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- EMDB-1587: ab initio 3D reconstruction of GroEL using 3DESS (3D alignment by... -

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Basic information

Entry
Database: EMDB / ID: EMD-1587
Titleab initio 3D reconstruction of GroEL using 3DESS (3D alignment by differential Evolution with Spectral Self-adaptation), which is a new high-resolution single-particle orientation refinement method based on spectrally self-adapting common lines
Map dataab initio 3D reconstruction of GroEL using 3DESS
Sample
  • Sample: GroEL data provided by National Resource for Automated Molecular Microscopy
  • Organelle or cellular component: GroEL
KeywordsGroEL / common lines / spectral self-adaptation
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.0 Å
AuthorsElmlund D / Elmlund H
CitationJournal: J Struct Biol / Year: 2009
Title: High-resolution single-particle orientation refinement based on spectrally self-adapting common lines.
Authors: Dominika Elmlund / Hans Elmlund /
Abstract: Three-dimensional (3D) structure determination from electron microscopic images of single molecules can be difficult for particles with low or no internal symmetry, and for images with low signal-to- ...Three-dimensional (3D) structure determination from electron microscopic images of single molecules can be difficult for particles with low or no internal symmetry, and for images with low signal-to-noise ratio (SNR), due to the existence of false maxima in the scoring function used for orientation search. In attempt to improve robustness of orientation parameter refinement towards noise and poor starting reconstruction quality, we have developed a method for common lines-based orientation search in Fourier space. The Fourier-space formulation enables inclusion of resolution (spatial frequency of the low-pass limit) as a variable that is adjusted in a particle-dependent, self-adaptive manner. The method allows for the underlying 3D structure to be estimated to high resolution, and requires only a crude, low-resolution reconstruction as starting-point for refinement. Benchmarking of the method is performed on experimental and synthetic data.
History
DepositionDec 15, 2008-
Header (metadata) releaseDec 15, 2008-
Map releaseApr 1, 2009-
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: 0.013
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.013
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-1oel
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-1oel
  • Surface level: 0.013
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1587.gif

Downloads & links

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Map

FileDownload / File: emd_1587.map.gz / Format: CCP4 / Size: 10.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationab initio 3D reconstruction of GroEL using 3DESS
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.63 Å/pix.
x 140 pix.
= 228.2 Å		1.63 Å/pix.
x 140 pix.
= 228.2 Å		1.63 Å/pix.
x 140 pix.
= 228.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.63 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.00689 / Movie #1: 0.013
Minimum - Maximum-0.0491726 - 0.0902491
Average (Standard dev.)0.000727468 (±0.00502245)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-70-70-70
Dimensions140140140
Spacing140140140
CellA=B=C: 228.2 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.631.631.63
M x/y/z140140140
origin x/y/z0.0000.0000.000
length x/y/z228.200228.200228.200
α/β/γ90.00090.00090.000
start NX/NY/NZ-100-100-99
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-70-70-70
NC/NR/NS140140140
D min/max/mean-0.0490.0900.001

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Supplemental data

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Sample components

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Entire : GroEL data provided by National Resource for Automated Molecular ...

EntireName: GroEL data provided by National Resource for Automated Molecular Microscopy
Components
  • Sample: GroEL data provided by National Resource for Automated Molecular Microscopy
  • Organelle or cellular component: GroEL

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Supramolecule #1000: GroEL data provided by National Resource for Automated Molecular ...

SupramoleculeName: GroEL data provided by National Resource for Automated Molecular Microscopy
type: sample / ID: 1000
Details: All sample details described in Stagg, S. M. et al. A test-bed for optimizing high-resolution single particle reconstructions, JSB 2008, 163(1), 29-39
Oligomeric state: 14-meric and d7 symmetric GroEL / Number unique components: 1

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Supramolecule #1: GroEL

SupramoleculeName: GroEL / type: organelle_or_cellular_component / ID: 1 / Name.synonym: GroEL / Recombinant expression: Yes
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

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 120 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
DetailsAll imaging details described in Stagg, S. M. et al. A test-bed for optimizing high-resolution single particle reconstructions, JSB 2008, 163(1), 29-39
Image recordingDetails: All image processing details described in Stagg, S. M. et al. A test-bed for optimizing high-resolution single particle
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: each micrograph, phase flipping only
Final reconstructionApplied symmetry - Point group: D7 (2x7 fold dihedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Evol-Align
DetailsAll experimental details described in Stagg, S. M. et al. A test-bed for optimizing high-resolution single particle reconstructions, JSB 2008, 163(1), 29-39

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