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- EMDB-1752: 3D reconstruction of the rotavirus VP6 trimer using the Fast Proj... -

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Basic information

Entry
Database: EMDB / ID: EMD-1752
Title3D reconstruction of the rotavirus VP6 trimer using the Fast Projection Matching (FPM) algorithm.
Map dataMap of rotavirus VP6 trimer (from EMD-1461) after icosahedral averaging and 13-fold non-icosahedral averaging
Sample
  • Sample: Rotavirus VP6 protein
  • Protein or peptide: VP6
  • Protein or peptide: VP1
  • Protein or peptide: VP2
  • Protein or peptide: VP3
  • RNA: dsRNA
KeywordsRotavirus VP6 protein / Methods / Projection Matching
Biological speciesBovine rotavirus
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsEstrozi LF / Navaza J
CitationJournal: J Struct Biol / Year: 2010
Title: Ab initio high-resolution single-particle 3D reconstructions: the symmetry adapted functions way.
Authors: Leandro F Estrozi / Jorge Navaza /
Abstract: A protocol to attain high-resolution single-particle reconstructions is presented. The protocol is the concatenation of two procedures: one to obtain an ab initio low-resolution reconstruction, the ...A protocol to attain high-resolution single-particle reconstructions is presented. The protocol is the concatenation of two procedures: one to obtain an ab initio low-resolution reconstruction, the other to determine a fixed point of the consecutive applications of fast projection matching and 3D reconstruction. It is a reciprocal space formulation where the Fourier coefficients of the 3D scattering density are expressed in terms of symmetry adapted functions and the 2D particle images are represented by their Fourier-Bessel transforms. The new protocol shows advantages in terms of speed and accuracy when compared to other methods currently in use. We illustrate its performance as applied to high-resolution cryo-electron micrographs of rotavirus.
History
DepositionJun 18, 2010-
Header (metadata) releaseOct 13, 2010-
Map releaseOct 13, 2010-
UpdateSep 26, 2012-
Current statusSep 26, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 460
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 460
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-1qhd
  • Surface level: 460
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_1752.png

Downloads & links

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Map

FileDownload / File: emd_1752.map.gz / Format: CCP4 / Size: 5.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMap of rotavirus VP6 trimer (from EMD-1461) after icosahedral averaging and 13-fold non-icosahedral averaging
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.14 Å/pix.
x 114 pix.
= 129.96 Å		1.14 Å/pix.
x 114 pix.
= 129.96 Å		1.14 Å/pix.
x 114 pix.
= 129.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.14 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 460.0 / Movie #1: 460
Minimum - Maximum-1774.839999999999918 - 2060.699999999999818
Average (Standard dev.)0.0000916213 (±158.209000000000003)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-57-57-57
Dimensions114114114
Spacing114114114
CellA=B=C: 129.96 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.141.141.14
M x/y/z114114114
origin x/y/z0.0000.0000.000
length x/y/z129.960129.960129.960
α/β/γ90.00090.00090.000
start NX/NY/NZ-100-100-100
NX/NY/NZ200200200
MAP C/R/S123
start NC/NR/NS-57-57-57
NC/NR/NS114114114
D min/max/mean-1774.8392060.6960.000

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Supplemental data

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Sample components

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Entire : Rotavirus VP6 protein

EntireName: Rotavirus VP6 protein
Components
  • Sample: Rotavirus VP6 protein
  • Protein or peptide: VP6
  • Protein or peptide: VP1
  • Protein or peptide: VP2
  • Protein or peptide: VP3
  • RNA: dsRNA

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Supramolecule #1000: Rotavirus VP6 protein

SupramoleculeName: Rotavirus VP6 protein / type: sample / ID: 1000
Oligomeric state: 780 molecules of VP6 form a DLP particle with 12 molecules of VP1, 120 molecules of VP2, 12 molecules of VP3 and 11 dsRNA molecules
Number unique components: 5

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Macromolecule #1: VP6

MacromoleculeName: VP6 / type: protein_or_peptide / ID: 1 / Name.synonym: VP6 / Recombinant expression: No
Source (natural)Organism: Bovine rotavirus / synonym: Rotavirus
Molecular weightTheoretical: 41 KDa

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Macromolecule #2: VP1

MacromoleculeName: VP1 / type: protein_or_peptide / ID: 2 / Name.synonym: VP1 / Recombinant expression: No
Source (natural)Organism: Bovine rotavirus / synonym: Rotavirus

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Macromolecule #3: VP2

MacromoleculeName: VP2 / type: protein_or_peptide / ID: 3 / Name.synonym: VP2 / Recombinant expression: No
Source (natural)Organism: Bovine rotavirus / synonym: Rotavirus

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Macromolecule #4: VP3

MacromoleculeName: VP3 / type: protein_or_peptide / ID: 4 / Name.synonym: VP3 / Recombinant expression: No
Source (natural)Organism: Bovine rotavirus / synonym: Rotavirus

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Macromolecule #5: dsRNA

MacromoleculeName: dsRNA / type: rna / ID: 5 / Name.synonym: dsRNA / Classification: OTHER / Structure: OTHER / Synthetic?: No
Source (natural)Organism: Bovine rotavirus / synonym: Rotavirus

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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

Concentration5 mg/mL
BufferpH: 7.4
GridDetails: Lacy carbon and C-flat
VitrificationCryogen name: ETHANE / Chamber humidity: 30 % / Instrument: HOMEMADE PLUNGER
Details: Vitrification instrument: Home-made. Vitrification carried out in air at room temperature
Method: Blot for 3 seconds before plunging

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Electron microscopy

MicroscopeFEI TECNAI F30
TemperatureAverage: 90 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected
DateJun 1, 2007
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 7 µm / Number real images: 386 / Average electron dose: 15 e/Å2 / Od range: 1 / Bits/pixel: 8
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 56540 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2 mm / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.1 µm / Nominal magnification: 59000
Sample stageSpecimen holder: Eucentric, side-entry / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Phase flipping for each particle
Final reconstructionApplied symmetry - Point group: I (icosahedral) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: OTHER / Software - Name: RIco / Number images used: 7000

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Atomic model buiding 1

Initial modelPDB ID:

1qhd


Chain - Chain ID: A
SoftwareName: URO
DetailsPDBEntryID_givenInChain. Protocol: Rigid body
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Target criteria: Correlation coefficient

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