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- EMDB-1928: Modular architecture of eukaryotic RNase P and RNase MRP revealed... -

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Basic information

Entry
Database: EMDB / ID: EMD-1928
TitleModular architecture of eukaryotic RNase P and RNase MRP revealed by electron microscopy
Map dataRNase MRP
Sample
  • Sample: RNase MRP
  • Protein or peptide: Ribonuclease MRP
KeywordsRNase P / RNA-processing / ribozyme
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 15.0 Å
AuthorsHipp K / Galani K / Batisse C / Prinz S / Bottcher B
CitationJournal: Nucleic Acids Res / Year: 2012
Title: Modular architecture of eukaryotic RNase P and RNase MRP revealed by electron microscopy.
Authors: Katharina Hipp / Kyriaki Galani / Claire Batisse / Simone Prinz / Bettina Böttcher /
Abstract: Ribonuclease P (RNase P) and RNase MRP are closely related ribonucleoprotein enzymes, which process RNA substrates including tRNA precursors for RNase P and 5.8 S rRNA precursors, as well as some ...Ribonuclease P (RNase P) and RNase MRP are closely related ribonucleoprotein enzymes, which process RNA substrates including tRNA precursors for RNase P and 5.8 S rRNA precursors, as well as some mRNAs, for RNase MRP. The structures of RNase P and RNase MRP have not yet been solved, so it is unclear how the proteins contribute to the structure of the complexes and how substrate specificity is determined. Using electron microscopy and image processing we show that eukaryotic RNase P and RNase MRP have a modular architecture, where proteins stabilize the RNA fold and contribute to cavities, channels and chambers between the modules. Such features are located at strategic positions for substrate recognition by shape and coordination of the cleaved-off sequence. These are also the sites of greatest difference between RNase P and RNase MRP, highlighting the importance of the adaptation of this region to the different substrates.
History
DepositionJul 7, 2011-
Header (metadata) releaseJan 20, 2012-
Map releaseJan 20, 2012-
UpdateAug 29, 2012-
Current statusAug 29, 2012Processing site: PDBe / 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
  • Download
  • 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

1928.png

Downloads & links

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Map

FileDownload / File: emd_1928.map.gz / Format: CCP4 / Size: 6.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRNase MRP
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.2 Å/pix.
x 120 pix.
= 264. Å		2.2 Å/pix.
x 120 pix.
= 264. Å		2.2 Å/pix.
x 120 pix.
= 264. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.2 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.9 / Movie #1: 0.9
Minimum - Maximum-2.80114 - 10.2021
Average (Standard dev.)0.0338696 (±0.389815)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-60-60-60
Dimensions120120120
Spacing120120120
CellA=B=C: 264 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.22.22.2
M x/y/z120120120
origin x/y/z-0.000-0.000-0.000
length x/y/z264.000264.000264.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-60-60-60
NC/NR/NS120120120
D min/max/mean-2.80110.2020.034

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Supplemental data

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Sample components

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Entire : RNase MRP

EntireName: RNase MRP
Components
  • Sample: RNase MRP
  • Protein or peptide: Ribonuclease MRP

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Supramolecule #1000: RNase MRP

SupramoleculeName: RNase MRP / type: sample / ID: 1000 / Number unique components: 1
Molecular weightTheoretical: 410 KDa

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Macromolecule #1: Ribonuclease MRP

MacromoleculeName: Ribonuclease MRP / type: protein_or_peptide / ID: 1 / Name.synonym: RNase MRP / Oligomeric state: monomer / Recombinant expression: No
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast) / synonym: Baker's yeast / Organelle: Nucleus
Molecular weightTheoretical: 410 KDa

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
Details: 50 mM Tris HCl pH 7.5, 100 mM NaCl, 10 mM MgCl2, 1 mM DTT
StainingType: NEGATIVE
Details: sandwich, cryo negative stain with 1% uranyl acetate
GridDetails: 400 mesh copper grid
VitrificationCryogen name: NITROGEN / Chamber temperature: 95 K / Instrument: OTHER
Method: samples were stained and frozen after partly drying, by dipping grids into liquid nitrogen

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG
TemperatureMin: 95 K / Max: 95 K / Average: 95 K
Alignment procedureLegacy - Astigmatism: astigmatism was corrected at 200000 times magnification on carbon film
Image recordingCategory: CCD / Film or detector model: GENERIC TVIPS (2k x 2k) / Number real images: 2006 / Average electron dose: 20 e/Å2 / Bits/pixel: 12
Tilt angle min0
Tilt angle max0
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: 1.1 µm / Nominal defocus min: 0.68 µm / Nominal magnification: 66000
Sample stageSpecimen holder: side entry, liquid nitrogen cooled / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

Detailsparticle were selected automatically, particle orientations were determined by projection matching
CTF correctionDetails: each particle, phase flipping
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: spider, imagic, xmipp
Details: final maps were calculated from 20 defocus groups, number of particles in certain orientations were limited to counterbalance preferred orientations
Number images used: 32232

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