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- EMDB-5242: B. subtilis RNase P RNA Specificity domain folding intermediate -

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Basic information

Entry
Database: EMDB / ID: 5242
TitleB. subtilis RNase P RNA Specificity domain folding intermediate
KeywordsRNA folding intermediate RNase P Specificity domain
SampleB. subtilis RNase P RNA Specificity domain folding intermediate
SourceBacillus subtilis / bacteria / バチルス・サブティリス, 枯草菌 /
Map dataThis is a map of the folding intermediate of B. subtilis RNase P Specificity domain
Methodsingle particle reconstruction, at 15.2 Å resolution
AuthorsBaird NJ / Ludtke SJ / Khant H / Chiu W / Pan T / Sosnick TR
CitationJ. Am. Chem. Soc., 2010, 132, 16352-16353

J. Am. Chem. Soc., 2010, 132, 16352-16353 Yorodumi Papers
Discrete structure of an RNA folding intermediate revealed by cryo-electron microscopy.
Nathan J Baird / Steven J Ludtke / Htet Khant / Wah Chiu / Tao Pan / Tobin R Sosnick

DateDeposition: Oct 27, 2010 / Header (metadata) release: Dec 22, 2010 / Map release: Dec 22, 2010 / Last update: Dec 3, 2014

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0623
  • Imaged by UCSF CHIMERA
  • Download
  • Surface view colored by radius
  • Surface level: 0.0623
  • Imaged by UCSF CHIMERA
  • Download
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Supplemental images

emd_5242_1.tif

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Map

Fileemd_5242.map.gz (map file in CCP4 format, 16001 KB)
Projections & slices

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AxesZ (Sec.)Y (Row.)X (Col.)
160 pix
1.81 Å/pix.
= 289.6 Å		160 pix
1.81 Å/pix.
= 289.6 Å		160 pix
1.81 Å/pix.
= 289.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 1.81 Å
Density

Histogram

Histogram (log scale)
Contour Level:0.0623 (by author), 0.0623 (movie #1):
Minimum - Maximum-0.08578543 - 2.46069574
Average (Standard dev.)0.00539513 (0.07407818)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions160160160
Origin-80-80-80
Limit797979
Spacing160160160
CellA=B=C: 289.59998 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.811.811.81
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z289.600289.600289.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-62-62-62
NX/NY/NZ125125125
MAP C/R/S123
start NC/NR/NS-80-80-80
NC/NR/NS160160160
D min/max/mean-0.0862.4610.005

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Supplemental data

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Sample components

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Entire B. subtilis RNase P RNA Specificity domain folding intermediate

EntireName: B. subtilis RNase P RNA Specificity domain folding intermediate
Details: none / Number of components: 1 / Oligomeric State: Monomer of Specificity domain
MassTheoretical: 50 kDa
Measured by: Calculation from nucleotide sequence, 154mer RNA

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Component #1: nucleic-acid, RNA

Nucleic-acidName: RNA / a.k.a: RNase P RNA Specificity domain / Class: RNA / Structure: OTHER
Sequence:
GCGAGCCUAG CGAAGUCAUA AGCUAGGGCA GUCUUUAGAG GCUGACGGCA GGAAAAAAGC CUACGUCUUC GGAUAUGGCU GAGUAUCCUU GAAAGUGCCA CAGUGACGAA GUCUCACUAG AAAUGGUGAG AGUGGAACGC GGUAAACCCC UCGC

Synthetic: No
MassTheoretical: 50 kDa
SourceSpecies: Bacillus subtilis / bacteria / バチルス・サブティリス, 枯草菌 /

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 1 mg/ml / Buffer solution: 1 mM MgCl2, 20 mM TrisHCl pH 8 / pH: 8
Support film400 mesh carbon grid
VitrificationInstrument: 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

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Electron microscopy imaging

ImagingMicroscope: JEOL 2010F / Date: Mar 10, 2006
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 16 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 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 HolderHolder: single tilt cryo-holder / Model: GATAN LIQUID NITROGEN / Temperature: 94.1 K ( 93 - 95 K)
CameraDetector: GATAN ULTRASCAN 4000 (4k x 4k)

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Image acquisition

Image acquisitionNumber of digital images: 100

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Image processing

ProcessingMethod: 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 reconstructionAlgorithm: 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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