelerating voltage: 120 kV / Illumination mode: OTHER
LensImaging mode: OTHER
Specimen HolderHolder: Eucentric / Model: GATAN LIQUID NITROGEN

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 20480 / Applied symmetry: C1 (asymmetric)
3D reconstructionResolution: 21 A / Resolution method: FSC 0.5

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