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- EMDB-1388: Averaging tens to hundreds of icosahedral particle images to reso... -

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Basic information

Entry
Database: EMDB / ID: EMD-1388
TitleAveraging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm.
Map dataThis is a P3A subunit of a RDV (Rice Dwarf Virus) map. It was reconstructed from the best 62 particles. For the full map, see accession code: EMD-1387.
Sample
  • Sample: Rice Dwarf Virus
  • Virus: Rice dwarf virus
Biological speciesRice dwarf virus
Methodsingle particle reconstruction / cryo EM / Resolution: 9.6 Å
AuthorsLiu X / Jiang W / Jakana J / Chiu W
CitationJournal: J Struct Biol / Year: 2007
Title: Averaging tens to hundreds of icosahedral particle images to resolve protein secondary structure elements using a Multi-Path Simulated Annealing optimization algorithm.
Authors: Xiangan Liu / Wen Jiang / Joanita Jakana / Wah Chiu /
Abstract: Accurately determining a cryoEM particle's alignment parameters is crucial to high resolution single particle 3-D reconstruction. We developed Multi-Path Simulated Annealing, a Monte-Carlo type of ...Accurately determining a cryoEM particle's alignment parameters is crucial to high resolution single particle 3-D reconstruction. We developed Multi-Path Simulated Annealing, a Monte-Carlo type of optimization algorithm, for globally aligning the center and orientation of a particle simultaneously. A consistency criterion was developed to ensure the alignment parameters are correct and to remove some bad particles from a large pool of images of icosahedral particles. Without using any a priori model, this procedure is able to reconstruct a structure from a random initial model. Combining the procedure above with a new empirical double threshold particle selection method, we are able to pick tens of best quality particles to reconstruct a subnanometer resolution map from scratch. Using the best 62 particles of rice dwarf virus, the reconstruction reached 9.6A resolution at which four helices of the P3A subunit of RDV are resolved. Furthermore, with the 284 best particles, the reconstruction is improved to 7.9A resolution, and 21 of 22 helices and six of seven beta sheets are resolved.
History
DepositionJun 25, 2007-
Header (metadata) releaseJun 25, 2007-
Map releaseJun 25, 2007-
UpdateAug 31, 2011-
Current statusAug 31, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.09
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.09
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1388.gif

Downloads & links

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Map

FileDownload / File: emd_1388.map.gz / Format: CCP4 / Size: 7.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationThis is a P3A subunit of a RDV (Rice Dwarf Virus) map. It was reconstructed from the best 62 particles. For the full map, see accession code: EMD-1387.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.49 Å/pix.
x 128 pix.
= 190.6 Å		1.49 Å/pix.
x 128 pix.
= 190.6 Å		1.49 Å/pix.
x 128 pix.
= 190.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.48906 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.018 / Movie #1: 0.09
Minimum - Maximum-0.345271 - 0.421653
Average (Standard dev.)0.00134742 (±0.0166201)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-64-64-64
Dimensions128128128
Spacing128128128
CellA=B=C: 190.6 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.48906251.48906251.4890625
M x/y/z128128128
origin x/y/z0.0000.0000.000
length x/y/z190.600190.600190.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-64-64-64
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-64-64-64
NC/NR/NS128128128
D min/max/mean-0.3450.4220.001

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Supplemental data

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Sample components

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Entire : Rice Dwarf Virus

EntireName: Rice Dwarf Virus
Components
  • Sample: Rice Dwarf Virus
  • Virus: Rice dwarf virus

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Supramolecule #1000: Rice Dwarf Virus

SupramoleculeName: Rice Dwarf Virus / type: sample / ID: 1000 / Number unique components: 1
Molecular weightTheoretical: 50 MDa

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Supramolecule #1: Rice dwarf virus

SupramoleculeName: Rice dwarf virus / type: virus / ID: 1 / NCBI-ID: 10991 / Sci species name: Rice dwarf virus / Virus type: OTHER / Virus isolate: OTHER / Virus enveloped: No / Virus empty: No
Host (natural)synonym: PLANTAE(HIGHER PLANTS)
Virus shellShell ID: 1 / Name: Inner Shell / Diameter: 550 Å / T number (triangulation number): 1

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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 / Chamber humidity: 27 % / Chamber temperature: 111 K

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Electron microscopy

MicroscopeJEOL 4000
TemperatureAverage: 109 K
DetailsMicroscope:JEOL 4000
DateJan 1, 1999
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 4 µm / Number real images: 100 / Average electron dose: 13 e/Å2 / Bits/pixel: 32
Electron beamAcceleration voltage: 400 kV / Electron source: LAB6
Electron opticsCalibrated magnification: 49495 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 4.1 mm / Nominal defocus max: 1.6 µm / Nominal defocus min: 0.3 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Gatan / Specimen holder model: GATAN LIQUID NITROGEN

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Image processing

CTF correctionDetails: Each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.6 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Multi-path SA
Details: The 5 alignment parameters (2 for center and 3 for orientation) were searched simultaneously for each particle image. The search is executed by a new optimizaiton algorithm, multi-path ...Details: The 5 alignment parameters (2 for center and 3 for orientation) were searched simultaneously for each particle image. The search is executed by a new optimizaiton algorithm, multi-path simulated annealing, based on Cross Common Lines. There were 4200 good particles discriminated from 4865 raw particles by a Consistency Criterion. The best 62 particles were empirically selected by a double threshold method from the 4200 good particles. The map's resolution was measured against the Known X-ray structure (PDB ID: 1UF2).
Number images used: 62

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