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- EMDB-1711: Pyrococcus furiosus RNA Polymerase -

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Basic information

Entry
Database: EMDB / ID: EMD-1711
TitlePyrococcus furiosus RNA Polymerase
Map dataPyrococus furiosus RNA Polymerase, threshold masked map, gaussian filtered to 13 Angstrom
Sample
  • Sample: Endogeneous RNA Polymerase from Pyrococcus furiosus
  • Protein or peptide: DNA directed RNA polymerase
KeywordsArchaea / RNA Polymerase
Biological speciesPyrococcus furiosus (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 13.0 Å
AuthorsKusser AG / Bertero MG / Naji S / Becker T / Thomm M / Beckmann R / Cramer P
CitationJournal: J Mol Biol / Year: 2008
Title: Structure of an archaeal RNA polymerase.
Authors: Anselm G Kusser / Michela G Bertero / Souad Naji / Thomas Becker / Michael Thomm / Roland Beckmann / Patrick Cramer /
Abstract: Related multisubunit RNA polymerases (RNAPs) carry out gene transcription in all kingdoms of life. Since structural information is limited to bacterial and eukaryotic RNAPs, we determined the cryo- ...Related multisubunit RNA polymerases (RNAPs) carry out gene transcription in all kingdoms of life. Since structural information is limited to bacterial and eukaryotic RNAPs, we determined the cryo-electron microscopic structure of the RNAP from the thermophilic archaeon Pyrococcus furiosus at 13 A resolution. Comparison with eukaryotic RNAP II reveals a conserved architecture, no homologues for subunits Rpb8 and Rpb9, and significant deviation in the polymerase foot, jaws, pore, and protrusion. The structural organization of the archaeal RNA polymerase serves as a reference for future structure-function analysis of the transcription mechanism and allows for evolutionary comparisons.
History
SupersessionID: EMD-1436
DepositionMar 31, 2010-
Header (metadata) releaseSep 30, 2011-
Map releaseSep 30, 2011-
UpdateJan 23, 2013-
Current statusJan 23, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.0E-6
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1.0E-6
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

em-1711.png

Downloads & links

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Map

FileDownload / File: emd_1711.map.gz / Format: CCP4 / Size: 21.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPyrococus furiosus RNA Polymerase, threshold masked map, gaussian filtered to 13 Angstrom
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.24 Å/pix.
x 180 pix.
= 222.75 Å		1.24 Å/pix.
x 180 pix.
= 222.75 Å		1.24 Å/pix.
x 180 pix.
= 222.75 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2375 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.000001 / Movie #1: 1.0E-6
Minimum - Maximum-0.000000111779 - 0.0000333932
Average (Standard dev.)0.000000621751 (±0.00000277957)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-90-90-90
Dimensions180180180
Spacing180180180
CellA=B=C: 222.75 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.23751.23751.2375
M x/y/z180180180
origin x/y/z-0.000-0.000-0.000
length x/y/z222.750222.750222.750
α/β/γ90.00090.00090.000
start NX/NY/NZ-61-61-60
NX/NY/NZ122122122
MAP C/R/S123
start NC/NR/NS-90-90-90
NC/NR/NS180180180
D min/max/mean-0.0000.0000.000

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Supplemental data

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Sample components

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Entire : Endogeneous RNA Polymerase from Pyrococcus furiosus

EntireName: Endogeneous RNA Polymerase from Pyrococcus furiosus
Components
  • Sample: Endogeneous RNA Polymerase from Pyrococcus furiosus
  • Protein or peptide: DNA directed RNA polymerase

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Supramolecule #1000: Endogeneous RNA Polymerase from Pyrococcus furiosus

SupramoleculeName: Endogeneous RNA Polymerase from Pyrococcus furiosus / type: sample / ID: 1000 / Details: The sample was monodisperse / Oligomeric state: Monomeric / Number unique components: 11
Molecular weightExperimental: 380 KDa / Theoretical: 380 KDa

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Macromolecule #1: DNA directed RNA polymerase

MacromoleculeName: DNA directed RNA polymerase / type: protein_or_peptide / ID: 1 / Name.synonym: RNA polymerase / Oligomeric state: Monomer / Recombinant expression: No
Source (natural)Organism: Pyrococcus furiosus (archaea) / Cell: Endogeneous
Molecular weightExperimental: 380 KDa / Theoretical: 380 KDa

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.1 mg/mL
BufferpH: 7
Details: 10 mM HEPES (pH 7.0), 150 mM KCl, 2.5 mM MgCl2, 5 mM DTT
GridDetails: Quantifoil R3/3 w. 2nm Carbon on top
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: Blot for 10 seconds

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Electron microscopy

MicroscopeFEI TECNAI F30
TemperatureAverage: 80 K
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 7 µm / Number real images: 23 / Average electron dose: 25 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 67000 / Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 67000
Sample stageSpecimen holder: Multi specimen / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Wiener filtering of defocus group volumes
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 13.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Details: Final back projection in real space / Number images used: 22240

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Atomic model buiding 1

Initial modelPDB ID:

1wcm

DetailsFitted using UCSF Chimera
RefinementSpace: REAL

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