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- EMDB-5243: B. subtilis RNase P RNA Specificity domain P9extension folding in... -

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Basic information

Entry
Database: EMDB / ID: EMD-5243
TitleB. subtilis RNase P RNA Specificity domain P9extension folding intermediate
Map dataThis is a reconstruction of the folding intermediate of a mutant RNase P RNA Specificity domain.
Sample
  • Sample: B. subtilis RNase P RNA Specificity domain P9extension folding intermediate
  • RNA: RNA
KeywordsRNA folding intermediate / RNase P Specificity domain
Biological speciesBacillus subtilis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 15.0 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: 0.9
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 0.9
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_5243.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a reconstruction of the folding intermediate of a mutant RNase P RNA Specificity domain.
Voxel sizeX=Y=Z: 1.81 Å
Density
Contour LevelBy AUTHOR: 0.9 / Movie #1: 0.9
Minimum - Maximum-0.09130166 - 23.091293329999999
Average (Standard dev.)0.0429409 (±0.5422262)
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-0.09123.0910.043

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Supplemental data

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Sample components

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Entire : B. subtilis RNase P RNA Specificity domain P9extension folding in...

EntireName: B. subtilis RNase P RNA Specificity domain P9extension folding intermediate
Components
  • Sample: B. subtilis RNase P RNA Specificity domain P9extension folding intermediate
  • RNA: RNA

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Supramolecule #1000: B. subtilis RNase P RNA Specificity domain P9extension folding in...

SupramoleculeName: B. subtilis RNase P RNA Specificity domain P9extension folding intermediate
type: sample / ID: 1000 / Details: none / Oligomeric state: monomer / Number unique components: 1
Molecular weightTheoretical: 61 KDa / Method: Calculation from nucleotide sequence, 186mer RNA

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Macromolecule #1: RNA

MacromoleculeName: RNA / type: rna / ID: 1 / Name.synonym: RNase P RNA Specificity domain P9extension / Classification: OTHER / Structure: OTHER / Synthetic?: No
Source (natural)Organism: Bacillus subtilis (bacteria) / synonym: Bacteria
Molecular weightTheoretical: 61 KDa
SequenceString:
GCGAGCCTAG CGAAGTCATA AGCTAGGGCA GTCTCTAGTC TAGCGTCAGC TTCGGCTGAC GCTAGGCTAG AGGCTGACGG CAGGAAAAAA GCCTACGTCT TCGGATATGG CTGAGTATCC TTGAAAGTGC CACAGTGACG AAGTCTCACT AGAAATGGTG AGAGTGGAAC GCGGTAAACC CCTCGC

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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: 200 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 for 1 seconds before plunging

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Electron microscopy

MicroscopeJEOL 2010F
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / 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
TemperatureMin: 96 K / Max: 98 K / Average: 97 K
Alignment procedureLegacy - Astigmatism: object astigmatism correction made at 400,000 times magnification
DateApr 18, 2007
Image recordingCategory: CCD / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k) / Number real images: 110 / Average electron dose: 18 e/Å2

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Image processing

Final two d classificationNumber classes: 60
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN
Details: FSC gives a resolution of approximately 15 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: 19800
DetailsThe particles were selected using an automatic selection program and then inspected manually

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