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- EMDB-5557: Structure of the EV71 strain 1095 procapsid -

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Basic information

Entry
Database: EMDB / ID: 5557
TitleStructure of the EV71 strain 1095 procapsid
Map dataReconstruction of EV71 strain 1095 procapsid
SampleEV71 strain 1095 procapsid:
virus
Keywordspicornavirus / enterovirus 71 / hand foot and mouth disease / cryo-EM / single particle reconstruction
SourceHuman enterovirus 71
Methodsingle particle reconstruction / cryo EM / 8.78 Å resolution
AuthorsCifuente JO / Lee H / Yoder JD / Shingler KL / Carnegie MS / Yoder JL / Ashley RE / Makhov AM / Conway JF / Hafenstein S
CitationJournal: J. Virol. / Year: 2013
Title: Structures of the procapsid and mature virion of enterovirus 71 strain 1095.
Authors: Javier O Cifuente / Hyunwook Lee / Joshua D Yoder / Kristin L Shingler / Michael S Carnegie / Jennifer L Yoder / Robert E Ashley / Alexander M Makhov / James F Conway / Susan Hafenstein
DateDeposition: Dec 21, 2012 / Header (metadata) release: Jul 3, 2013 / Map release: Jul 17, 2013 / Last update: Jul 17, 2013

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by radius
  • Surface level: 1
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

Fileemd_5557.map.gz (map file in CCP4 format, 161805 KB)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
346 pix
1.25 Å/pix.
= 434.057 Å
346 pix
1.25 Å/pix.
= 434.057 Å
346 pix
1.25 Å/pix.
= 434.057 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2545 Å
Density
Contour Level:1 (by author), 1 (movie #1):
Minimum - Maximum-1.61199939 - 4.57805777
Average (Standard dev.)0.00143825 (0.99987930)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions346346346
Origin-173-173-173
Limit172172172
Spacing346346346
CellA=B=C: 434.057 Å
α=β=γ: 90.0 deg.

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.25451.25451.2545
M x/y/z346346346
origin x/y/z0.0000.0000.000
length x/y/z434.057434.057434.057
α/β/γ90.00090.00090.000
start NX/NY/NZ-5029166
NX/NY/NZ106122134
MAP C/R/S123
start NC/NR/NS-173-173-173
NC/NR/NS346346346
D min/max/mean-1.6124.5780.001

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Supplemental data

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Sample components

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Entire EV71 strain 1095 procapsid

EntireName: EV71 strain 1095 procapsid / Number of components: 1

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Component #1: virus, Human enterovirus 71

VirusName: Human enterovirus 71 / Class: VIRION / Empty: Yes / Enveloped: No / Isolate: STRAIN
MassTheoretical: 8 MDa
SpeciesSpecies: Human enterovirus 71
Source (natural)Host Species: Homo sapiens (human) / Host category: VERTEBRATES

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Experimental details

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Sample preparation

SpecimenSpecimen state: particle / Method: cryo EM
Sample solutionBuffer solution: 10mM Tris-HCl, 200mM NaCl, 50mM MgCl2 / pH: 7.4
VitrificationInstrument: FEI VITROBOT MARK I / Cryogen name: ETHANE-PROPANE MIXTURE / Temperature: 120 K

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Electron microscopy imaging

Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company
ImagingMicroscope: FEI TECNAI F20 / Date: Aug 15, 2011
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal), 50400 X (calibrated)
Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 790 - 3910 nm / Energy filter: FEI
Specimen HolderModel: GATAN LIQUID NITROGEN / Temperature: K ( 83 - K)
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 20 / Scanner: NIKON SUPER COOLSCAN 9000 / Sampling size: 6.35 microns

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 8805
Details: Semi-automatic particle selection was performed using e2boxer.py to obtain the particle coordinates, followed by particle boxing, linearization, normalization, and apodization of the images using Robem. Defocus and astigmatism values to perform contrast transfer function (CTF) correction were assessed using Robem for the extracted particles. The icosahedrally averaged reconstructions were initiated using a random model generated with setup_rmc and reached better than 10 A resolution estimated at a Fourier Shell Correlation, FSC=0.5. For the last step of refinement, the final maps were CTF corrected using a B factor of 300 A2.
Applied symmetry: I (icosahedral)
3D reconstructionAlgorithm: Cross-common lines / Euler angles: AUTO3DEM / Software: Auto3dem, EMAN2 / CTF correction: Each particle / Resolution: 8.78 Å / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Software: VEDA / Refinement protocol: rigid body / Target criteria: R-factor / Refinement space: RECIPROCAL / Details: Protocol: Rigid body
Input PDB model: 3VBU
Chain ID: A, B, C

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