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- EMDB-5529: 6.3 A Cryo-EM Structure of a Novel Calicivirus, Tulane Virus -

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Basic information

Entry
Database: EMDB / ID: EMD-5529
Title6.3 A Cryo-EM Structure of a Novel Calicivirus, Tulane Virus
Map dataReconstruction of TV virion
Sample
  • Sample: Tulane virus
  • Virus: Tulane virus
KeywordsTulane virus / calicivirus / conformational flexibility / single particle cryo-EM / 3-D reconstruction
Biological speciesTulane virus
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 6.3 Å
AuthorsYu G / Zhang D / Guo F / Tan M / Jiang X / Jiang W
CitationJournal: PLoS One / Year: 2013
Title: Cryo-EM structure of a novel calicivirus, Tulane virus.
Authors: Guimei Yu / Dongsheng Zhang / Fei Guo / Ming Tan / Xi Jiang / Wen Jiang /
Abstract: Tulane virus (TV) is a newly isolated cultivatable calicivirus that infects juvenile rhesus macaques. Here we report a 6.3 Å resolution cryo-electron microscopy structure of the TV virion. The TV ...Tulane virus (TV) is a newly isolated cultivatable calicivirus that infects juvenile rhesus macaques. Here we report a 6.3 Å resolution cryo-electron microscopy structure of the TV virion. The TV virion is about 400 Å in diameter and consists of a T = 3 icosahedral protein capsid enclosing the RNA genome. 180 copies of the major capsid protein VP1 (∼57 KDa) are organized into two types of dimers A/B and C/C and form a thin, smooth shell studded with 90 dimeric protrusions. The overall capsid organization and the capsid protein fold of TV closely resemble that of other caliciviruses, especially of human Norwalk virus, the prototype human norovirus. These close structural similarities support TV as an attractive surrogate for the non-cultivatable human noroviruses. The most distinctive feature of TV is that its C/C dimers are in a highly flexible conformation with significantly reduced interactions between the shell (S) domain and the protruding (P) domain of VP1. A comparative structural analysis indicated that the P domains of TV C/C dimers were much more flexible than those of other caliciviruses. These observations, combined with previous studies on other caliciviruses, led us to hypothesize that the enhanced flexibility of C/C dimer P domains are likely required for efficient calicivirus-host cell interactions and the consequent uncoating and genome release. Residues in the S-P1 hinge between the S and P domain may play a critical role in the flexibility of P domains of C/C dimers.
History
DepositionNov 30, 2012-
Header (metadata) releaseDec 12, 2012-
Map releaseApr 3, 2013-
UpdateApr 3, 2013-
Current statusApr 3, 2013Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 4
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 4
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5529.tif

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Map

FileDownload / File: emd_5529.map.gz / Format: CCP4 / Size: 162.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of TV virion
Voxel sizeX=Y=Z: 1.74 Å
Density
Contour LevelBy AUTHOR: 4.0 / Movie #1: 4
Minimum - Maximum-14.32884121 - 20.855964660000001
Average (Standard dev.)0.08813742 (±1.26044631)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions352352352
Spacing352352352
CellA=B=C: 612.48 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.741.741.74
M x/y/z352352352
origin x/y/z0.0000.0000.000
length x/y/z612.480612.480612.480
α/β/γ90.00090.00090.000
start NX/NY/NZ-5029166
NX/NY/NZ106122134
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS352352352
D min/max/mean-14.32920.8560.088

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Supplemental data

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Sample components

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Entire : Tulane virus

EntireName: Tulane virus
Components
  • Sample: Tulane virus
  • Virus: Tulane virus

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Supramolecule #1000: Tulane virus

SupramoleculeName: Tulane virus / type: sample / ID: 1000
Oligomeric state: One Tulane virus has 90 dimers forming its icosahedral capsid (T=3).
Number unique components: 1
Molecular weightTheoretical: 10.4 MDa

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Supramolecule #1: Tulane virus

SupramoleculeName: Tulane virus / type: virus / ID: 1 / NCBI-ID: 512169 / Sci species name: Tulane virus / Database: NCBI / Virus type: VIRION / Virus isolate: SPECIES / Virus enveloped: No / Virus empty: No
Host (natural)Organism: Macaca mulatta (Rhesus monkey) / synonym: VERTEBRATES
Molecular weightTheoretical: 10.4 MDa
Virus shellShell ID: 1 / Name: VP1 / Diameter: 400 Å / T number (triangulation number): 3

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.4
Details: 137mM NaCl, 2.7mM KCl, 10mM Na2HPO4, 2mM KH2PO4, pH 7.4
StainingType: NEGATIVE
Details: Grids with sample floated on 2% uranyl acetate for 30 seconds.
GridDetails: 400 mesh copper grid with one lacy carbon layer and one layer of ultra thin carbon on top.
VitrificationCryogen name: ETHANE / Chamber temperature: 85 K / Instrument: HOMEMADE PLUNGER

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 36475 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.891 µm / Nominal defocus min: 1.347 µm / Nominal magnification: 37000
Sample stageSpecimen holder: Liquid nitrogen cooled / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
TemperatureMin: 80 K / Max: 85 K / Average: 80 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 250,000 magnification using quadrupole stigmator.
Legacy - Electron beam tilt params: 0
DateJul 29, 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: 190 / Average electron dose: 25 e/Å2 / Bits/pixel: 16
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: each particle
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 6.3 Å / Resolution method: OTHER / Software - Name: jspr.py, EMAN, EMAN2 / Number images used: 4338
Details4702 Tulane virus particles were selected using combined automated selection with ethan program and manual screening with boxer program in EMAN. The microscope contrast transfer function parameters for each micrograph were first determined using an automated fitting method and then manually verified/corrected using EMAN ctfit graphic program. The entire TV dataset was divided into two halves and processed independently for all the subsequent steps including construction of initial model, 2-D alignment and 3-D reconstruction. De novo initial models were constructed using the random model method in which random particle orientations were assigned and subsequently refined iteratively until convergence. The iterative refinement process including particle alignment and 3-D icosahedral reconstruction was performed using an in-house developed program jspr.py utilizing the EMAN/EMAN2 programs and library functions. The resolution was determined based on the 0.143 cutoff criterion for two truly independent reconstructions.

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Atomic model buiding 1

Initial modelPDB ID:

1ihm


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B / Chain - #2 - Chain ID: C
SoftwareName: Chimera
DetailsProtocol: rigid body. The three chains from 1IHM were first fitted into TV density as a whole rigid body and then divided into dimers, specific chains, domains, and subdomains and fitted.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Correlation

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