+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-1435 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | Functional architecture of RNA polymerase I. | |||||||||
Map data | This is the final reconstruction of RNA polymerase I in ccp4 format. | |||||||||
Sample |
| |||||||||
Function / homology | RNA polymerase I complex Function and homology information | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / negative staining / Resolution: 11.9 Å | |||||||||
Authors | Kuhn C-D / Geiger SR / Baumli S / Gartmann M / Gerber J / Jennebach S / Mielke T / Tschochner H / Beckmann R / Cramer P | |||||||||
Citation | Journal: Cell / Year: 2007 Title: Functional architecture of RNA polymerase I. Authors: Claus-D Kuhn / Sebastian R Geiger / Sonja Baumli / Marco Gartmann / Jochen Gerber / Stefan Jennebach / Thorsten Mielke / Herbert Tschochner / Roland Beckmann / Patrick Cramer / Abstract: Synthesis of ribosomal RNA (rRNA) by RNA polymerase (Pol) I is the first step in ribosome biogenesis and a regulatory switch in eukaryotic cell growth. Here we report the 12 A cryo-electron ...Synthesis of ribosomal RNA (rRNA) by RNA polymerase (Pol) I is the first step in ribosome biogenesis and a regulatory switch in eukaryotic cell growth. Here we report the 12 A cryo-electron microscopic structure for the complete 14-subunit yeast Pol I, a homology model for the core enzyme, and the crystal structure of the subcomplex A14/43. In the resulting hybrid structure of Pol I, A14/43, the clamp, and the dock domain contribute to a unique surface interacting with promoter-specific initiation factors. The Pol I-specific subunits A49 and A34.5 form a heterodimer near the enzyme funnel that acts as a built-in elongation factor and is related to the Pol II-associated factor TFIIF. In contrast to Pol II, Pol I has a strong intrinsic 3'-RNA cleavage activity, which requires the C-terminal domain of subunit A12.2 and, apparently, enables ribosomal RNA proofreading and 3'-end trimming. | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_1435.map.gz | 710.6 KB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-1435-v30.xml emd-1435.xml | 9.7 KB 9.7 KB | Display Display | EMDB header |
Images | 1435.gif | 20.6 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-1435 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1435 | HTTPS FTP |
-Validation report
Summary document | emd_1435_validation.pdf.gz | 212.6 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_1435_full_validation.pdf.gz | 211.7 KB | Display | |
Data in XML | emd_1435_validation.xml.gz | 5.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1435 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-1435 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_1435.map.gz / Format: CCP4 / Size: 6.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | This is the final reconstruction of RNA polymerase I in ccp4 format. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.23 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : S. cerevisiae RNA polymerase I
Entire | Name: S. cerevisiae RNA polymerase I |
---|---|
Components |
|
-Supramolecule #1000: S. cerevisiae RNA polymerase I
Supramolecule | Name: S. cerevisiae RNA polymerase I / type: sample / ID: 1000 / Oligomeric state: monomeric / Number unique components: 1 |
---|---|
Molecular weight | Experimental: 600 KDa / Theoretical: 600 KDa |
-Macromolecule #1: RNA polymerase I
Macromolecule | Name: RNA polymerase I / type: protein_or_peptide / ID: 1 / Name.synonym: DNA-dependant RNA polymerase I / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) / Strain: GPY2 / synonym: Budding yeast / Cell: Yeast / Organelle: Nucleus / Location in cell: Nucleus |
Molecular weight | Experimental: 600 KDa / Theoretical: 600 KDa |
Recombinant expression | Organism: Saccharomyces cerevisiae (brewer's yeast) / Recombinant plasmid: pAS22 |
Sequence | GO: RNA polymerase I complex |
-Experimental details
-Structure determination
Method | negative staining, cryo EM |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.1 mg/mL |
---|---|
Buffer | pH: 7.8 Details: 60mM ammonium sulfate, 5mM HEPES pH 7.8, 1mM magnesium chloride, 0.1mM zinc chloride |
Staining | Type: NEGATIVE / Details: Vitrification |
Grid | Details: Carbon holey grids |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Instrument: OTHER / Details: Vitrification instrument: Vitrobot |
-Electron microscopy
Microscope | FEI TECNAI F30 |
---|---|
Temperature | Average: 100 K |
Date | Mar 20, 2006 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Average electron dose: 20 e/Å2 / Details: Heidelberg Drum Scanner / Bits/pixel: 16 |
Tilt angle min | 0 |
Tilt angle max | 0 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal magnification: 39000 |
Sample stage | Specimen holder: Eucentric / Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
Details | Quantifoil |
---|---|
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 11.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 46056 |
-Atomic model buiding 1
Initial model | PDB ID: |
---|---|
Details | Protocol: rigid body. 1WCM (lacking Rpb4/7 and the foot domain) was fitted by manual docking using program O. |
Refinement | Protocol: RIGID BODY FIT |