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- EMDB-3364: Sub-tomogram averaging of Tula virus glycoprotein spike -

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Basic information

Entry
Database: EMDB / ID: EMD-3364
TitleSub-tomogram averaging of Tula virus glycoprotein spike
Map dataSub-tomogram average of Tula virus surface
Sample
  • Sample: Glycoprotein spike of Tula hantavirus
  • Virus: Tula virus
KeywordsTula virus / membrane protein / glycoprotein / hantavirus / bunyavirus / receptor binding
Function / homology
Function and homology information


symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / host cell surface / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / virus-mediated perturbation of host defense response / virion membrane / cell surface / signal transduction ...symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / host cell surface / host cell endoplasmic reticulum membrane / symbiont-mediated suppression of host innate immune response / virus-mediated perturbation of host defense response / virion membrane / cell surface / signal transduction / membrane / metal ion binding
Similarity search - Function
Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / : / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / Hantavirus glycoprotein Gn, base / ITAM motif hantavirus type profile. / Hantavirus glycoprotein Gc / : ...Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / : / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / Hantavirus glycoprotein Gn, base / ITAM motif hantavirus type profile. / Hantavirus glycoprotein Gc / : / Hantavirus glycoprotein Gc, N-terminal / Hantavirus glycoprotein Gc, C-terminal
Similarity search - Domain/homology
Envelopment polyprotein
Similarity search - Component
Biological speciesTula virus
Methodsubtomogram averaging / cryo EM / Resolution: 15.6 Å
AuthorsLi S / Rissanen I / Zeltina A / Hepojoki J / Raghwani J / Harlos K / Pybus OG / Huiskonen JT / Bowden TA
CitationJournal: Cell Rep / Year: 2016
Title: A Molecular-Level Account of the Antigenic Hantaviral Surface.
Authors: Sai Li / Ilona Rissanen / Antra Zeltina / Jussi Hepojoki / Jayna Raghwani / Karl Harlos / Oliver G Pybus / Juha T Huiskonen / Thomas A Bowden /
Abstract: Hantaviruses, a geographically diverse group of zoonotic pathogens, initiate cell infection through the concerted action of Gn and Gc viral surface glycoproteins. Here, we describe the high- ...Hantaviruses, a geographically diverse group of zoonotic pathogens, initiate cell infection through the concerted action of Gn and Gc viral surface glycoproteins. Here, we describe the high-resolution crystal structure of the antigenic ectodomain of Gn from Puumala hantavirus (PUUV), a causative agent of hemorrhagic fever with renal syndrome. Fitting of PUUV Gn into an electron cryomicroscopy reconstruction of intact Gn-Gc spike complexes from the closely related but non-pathogenic Tula hantavirus localized Gn tetramers to the membrane-distal surface of the virion. The accuracy of the fitting was corroborated by epitope mapping and genetic analysis of available PUUV sequences. Interestingly, Gn exhibits greater non-synonymous sequence diversity than the less accessible Gc, supporting a role of the host humoral immune response in exerting selective pressure on the virus surface. The fold of PUUV Gn is likely to be widely conserved across hantaviruses.
History
DepositionMar 7, 2016-
Header (metadata) releaseApr 13, 2016-
Map releaseMay 4, 2016-
UpdateJun 8, 2016-
Current statusJun 8, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view colored by radius
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5fyn
  • Surface level: 1.5
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5fyn
  • Surface level: 1.6
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-5fyn
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3364.tif

Downloads & links

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Map

FileDownload / File: emd_3364.map.gz / Format: CCP4 / Size: 15.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSub-tomogram average of Tula virus surface
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.7 Å/pix.
x 160 pix.
= 432. Å		2.7 Å/pix.
x 160 pix.
= 432. Å		2.7 Å/pix.
x 160 pix.
= 432. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.7 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 1.5 / Movie #1: 1.5
Minimum - Maximum-4.09631443 - 4.94078588
Average (Standard dev.)0.01067896 (±0.68623537)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-80-80-80
Dimensions160160160
Spacing160160160
CellA=B=C: 432.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.72.72.7
M x/y/z160160160
origin x/y/z0.0000.0000.000
length x/y/z432.000432.000432.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS-80-80-80
NC/NR/NS160160160
D min/max/mean-4.0964.9410.011

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Supplemental data

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Sample components

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Entire : Glycoprotein spike of Tula hantavirus

EntireName: Glycoprotein spike of Tula hantavirus
Components
  • Sample: Glycoprotein spike of Tula hantavirus
  • Virus: Tula virus

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Supramolecule #1000: Glycoprotein spike of Tula hantavirus

SupramoleculeName: Glycoprotein spike of Tula hantavirus / type: sample / ID: 1000 / Oligomeric state: Lattice of GnGc tetramers / Number unique components: 1

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Supramolecule #1: Tula virus

SupramoleculeName: Tula virus / type: virus / ID: 1 / Name.synonym: Tula hantavirus / NCBI-ID: 37133 / Sci species name: Tula virus / Sci species strain: Moravia / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No / Syn species name: Tula hantavirus
Host (natural)Organism: Microtus (meadow voles) / synonym: VERTEBRATES
Host systemOrganism: Chlorocebus / Recombinant cell: Vero E6

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Experimental details

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Structure determination

Methodcryo EM
Processingsubtomogram averaging
Aggregation stateparticle

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Sample preparation

BufferpH: 8 / Details: 25 mM Tris, 75 mM NaCl
GridDetails: Grids (Cflat CF-2/1-2C-T) were glow-discharged for 15 s. 10-nm gold particles were added.
VitrificationCryogen name: ETHANE-PROPANE MIXTURE / Chamber humidity: 80 % / Chamber temperature: 120 K / Instrument: GATAN CRYOPLUNGE 3 / Method: Blot for 3 seconds before plunging.

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Electron microscopy

MicroscopeFEI POLARA 300
TemperatureMin: 80 K / Max: 120 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 160,000 times magnification.
Specialist opticsEnergy filter - Name: GIF QUANTUM LS / Energy filter - Lower energy threshold: 0.0 eV / Energy filter - Upper energy threshold: 20.0 eV
DetailsSuper-resolution counting mode
DateAug 14, 2014
Image recordingCategory: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Digitization - Sampling interval: 5 µm / Number real images: 30 / Average electron dose: 60 e/Å2
Details: Each image is a tilt series of 19 movies, acquired at 5 degree intervals. Each movie consists of 8 frames.
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 37037 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.8 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 160000
Sample stageSpecimen holder: Liquid nitrogen cooled / Specimen holder model: OTHER / Tilt series - Axis1 - Min angle: -45 ° / Tilt series - Axis1 - Max angle: 45 °
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsSubtomograms were selected using template-based picking.
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 15.6 Å / Resolution method: OTHER / Software - Name: IMOD, Dynamo / Number subtomograms used: 5449
CTF correctionDetails: Each tilted image
Final 3D classificationNumber classes: 1
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

5fxu


Chain - #0 - Chain ID: A / Chain - #1 - Chain ID: B
SoftwareName: Chimera, Segger
DetailsDensity was segmented in 6 segments and 1000 evenly rotated fits were considered for each segment.
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation
Output model

PDB-5fyn:
Sub-tomogram averaging of Tula virus glycoprotein spike

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