+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-5242 | |||||||||
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Title | B. subtilis RNase P RNA Specificity domain folding intermediate | |||||||||
Map data | This is a map of the folding intermediate of B. subtilis RNase P Specificity domain | |||||||||
Sample |
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Keywords | RNA folding intermediate RNase P Specificity domain | |||||||||
Biological species | Bacillus subtilis (bacteria) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 15.2 Å | |||||||||
Authors | Baird NJ / Ludtke SJ / Khant H / Chiu W / Pan T / Sosnick TR | |||||||||
Citation | Journal: J Am Chem Soc / Year: 2010 Title: Discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy. Authors: Nathan J Baird / Steven J Ludtke / Htet Khant / Wah Chiu / Tao Pan / Tobin R Sosnick / Abstract: RNA folding occurs via a series of transitions between metastable intermediate states. It is unknown whether folding intermediates are discrete structures folding along defined pathways or ...RNA folding occurs via a series of transitions between metastable intermediate states. It is unknown whether folding intermediates are discrete structures folding along defined pathways or heterogeneous ensembles folding along broad landscapes. We use cryo-electron microscopy and single-particle image reconstruction to determine the structure of the major folding intermediate of the specificity domain of a ribonuclease P ribozyme. Our results support the existence of a discrete conformation for this folding intermediate. | |||||||||
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_5242.map.gz | 14.1 MB | EMDB map data format | |
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Header (meta data) | emd-5242-v30.xml emd-5242.xml | 10.1 KB 10.1 KB | Display Display | EMDB header |
Images | emd_5242_1.tif | 34.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-5242 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-5242 | HTTPS FTP |
-Validation report
Summary document | emd_5242_validation.pdf.gz | 77.9 KB | Display | EMDB validaton report |
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Full document | emd_5242_full_validation.pdf.gz | 77 KB | Display | |
Data in XML | emd_5242_validation.xml.gz | 492 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5242 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-5242 | HTTPS FTP |
-Related structure data
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_5242.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is a map of the folding intermediate of B. subtilis RNase P Specificity domain | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.81 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 : B. subtilis RNase P RNA Specificity domain folding intermediate
Entire | Name: B. subtilis RNase P RNA Specificity domain folding intermediate |
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Components |
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-Supramolecule #1000: B. subtilis RNase P RNA Specificity domain folding intermediate
Supramolecule | Name: B. subtilis RNase P RNA Specificity domain folding intermediate type: sample / ID: 1000 / Details: none / Oligomeric state: Monomer of Specificity domain / Number unique components: 1 |
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Molecular weight | Theoretical: 50 KDa / Method: Calculation from nucleotide sequence, 154mer RNA |
-Macromolecule #1: RNA
Macromolecule | Name: RNA / type: rna / ID: 1 / Name.synonym: RNase P RNA Specificity domain / Classification: OTHER / Structure: OTHER / Synthetic?: No |
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Source (natural) | Organism: Bacillus subtilis (bacteria) / synonym: Bacteria |
Molecular weight | Theoretical: 50 KDa |
Sequence | String: GCGAGCCUAG CGAAGUCAUA AGCUAGGGCA GUCUUUAGAG GCUGACGGCA GGAAAAAAGC CUACGUCUUC GGAUAUGGCU GAGUAUCCUU GAAAGUGCCA CAGUGACGAA GUCUCACUAG AAAUGGUGAG AGUGGAACGC GGUAAACCCC UCGC |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1 mg/mL |
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Buffer | pH: 8 / Details: 1 mM MgCl2, 20 mM TrisHCl pH 8 |
Grid | Details: 400 mesh carbon grid |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 77 K / Instrument: FEI VITROBOT MARK III / Details: Vitrification instrument: FEI Vitrobot mark III / Method: 2 blots 1 second each before plunging |
-Electron microscopy
Microscope | JEOL 2010F |
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Temperature | Min: 93 K / Max: 95 K / Average: 94.1 K |
Alignment procedure | Legacy - Astigmatism: object astigmatism correction made at 400,000 times magnification |
Date | Mar 10, 2006 |
Image recording | Category: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 100 / Average electron dose: 16 e/Å2 |
Electron beam | Acceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.0 µm / Nominal magnification: 60000 |
Sample stage | Specimen holder: single tilt cryo-holder / Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
Details | The particles were selected using an automatic selection program and then inspected manually |
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Final reconstruction | Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.2 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN Details: FSC gives a resolution of 15.2 A, but the model was low-pass filtered to 26 A, corresponding to the first zero-crossing of the data. CTF correction was not performed. Number images used: 11600 |
Final two d classification | Number classes: 60 |