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- EMDB-1921: Improved ab initio 3D reconstruction of the EF-G lacking E. coli ... -

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Basic information

Entry
Database: EMDB / ID: EMD-1921
TitleImproved ab initio 3D reconstruction of the EF-G lacking E. coli ribosome by SIMPLE
Map dataThis is a volume of the EF-G-lacking E. coli ribosome reconstructed by SIMPLE
Sample
  • Sample: EF-G ribosome test data
  • Complex: Ribosome
Keywordsab initio
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM
AuthorsElmlund H
CitationJournal: Ultramicroscopy / Year: 2001
Title: Strul--a method for 3D alignment of single-particle projections based on common line correlation in Fourier space.
Authors: M Lindahl /
Abstract: A central problem of 3D reconstruction in single-particle electron microscopy is the determination of relative orientations of the individual projections contributing to the reconstruction. This ...A central problem of 3D reconstruction in single-particle electron microscopy is the determination of relative orientations of the individual projections contributing to the reconstruction. This article describes an implementation of the method of common lines correlation in Fourier space that allows generation of common lines between an arbitrary number of projections which might posses an arbitrary point group symmetry. Based on this method, it is possible to optimize rotational and translational alignment parameters for individual single-particle projections. The underlying philosophy and details of implementation are discussed, and as an illustration a 3D reconstruction in ice of peroxisomal alcohol oxidase from Pichia pastoris, an octameric assembly with 422-symmetry and a molecular weight of 592 kDa is presented.
History
DepositionJul 2, 2011-
Header (metadata) releaseSep 26, 2012-
Map releaseSep 26, 2012-
UpdateApr 9, 2014-
Current statusApr 9, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.112
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.112
  • 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_1921.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a volume of the EF-G-lacking E. coli ribosome reconstructed by SIMPLE
Voxel sizeX=Y=Z: 2.82 Å
Density
Contour LevelBy AUTHOR: 0.112 / Movie #1: 0.112
Minimum - Maximum-3.98637533 - 6.75133562
Average (Standard dev.)0.04442283 (±0.26333624)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 360.96 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.822.822.82
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z360.960360.960360.960
α/β/γ90.00090.00090.000
start NX/NY/NZ-56-56-55
NX/NY/NZ112112112
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-3.9866.7510.044

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Supplemental data

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Sample components

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Entire : EF-G ribosome test data

EntireName: EF-G ribosome test data
Components
  • Sample: EF-G ribosome test data
  • Complex: Ribosome

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Supramolecule #1000: EF-G ribosome test data

SupramoleculeName: EF-G ribosome test data / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Ribosome

SupramoleculeName: Ribosome / type: complex / ID: 1 / Name.synonym: Ribosome / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL
Source (natural)Organism: Escherichia coli (E. coli)

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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 / Instrument: OTHER

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Electron microscopy

MicroscopeOTHER
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Software - Name: SIMPLE

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