[English] 日本語
Yorodumi- EMDB-2829: The interaction of an essential DNA helicase with RNA polymerase -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2829 | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | The interaction of an essential DNA helicase with RNA polymerase | |||||||||
Map data | Reconstruction of RNAP-PcrA complex | |||||||||
Sample |
| |||||||||
Keywords | Transcription / RNA polymerase / helicase | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | single particle reconstruction / negative staining / Resolution: 25.0 Å | |||||||||
Authors | Harriott K / Yang X / Mervelet P / Buncherd H / Noirot P / de Jong L / Noirot Gros MF / Lewis PJ | |||||||||
Citation | Journal: To Be Published Title: The interaction of an essential DNA helicase with RNA polymerase Authors: Harriott K / Yang X / Mervelet P / Buncherd H / Noirot P / de Jong L / Noirot Gros MF / Lewis PJ | |||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2829.map.gz | 1.3 MB | EMDB map data format | |
---|---|---|---|---|
Header (meta data) | emd-2829-v30.xml emd-2829.xml | 9 KB 9 KB | Display Display | EMDB header |
Images | EMD-2829.png | 122.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2829 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2829 | HTTPS FTP |
-Validation report
Summary document | emd_2829_validation.pdf.gz | 202.2 KB | Display | EMDB validaton report |
---|---|---|---|---|
Full document | emd_2829_full_validation.pdf.gz | 201.4 KB | Display | |
Data in XML | emd_2829_validation.xml.gz | 5.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2829 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2829 | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
---|
-Map
File | Download / File: emd_2829.map.gz / Format: CCP4 / Size: 1.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Annotation | Reconstruction of RNAP-PcrA complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.9 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
|
-Supplemental data
-Sample components
-Entire : RNAP-PcrA complex
Entire | Name: RNAP-PcrA complex |
---|---|
Components |
|
-Supramolecule #1000: RNAP-PcrA complex
Supramolecule | Name: RNAP-PcrA complex / type: sample / ID: 1000 / Details: complex was made with in vitro purified proteins / Oligomeric state: 1 / Number unique components: 2 |
---|---|
Molecular weight | Experimental: 370 KDa / Theoretical: 370 KDa |
-Macromolecule #1: RNAP
Macromolecule | Name: RNAP / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: 1 / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Bacillus subtilis (bacteria) |
Molecular weight | Experimental: 370 KDa / Theoretical: 370 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: MCC217 / Recombinant plasmid: pSMG69 |
-Macromolecule #2: PcrA
Macromolecule | Name: PcrA / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Oligomeric state: 1 / Recombinant expression: Yes |
---|---|
Source (natural) | Organism: Bacillus subtilis (bacteria) |
Molecular weight | Experimental: 370 KDa / Theoretical: 370 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) / Recombinant strain: MCC217 / Recombinant plasmid: pSMG69 |
-Experimental details
-Structure determination
Method | negative staining |
---|---|
Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
---|---|
Buffer | pH: 7.8 / Details: 20 mM Tris, 150 mM NaCl, 10 mM MgCl2, 0.1 mM DTT |
Staining | Type: NEGATIVE Details: Grids were stained with 1% uranyl formate for 30 seconds |
Vitrification | Cryogen name: NONE / Instrument: OTHER |
-Electron microscopy
Microscope | FEI TECNAI F30 |
---|---|
Date | Dec 3, 2008 |
Image recording | Category: CCD / Film or detector model: GATAN K2 (4k x 4k) / Digitization - Sampling interval: 3.9 µm / Number real images: 240 / Bits/pixel: 16 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN |
Experimental equipment | Model: Tecnai F30 / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: OTHER / Software - Name: EMAN / Number images used: 14266 |
---|---|
Final two d classification | Number classes: 1178 |