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- EMDB-5558: Structure of the EV71 strain 1095 mature virion -

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Basic information

Entry
Database: EMDB / ID: EMD-5558
TitleStructure of the EV71 strain 1095 mature virion
Map dataReconstruction of EV71 virion
Sample
  • Sample: EV71 strain 1095 capsid
  • Virus: Human enterovirus 71
Keywordspicornavirus / enterovirus 71 / hand foot and mouth disease / cryo-EM / single particle reconstruction
Biological speciesHuman enterovirus 71
Methodsingle particle reconstruction / cryo EM / Resolution: 9.76 Å
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 /
Abstract: Enterovirus 71 (EV71) is an important emerging human pathogen with a global distribution and presents a disease pattern resembling poliomyelitis with seasonal epidemics that include cases of severe ...Enterovirus 71 (EV71) is an important emerging human pathogen with a global distribution and presents a disease pattern resembling poliomyelitis with seasonal epidemics that include cases of severe neurological complications, such as acute flaccid paralysis. EV71 is a member of the Picornaviridae family, which consists of icosahedral, nonenveloped, single-stranded RNA viruses. Here we report structures derived from X-ray crystallography and cryoelectron microscopy (cryo-EM) for the 1095 strain of EV71, including a putative precursor in virus assembly, the procapsid, and the mature virus capsid. The cryo-EM map of the procapsid provides new structural information on portions of the capsid proteins VP0 and VP1 that are disordered in the higher-resolution crystal structures. Our structures solved from virus particles in solution are largely in agreement with those from prior X-ray crystallographic studies; however, we observe small but significant structural differences for the 1095 procapsid compared to a structure solved in a previous study (X. Wang, W. Peng, J. Ren, Z. Hu, J. Xu, Z. Lou, X. Li, W. Yin, X. Shen, C. Porta, T. S. Walter, G. Evans, D. Axford, R. Owen, D. J. Rowlands, J. Wang, D. I. Stuart, E. E. Fry, and Z. Rao, Nat. Struct. Mol. Biol. 19:424-429, 2012) for a different strain of EV71. For both EV71 strains, the procapsid is significantly larger in diameter than the mature capsid, unlike in any other picornavirus. Nonetheless, our results demonstrate that picornavirus capsid expansion is possible without RNA encapsidation and that picornavirus assembly may involve an inward radial collapse of the procapsid to yield the native virion.
History
DepositionDec 21, 2012-
Header (metadata) releaseJul 3, 2013-
Map releaseJul 17, 2013-
UpdateJul 17, 2013-
Current statusJul 17, 2013Processing site: RCSB / Status: Released

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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

emd_5558_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5558.map.gz / Format: CCP4 / Size: 172.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of EV71 virion
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.25 Å/pix.
x 359 pix.
= 448.75 Å		1.25 Å/pix.
x 359 pix.
= 448.75 Å		1.25 Å/pix.
x 359 pix.
= 448.75 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.25 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-1.20558047 - 4.22272682
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-179-179-179
Dimensions359359359
Spacing359359359
CellA=B=C: 448.75 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.251.251.25
M x/y/z359359359
origin x/y/z0.0000.0000.000
length x/y/z448.750448.750448.750
α/β/γ90.00090.00090.000
start NX/NY/NZ-5029166
NX/NY/NZ106122134
MAP C/R/S123
start NC/NR/NS-179-179-179
NC/NR/NS359359359
D min/max/mean-1.2064.2230.000

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Supplemental data

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Sample components

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Entire : EV71 strain 1095 capsid

EntireName: EV71 strain 1095 capsid
Components
  • Sample: EV71 strain 1095 capsid
  • Virus: Human enterovirus 71

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Supramolecule #1000: EV71 strain 1095 capsid

SupramoleculeName: EV71 strain 1095 capsid / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: Human enterovirus 71

SupramoleculeName: Human enterovirus 71 / type: virus / ID: 1 / NCBI-ID: 39054 / Sci species name: Human enterovirus 71 / Database: NCBI / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES
Molecular weightTheoretical: 9 MDa
Virus shellShell ID: 1 / Diameter: 300 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

BufferpH: 7.4 / Details: 10mM Tris-HCl, 200mM NaCl, 50mM MgCl2
VitrificationCryogen name: ETHANE-PROPANE MIXTURE / Chamber temperature: 120 K / Instrument: FEI VITROBOT MARK I

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMin: 83 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
Specialist opticsEnergy filter - Name: FEI
DateNov 14, 2011
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000 / Digitization - Sampling interval: 6.35 µm / Number real images: 24
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50400 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.94 µm / Nominal defocus min: 2.36 µm / Nominal magnification: 50000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

DetailsSemi-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.
CTF correctionDetails: Each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.76 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Auto3dem, EMAN2 / Number images used: 6168
Final angle assignmentDetails: AUTO3DEM

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Atomic model buiding 1

Initial modelPDB ID:

3vbs


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C / Chain - #3 - Chain ID: D
SoftwareName: VEDA
DetailsProtocol: Rigid body
RefinementSpace: RECIPROCAL / Protocol: RIGID BODY FIT / Target criteria: R-factor

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