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- EMDB-1125: Localization and dynamic behavior of ribosomal protein L30e. -

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Basic information

Entry
Database: EMDB / ID: EMD-1125
TitleLocalization and dynamic behavior of ribosomal protein L30e.
Map data80s wheat germ ribosome
Sample
  • Sample: 80s wheat germ ribosome
  • Complex: 80s
Function / homology
Function and homology information


plastid / cytosolic small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / nucleolus / RNA binding ...plastid / cytosolic small ribosomal subunit / small ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / ribosome / structural constituent of ribosome / translation / ribonucleoprotein complex / nucleolus / RNA binding / zinc ion binding / metal ion binding
Similarity search - Function
Ribosomal protein L30e signature 1. / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein L30/YlxQ / Ribosomal protein L37ae / Ribosomal L37ae protein family / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal S13/S15 N-terminal domain ...Ribosomal protein L30e signature 1. / Ribosomal protein L30e signature 2. / Ribosomal protein L30e, conserved site / Ribosomal protein L30/YlxQ / Ribosomal protein L37ae / Ribosomal L37ae protein family / Ribosomal protein S13/S15, N-terminal / Ribosomal protein S15P / Ribosomal S13/S15 N-terminal domain / Ribosomal S13/S15 N-terminal domain / Ribosomal protein L37ae/L37e / Ribosomal protein L7Ae/L30e/S12e/Gadd45 / Ribosomal protein L7Ae/L30e/S12e/Gadd45 family / 50S ribosomal protein L30e-like / Ribosomal protein S15 signature. / Ribosomal protein S15 / Ribosomal_S15 / Ribosomal protein S15 / S15/NS1, RNA-binding / Zinc-binding ribosomal protein
Similarity search - Domain/homology
Large ribosomal subunit protein eL43z / Large ribosomal subunit protein eL30 / 60S ribosomal protein L37a-1 / Small ribosomal subunit protein uS15z
Similarity search - Component
Biological speciesTriticum sp. (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.5 Å
AuthorsHalic M
CitationJournal: Nat Struct Mol Biol / Year: 2005
Title: Localization and dynamic behavior of ribosomal protein L30e.
Authors: Mario Halic / Thomas Becker / Joachim Frank / Christian M T Spahn / Roland Beckmann /
Abstract: The ribosomal protein L30e is an indispensable component of the eukaryotic 80S ribosome, where it is part of the large (60S) ribosomal subunit. Here, we determined the localization of L30e in the ...The ribosomal protein L30e is an indispensable component of the eukaryotic 80S ribosome, where it is part of the large (60S) ribosomal subunit. Here, we determined the localization of L30e in the cryo-EM map of the 80S wheat germ (wg) ribosome at a resolution of 9.5 A. L30e is part of the interface between large and small subunits, where it dynamically participates in the formation of the two intersubunit bridges eB9 and B4.
History
DepositionFeb 7, 2005-
Header (metadata) releaseMay 2, 2005-
Map releaseMay 2, 2007-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0003
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0003
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-1ysh
  • Surface level: 0.0003
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1ysh
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1125.gif

Downloads & links

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Map

FileDownload / File: emd_1125.map.gz / Format: CCP4 / Size: 40.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation80s wheat germ ribosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.05 Å/pix.
x 221 pix.
= 453.05 Å		2.05 Å/pix.
x 221 pix.
= 453.05 Å		2.05 Å/pix.
x 221 pix.
= 453.05 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.05 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.000155 / Movie #1: 0.0003
Minimum - Maximum-0.000958881 - 0.00212884
Average (Standard dev.)0.0000263569 (±0.000171384)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-110-110-110
Dimensions221221221
Spacing221221221
CellA=B=C: 453.05 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.052.052.05
M x/y/z221221221
origin x/y/z0.0000.0000.000
length x/y/z453.050453.050453.050
α/β/γ90.00090.00090.000
start NX/NY/NZ-220-220-220
NX/NY/NZ441441441
MAP C/R/S123
start NC/NR/NS-110-110-110
NC/NR/NS221221221
D min/max/mean-0.0010.0020.000

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Supplemental data

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Sample components

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Entire : 80s wheat germ ribosome

EntireName: 80s wheat germ ribosome
Components
  • Sample: 80s wheat germ ribosome
  • Complex: 80s

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Supramolecule #1000: 80s wheat germ ribosome

SupramoleculeName: 80s wheat germ ribosome / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: 80s

SupramoleculeName: 80s / type: complex / ID: 1 / Name.synonym: 80s / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL
Source (natural)Organism: Triticum sp. (plant) / synonym: Bread wheat

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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
Image recordingDigitization - Scanner: OTHER / Digitization - Sampling interval: 1.6 µm
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD
Sample stageSpecimen holder: gg / Specimen holder model: GATAN HELIUM
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 9.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: spider

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