|Entry||Database: EMDB / ID: 5242|
|Title||B. subtilis RNase P RNA Specificity domain folding intermediate|
|Keywords||RNA folding intermediate RNase P Specificity domain|
|Sample||B. subtilis RNase P RNA Specificity domain folding intermediate|
|Source||Bacillus subtilis / bacteria / バチルス・サブティリス, 枯草菌 /|
|Map data||This is a map of the folding intermediate of B. subtilis RNase P Specificity domain|
|Method||single particle reconstruction, at 15.2 Å resolution|
|Authors||Baird NJ / Ludtke SJ / Khant H / Chiu W / Pan T / Sosnick TR|
|Citation||J. Am. Chem. Soc., 2010, 132, 16352-16353|
|Date||Deposition: Oct 27, 2010 / Header (metadata) release: Dec 22, 2010 / Map release: Dec 22, 2010 / Last update: Dec 3, 2014|
Downloads & links
|File||emd_5242.map.gz (map file in CCP4 format, 16001 KB)|
|Projections & slices|
Images are generated by Spider package.
|Voxel size||X=Y=Z: 1.81 Å|
CCP4 map header:
-Entire B. subtilis RNase P RNA Specificity domain folding intermediate
|Entire||Name: B. subtilis RNase P RNA Specificity domain folding intermediate|
Details: none / Number of components: 1 / Oligomeric State: Monomer of Specificity domain
|Mass||Theoretical: 50 kDa|
Measured by: Calculation from nucleotide sequence, 154mer RNA
-Component #1: nucleic-acid, RNA
|Nucleic-acid||Name: RNA / a.k.a: RNase P RNA Specificity domain / Class: RNA / Structure: OTHER|
GCGAGCCUAG CGAAGUCAUA AGCUAGGGCA GUCUUUAGAG GCUGACGGCA GGAAAAAAGC CUACGUCUUC GGAUAUGGCU GAGUAUCCUU GAAAGUGCCA CAGUGACGAA GUCUCACUAG AAAUGGUGAG AGUGGAACGC GGUAAACCCC UCGC
|Mass||Theoretical: 50 kDa|
|Source||Species: Bacillus subtilis / bacteria / バチルス・サブティリス, 枯草菌 /|
|Sample solution||Specimen conc.: 1 mg/ml / Buffer solution: 1 mM MgCl2, 20 mM TrisHCl pH 8 / pH: 8|
|Support film||400 mesh carbon grid|
|Vitrification||Instrument: FEI VITROBOT MARK III / Cryogen name: ETHANE / Temperature: 77 K / Humidity: 100 % / Method: 2 blots 1 second each before plunging / Details: Vitrification instrument: FEI Vitrobot mark III|
-Electron microscopy imaging
|Imaging||Microscope: JEOL 2010F / Date: Mar 10, 2006|
|Electron gun||Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 16 e/Å2 / Illumination mode: FLOOD BEAM|
|Lens||Magnification: 60000 X (nominal)|
Astigmatism: object astigmatism correction made at 400,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 1000 - 3500 nm
|Specimen Holder||Holder: single tilt cryo-holder / Model: GATAN LIQUID NITROGEN / Temperature: 94.1 K ( 93 - 95 K)|
|Camera||Detector: GATAN ULTRASCAN 4000 (4k x 4k)|
|Image acquisition||Number of digital images: 100|
|Processing||Method: single particle reconstruction / Number of class averages: 60 / Number of projections: 11600|
Details: The particles were selected using an automatic selection program and then inspected manually
Applied symmetry: C1 (asymmetric)
|3D reconstruction||Algorithm: Cross-common lines / Software: 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.
Resolution: 15.2 Å / Resolution method: FSC 0.5
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Three pioneers of this field were awarded Nobel Prize in Chemistry 2017
- Jacques Dubochet (University of Lausanne, Switzerland) is a pioneer of ice-embedding method of EM specimen (as known as cryo-EM), Most of 3DEM structures in EMDB and PDB are obtained using his method.
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- Richard Henderson (MRC Laboratory of Molecular Biology, Cambridge, UK) was determined the first biomolecule structure by EM. The first EM entry in PDB, PDB-1brd is determinedby him.
External links: The 2017 Nobel Prize in Chemistry - Press Release
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