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- EMDB-1092: Cryo-EM visualization of a viral internal ribosome entry site bou... -

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Basic information

Entry
Database: EMDB / ID: EMD-1092
TitleCryo-EM visualization of a viral internal ribosome entry site bound to human ribosomes: the IRES functions as an RNA-based translation factor.
Map datamap
Sample
  • Sample: Human ribosome 40s subunit
  • Complex: Human ribosome 40s subunit
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 25.3 Å
AuthorsSpahn CM / Frank J
CitationJournal: Cell / Year: 2004
Title: Cryo-EM visualization of a viral internal ribosome entry site bound to human ribosomes: the IRES functions as an RNA-based translation factor.
Authors: Christian M T Spahn / Eric Jan / Anke Mulder / Robert A Grassucci / Peter Sarnow / Joachim Frank /
Abstract: Internal initiation of protein synthesis in eukaryotes is accomplished by recruitment of ribosomes to structured internal ribosome entry sites (IRESs), which are located in certain viral and cellular ...Internal initiation of protein synthesis in eukaryotes is accomplished by recruitment of ribosomes to structured internal ribosome entry sites (IRESs), which are located in certain viral and cellular messenger RNAs. An IRES element in cricket paralysis virus (CrPV) can directly assemble 80S ribosomes in the absence of canonical initiation factors and initiator tRNA. Here we present cryo-EM structures of the CrPV IRES bound to the human ribosomal 40S subunit and to the 80S ribosome. The CrPV IRES adopts a defined, elongate structure within the ribosomal intersubunit space and forms specific contacts with components of the ribosomal A, P, and E sites. Conformational changes in the ribosome as well as within the IRES itself show that CrPV IRES actively manipulates the ribosome. CrPV-like IRES elements seem to act as RNA-based translation factors.
History
DepositionAug 10, 2004-
Header (metadata) releaseAug 10, 2004-
Map releaseNov 10, 2004-
UpdateOct 17, 2012-
Current statusOct 17, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0005
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0005
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1092.gif

Downloads & links

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Map

FileDownload / File: emd_1092.map.gz / Format: CCP4 / Size: 7.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmap
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.66 Å/pix.
x 125 pix.
= 457.5 Å		3.66 Å/pix.
x 125 pix.
= 457.5 Å		3.66 Å/pix.
x 125 pix.
= 457.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.66 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.0000843 / Movie #1: 0.0005
Minimum - Maximum-0.00128077 - 0.00278893
Average (Standard dev.)0.0000147812 (±0.000198816)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-62-62-62
Dimensions125125125
Spacing125125125
CellA=B=C: 457.5 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.663.663.66
M x/y/z125125125
origin x/y/z0.0000.0000.000
length x/y/z457.500457.500457.500
α/β/γ90.00090.00090.000
start NX/NY/NZ-96-56-288
NX/NY/NZ192112576
MAP C/R/S123
start NC/NR/NS-62-62-62
NC/NR/NS125125125
D min/max/mean-0.0010.0030.000

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Supplemental data

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Sample components

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Entire : Human ribosome 40s subunit

EntireName: Human ribosome 40s subunit
Components
  • Sample: Human ribosome 40s subunit
  • Complex: Human ribosome 40s subunit

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Supramolecule #1000: Human ribosome 40s subunit

SupramoleculeName: Human ribosome 40s subunit / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Human ribosome 40s subunit

SupramoleculeName: Human ribosome 40s subunit / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL
Source (natural)Organism: Homo sapiens (human) / synonym: Human

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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

VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TECNAI F30
TemperatureMax: 84 K
Alignment procedureLegacy - Astigmatism: objective lens astigmatism was corrected at 100,000 times magnification
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Average electron dose: 20 e/Å2
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 38000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal magnification: 39000
Sample stageSpecimen holder: FEI Polara cartridge system / Specimen holder model: OTHER
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: defocus group volumes
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.3 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER

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