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Yorodumi- EMDB-1883: Three-dimensional structure of the RNA polymerase II-Iwr1 complex -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1883 | |||||||||
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Title | Three-dimensional structure of the RNA polymerase II-Iwr1 complex | |||||||||
Map data | This is a map of the RNA Polymerase II-Iwr1 complex. | |||||||||
Sample |
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Keywords | transcription / Pol II / nuclear import | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 20.9 Å | |||||||||
Authors | Czeko E / Seizl M / Augsberger C / Mielke T / Cramer P | |||||||||
Citation | Journal: Mol Cell / Year: 2011 Title: Iwr1 directs RNA polymerase II nuclear import. Authors: Elmar Czeko / Martin Seizl / Christian Augsberger / Thorsten Mielke / Patrick Cramer / Abstract: RNA polymerase (Pol) II transcribes protein-coding genes in the nucleus of eukaryotic cells and consists of 12 polypeptide subunits. It is unknown how Pol II is imported into the nucleus. Here we ...RNA polymerase (Pol) II transcribes protein-coding genes in the nucleus of eukaryotic cells and consists of 12 polypeptide subunits. It is unknown how Pol II is imported into the nucleus. Here we show that Pol II nuclear import requires the protein Iwr1 and provide evidence for cyclic Iwr1 function. Iwr1 binds Pol II in the active center cleft between the two largest subunits, maybe facilitating or sensing complete Pol II assembly in the cytoplasm. Iwr1 then uses an N-terminal bipartite nuclear localization signal that is recognized by karyopherin α to direct Pol II nuclear import. In the nucleus, Iwr1 is displaced from Pol II by transcription initiation factors and nucleic acids, enabling its export and recycling. Iwr1 function is Pol II specific, transcription independent, and apparently conserved from yeast to human. | |||||||||
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_1883.map.gz | 1.2 MB | EMDB map data format | |
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Header (meta data) | emd-1883-v30.xml emd-1883.xml | 10 KB 10 KB | Display Display | EMDB header |
Images | EMD-1883.jpg | 65.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1883 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1883 | HTTPS FTP |
-Validation report
Summary document | emd_1883_validation.pdf.gz | 219.7 KB | Display | EMDB validaton report |
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Full document | emd_1883_full_validation.pdf.gz | 218.8 KB | Display | |
Data in XML | emd_1883_validation.xml.gz | 4.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1883 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1883 | 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_1883.map.gz / Format: CCP4 / Size: 1.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a map of the RNA Polymerase II-Iwr1 complex. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.71 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 : RNA polymerase II-Iwr1
Entire | Name: RNA polymerase II-Iwr1 |
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Components |
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-Supramolecule #1000: RNA polymerase II-Iwr1
Supramolecule | Name: RNA polymerase II-Iwr1 / type: sample / ID: 1000 / Oligomeric state: Monomeric / Number unique components: 2 |
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Molecular weight | Theoretical: 550 KDa |
-Macromolecule #1: DNA-directed RNA polymerase
Macromolecule | Name: DNA-directed RNA polymerase / type: protein_or_peptide / ID: 1 / Name.synonym: Pol II / Number of copies: 1 / Recombinant expression: No |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast / Organelle: Nucleus |
Molecular weight | Theoretical: 510 KDa |
-Macromolecule #2: Import adaptor
Macromolecule | Name: Import adaptor / type: protein_or_peptide / ID: 2 / Name.synonym: Iwr1 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's Yeast |
Molecular weight | Theoretical: 40 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant plasmid: pET21b |
-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: 7.25 Details: 5 mM HEPES, 40 mM Ammonium sulfate, 10 microM Zinc chloride, 10 mM DTT |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 80 K / Instrument: OTHER / Details: Vitrification instrument: FEI Vitrobot / Method: Blot for 10 s before plunging |
-Electron microscopy
Microscope | FEI POLARA 300 |
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Temperature | Average: 80 K |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Number real images: 35 / Average electron dose: 25 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | 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: Multispecimen holder / Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Details | Particles were selected using Signature and thereafter checked manually |
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CTF correction | Details: Defocus groups |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 20.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 25206 |
Final angle assignment | Details: SPIDER |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: Chimera |
Details | Protocol: Rigid body |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Least-square |