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- EMDB-8252: 2.6A 3D reconstruction of Tulane virus -

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Basic information

Entry
Database: EMDB / ID: EMD-8252
Title2.6A 3D reconstruction of Tulane virus
Map datareconstruction of Tulane virus
Sample
  • Virus: Tulane virus
Function / homologyCalicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / virion component / Viral coat protein subunit / host cell cytoplasm / Capsid protein
Function and homology information
Biological speciesTulane virus
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsYu G / Li K / Jiang W
CitationJournal: Structure / Year: 2016
Title: Antibody-Based Affinity Cryoelectron Microscopy at 2.6-Å Resolution.
Authors: Guimei Yu / Kunpeng Li / Pengwei Huang / Xi Jiang / Wen Jiang /
Abstract: The affinity cryoelectron microscopy (cryo-EM) approach has been explored in recent years to simplify and/or improve the sample preparation for cryo-EM, which can bring previously challenging ...The affinity cryoelectron microscopy (cryo-EM) approach has been explored in recent years to simplify and/or improve the sample preparation for cryo-EM, which can bring previously challenging specimens such as those of low abundance and/or unpurified ones within reach of the cryo-EM technique. Despite the demonstrated successes for solving structures to low to intermediate resolutions, the lack of near-atomic structures using this approach has led to a common perception of affinity cryo-EM as a niche technique incapable of reaching high resolutions. Here, we report a ∼2.6-Å structure solved using the antibody-based affinity grid approach with low-concentration Tulane virus purified from a low-yield cell-culture system that has been challenging to standard cryo-EM grid preparation. Quantitative analyses of the structure indicate data and reconstruction quality comparable with the conventional grid preparation method using samples at high concentration.
History
DepositionJun 15, 2016-
Header (metadata) releaseJul 20, 2016-
Map releaseNov 16, 2016-
UpdateFeb 14, 2018-
Current statusFeb 14, 2018Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 11
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 11
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 11
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_8252.png

Downloads & links

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Map

FileDownload / File: emd_8252.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationreconstruction of Tulane virus
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.98 Å/pix.
x 640 pix.
= 624. Å		0.98 Å/pix.
x 640 pix.
= 624. Å		0.98 Å/pix.
x 640 pix.
= 624. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.975 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 11. / Movie #1: 11
Minimum - Maximum-19.618842999999998 - 45.136246
Average (Standard dev.)0.053495932 (±2.4022765)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-320-320-320
Dimensions640640640
Spacing640640640
CellA=B=C: 624.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.9750.9750.975
M x/y/z640640640
origin x/y/z0.0000.0000.000
length x/y/z624.000624.000624.000
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ281156
MAP C/R/S123
start NC/NR/NS-320-320-320
NC/NR/NS640640640
D min/max/mean-19.61945.1360.053

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Supplemental data

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Sample components

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Entire : Tulane virus

EntireName: Tulane virus
Components
  • Virus: Tulane virus

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Supramolecule #1: Tulane virus

SupramoleculeName: Tulane virus / type: virus / ID: 1 / Parent: 0 / Details: Purified from cell cultures / NCBI-ID: 512169 / Sci species name: Tulane virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Macaca mulatta (Rhesus monkey)
Host systemOrganism: Platyrrhini (New World monkeys) / Recombinant cell: Monkey kidney cells / Recombinant plasmid: pBR322
Molecular weightTheoretical: 10 MDa
Virus shellShell ID: 1 / Diameter: 400.0 Å / T number (triangulation number): 3

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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

BufferpH: 7.4 / Details: 1x PBS
GridModel: Ted Pella ultrathin carbon / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 3.0 nm / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 60 % / Chamber temperature: 298 K / Instrument: GATAN CRYOPLUNGE 3

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 2-25 / Number grids imaged: 1 / Number real images: 1000 / Average electron dose: 5.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 100.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 22500
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 20000
CTF correctionSoftware - Name: fitctf2.py
Software - details: http://jiang.bio.purdue.edu/software.php
Details: Amplitude correction was performed during 3D reconstruction.
Startup modelType of model: OTHER
Details: Random initial models were generated using a small fraction of the boxed particles.
Final reconstructionAlgorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: jspr
Software - details: http://jiang.bio.purdue.edu/software.php
Number images used: 14154
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: jspr
Software - details: http://jiang.bio.purdue.edu/software.php
Final angle assignmentType: PROJECTION MATCHING / Software - Name: jspr
Software - details: http://jiang.bio.purdue.edu/software.php
FSC plot (resolution estimation)

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