+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1711 | ||||||||||||
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Title | Pyrococcus furiosus RNA Polymerase | ||||||||||||
Map data | Pyrococus furiosus RNA Polymerase, threshold masked map, gaussian filtered to 13 Angstrom | ||||||||||||
Sample |
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Keywords | Archaea / RNA Polymerase | ||||||||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 13.0 Å | ||||||||||||
Authors | Kusser AG / Bertero MG / Naji S / Becker T / Thomm M / Beckmann R / Cramer P | ||||||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1711.map.gz | 21.2 MB | EMDB map data format | |
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Header (meta data) | emd-1711-v30.xml emd-1711.xml | 9.5 KB 9.5 KB | Display Display | EMDB header |
Images | em-1711.png | 86.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1711 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1711 | HTTPS FTP |
-Validation report
Summary document | emd_1711_validation.pdf.gz | 196.8 KB | Display | EMDB validaton report |
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Full document | emd_1711_full_validation.pdf.gz | 196 KB | Display | |
Data in XML | emd_1711_validation.xml.gz | 5.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1711 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1711 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_1711.map.gz / Format: CCP4 / Size: 21.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Pyrococus furiosus RNA Polymerase, threshold masked map, gaussian filtered to 13 Angstrom | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.2375 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Endogeneous RNA Polymerase from Pyrococcus furiosus
Entire | Name: Endogeneous RNA Polymerase from Pyrococcus furiosus |
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Components |
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-Supramolecule #1000: Endogeneous RNA Polymerase from Pyrococcus furiosus
Supramolecule | Name: Endogeneous RNA Polymerase from Pyrococcus furiosus / type: sample / ID: 1000 / Details: The sample was monodisperse / Oligomeric state: Monomeric / Number unique components: 11 |
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Molecular weight | Experimental: 380 KDa / Theoretical: 380 KDa |
-Macromolecule #1: DNA directed RNA polymerase
Macromolecule | Name: DNA directed RNA polymerase / type: protein_or_peptide / ID: 1 / Name.synonym: RNA polymerase / Oligomeric state: Monomer / Recombinant expression: No |
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Source (natural) | Organism: Pyrococcus furiosus (archaea) / Cell: Endogeneous |
Molecular weight | Experimental: 380 KDa / Theoretical: 380 KDa |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
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Buffer | pH: 7 Details: 10 mM HEPES (pH 7.0), 150 mM KCl, 2.5 mM MgCl2, 5 mM DTT |
Grid | Details: Quantifoil R3/3 w. 2nm Carbon on top |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: Blot for 10 seconds |
-Electron microscopy
Microscope | FEI TECNAI F30 |
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Temperature | Average: 80 K |
Image recording | Category: 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 beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated 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 stage | Specimen holder: Multi specimen / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
CTF correction | Details: Wiener filtering of defocus group volumes |
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Final reconstruction | Applied 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 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Details | Fitted using UCSF Chimera |
Refinement | Space: REAL |