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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: EMD-5242
TitleB. subtilis RNase P RNA Specificity domain folding intermediate
Map dataThis is a map of the folding intermediate of B. subtilis RNase P Specificity domain
Sample
  • Sample: B. subtilis RNase P RNA Specificity domain folding intermediate
  • RNA: RNA
KeywordsRNA folding intermediate RNase P Specificity domain
Biological speciesBacillus subtilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 15.2 Å
AuthorsBaird NJ / Ludtke SJ / Khant H / Chiu W / Pan T / Sosnick TR
CitationJournal: 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
DepositionOct 27, 2010-
Header (metadata) releaseDec 22, 2010-
Map releaseDec 22, 2010-
UpdateDec 3, 2014-
Current statusDec 3, 2014Processing site: RCSB / Status: Released

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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
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5242_1.tif

Downloads & links

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Map

FileDownload / File: emd_5242.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a map of the folding intermediate of B. subtilis RNase P Specificity domain
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.81 Å/pix.
x 160 pix.
= 289.6 Å		1.81 Å/pix.
x 160 pix.
= 289.6 Å		1.81 Å/pix.
x 160 pix.
= 289.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0623 / Movie #1: 0.0623
Minimum - Maximum-0.08578543 - 2.46069574
Average (Standard dev.)0.00539513 (±0.07407818)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-80-80-80
Dimensions160160160
Spacing160160160
CellA=B=C: 289.59998 Å
α=β=γ: 90.0 °

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
Components
  • Sample: B. subtilis RNase P RNA Specificity domain folding intermediate
  • RNA: RNA

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Supramolecule #1000: B. subtilis RNase P RNA Specificity domain folding intermediate

SupramoleculeName: 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
Molecular weightTheoretical: 50 KDa / Method: Calculation from nucleotide sequence, 154mer RNA

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Macromolecule #1: RNA

MacromoleculeName: RNA / type: rna / ID: 1 / Name.synonym: RNase P RNA Specificity domain / Classification: OTHER / Structure: OTHER / Synthetic?: No
Source (natural)Organism: Bacillus subtilis (bacteria) / synonym: Bacteria
Molecular weightTheoretical: 50 KDa
SequenceString:
GCGAGCCUAG CGAAGUCAUA AGCUAGGGCA GUCUUUAGAG GCUGACGGCA GGAAAAAAGC CUACGUCUUC GGAUAUGGCU GAGUAUCCUU GAAAGUGCCA CAGUGACGAA GUCUCACUAG AAAUGGUGAG AGUGGAACGC GGUAAACCCC UCGC

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration1 mg/mL
BufferpH: 8 / Details: 1 mM MgCl2, 20 mM TrisHCl pH 8
GridDetails: 400 mesh carbon grid
VitrificationCryogen 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

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Electron microscopy

MicroscopeJEOL 2010F
TemperatureMin: 93 K / Max: 95 K / Average: 94.1 K
Alignment procedureLegacy - Astigmatism: object astigmatism correction made at 400,000 times magnification
DateMar 10, 2006
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 100 / Average electron dose: 16 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination 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 stageSpecimen holder: single tilt cryo-holder / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

DetailsThe particles were selected using an automatic selection program and then inspected manually
Final reconstructionAlgorithm: 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 classificationNumber classes: 60

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