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- EMDB-1435: Functional architecture of RNA polymerase I. -

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Basic information

Entry
Database: EMDB / ID: 1435
TitleFunctional architecture of RNA polymerase I.
SampleS. cerevisiae RNA polymerase I
SourceSaccharomyces cerevisiae / yeast / Budding yeast / サッカロミセス・セレビシエ /
Map dataThis is the final reconstruction of RNA polymerase I in ccp4 format.
Methodsingle particle reconstruction, at 11.9 A resolution
AuthorsKuhn C-D / Geiger SR / Baumli S / Gartmann M / Gerber J / Jennebach S / Mielke T / Tschochner H / Beckmann R / Cramer P
CitationCell, 2007, 131, 1260-1272

Cell, 2007, 131, 1260-1272 StrPapers
Functional architecture of RNA polymerase I.
Claus-D Kuhn / Sebastian R Geiger / Sonja Baumli / Marco Gartmann / Jochen Gerber / Stefan Jennebach / Thorsten Mielke / Herbert Tschochner / Roland Beckmann / Patrick Cramer

DateDeposition: Sep 27, 2007 / Header (metadata) release: Sep 27, 2007 / Map release: Jan 8, 2008 / Last update: Sep 27, 2007

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.22
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.22
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

Downloads & links

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Map

Fileemd_1435.map.gz (map file in CCP4 format, 6751 KB)
Projections & slices
Size
Brightness
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Others
AxesZ (Sec.)X (Row.)Y (Col.)
120 pix
1.23 A/pix
= 147.6 A
120 pix
1.23 A/pix
= 147.6 A
120 pix
1.23 A/pix
= 147.6 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.23 A
Density
Contour Level:0.512, 0.22 (movie #1):
Minimum - Maximum-1.60931 - 3.05404
Average (Standard dev.)0.0329902 (0.252014)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderYXZ
Dimensions120120120
Origin-60-60-59
Limit595960
Spacing120120120
CellA=B=C: 147.6 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/pix X/Y/Z1.231.231.23
M x/y/z120120120
origin x/y/z0.0000.0000.000
length x/y/z147.600147.600147.600
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-60-60-59
NX/NY/NZ120120120
MAP C/R/S213
start NC/NR/NS-60-60-59
NC/NR/NS120120120
D min/max/mean-1.6093.0540.033

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Supplemental data

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Sample components

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Entire S. cerevisiae RNA polymerase I

EntireName: S. cerevisiae RNA polymerase I / Oligomeric State: monomeric / Number of components: 1
MassTheoretical: 600 kDa / Experimental: 600 kDa

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Component #1: protein, RNA polymerase I

ProteinName: RNA polymerase I / a.k.a: DNA-dependant RNA polymerase I / Oligomeric Details: Monomer / Recombinant expression: Yes / Number of Copies: 1
MassTheoretical: 600 kDa / Experimental: 600 kDa
SourceSpecies: Saccharomyces cerevisiae / yeast / Budding yeast / サッカロミセス・セレビシエ /
Strain: GPY2
Source (engineered)Expression System: Saccharomyces cerevisiae / yeast / サッカロミセス・セレビシエ /
Vector: pAS22
Source (natural)Organelle: Nucleus / Location in cell: Nucleus / Cell: Yeast
External referencesGene Ontology: GO: 0005736

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.1 mg/ml
Buffer solution: 60mM ammonium sulfate, 5mM HEPES pH 7.8, 1mM magnesium chloride, 0.1mM zinc chloride
pH: 7.8
Support filmCarbon holey grids
StainingVitrification
VitrificationInstrument: FEI VITROBOT / Cryogen name: ETHANE / Humidity: 95 % / Details: Vitrification instrument: Vitrobot

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI F30 / Date: Mar 20, 2006
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 20 e/A2 / Illumination mode: OTHER
LensMagnification: 39000 X (nominal) / Imaging mode: BRIGHT FIELD
Specimen HolderHolder: Eucentric / Model: OTHER / Temperature: 100 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionScanner: PRIMESCAN / Bit depth: 16 / Details: Heidelberg Drum Scanner

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 46056 / Details: Quantifoil / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Projection matching / Software: SPIDER / Resolution: 11.9 A / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Refinement protocol: rigid body
Details: Protocol: rigid body. 1WCM (lacking Rpb4/7 and the foot domain) was fitted by manual docking using program O.
Input PDB model: 1WCM

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