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- EMDB-2056: Electron cryo-microscopy of the Hantaan virus glycoprotein spike -

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Basic information

Entry
Database: EMDB / ID: EMD-2056
TitleElectron cryo-microscopy of the Hantaan virus glycoprotein spike
Map dataReconstruction of the Hantaan virus Gn-Gc glycoprotein spike complex
Sample
  • Sample: Hantaan virus Gn-Gc glycoprotein spike complex
  • Virus: Hantaan virus
Keywordsglycoprotein complex / viral membrane / fusion
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 / virion membrane / signal transduction / membrane / metal ion binding
Similarity search - Function
: / Hantavirus glycoprotein Gn, base / Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / ITAM motif hantavirus type profile. / : / Hantavirus glycoprotein Gc, C-terminal ...: / Hantavirus glycoprotein Gn, base / Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / ITAM motif hantavirus type profile. / : / Hantavirus glycoprotein Gc, C-terminal / Hantavirus glycoprotein Gc / Hantavirus glycoprotein Gc, N-terminal
Similarity search - Domain/homology
Envelopment polyprotein
Similarity search - Component
Biological speciesHantaan virus
Methodsingle particle reconstruction / cryo EM / Resolution: 25.0 Å
AuthorsBattisti AJ / Chu YK / Chipman PR / Kaufmann B / Jonsson CB / Rossmann MG
CitationJournal: J Virol / Year: 2011
Title: Structural studies of Hantaan virus.
Authors: Anthony J Battisti / Yong-Kyu Chu / Paul R Chipman / Bärbel Kaufmann / Colleen B Jonsson / Michael G Rossmann /
Abstract: Hantaan virus is the prototypic member of the Hantavirus genus within the family Bunyaviridae and is a causative agent of the potentially fatal hemorrhagic fever with renal syndrome. The Bunyaviridae ...Hantaan virus is the prototypic member of the Hantavirus genus within the family Bunyaviridae and is a causative agent of the potentially fatal hemorrhagic fever with renal syndrome. The Bunyaviridae are a family of negative-sense RNA viruses with three-part segmented genomes. Virions are enveloped and decorated with spikes derived from a pair of glycoproteins (Gn and Gc). Here, we present cryo-electron tomography and single-particle cryo-electron microscopy studies of Hantaan virus virions. We have determined the structure of the tetrameric Gn-Gc spike complex to a resolution of 2.5 nm and show that spikes are ordered in lattices on the virion surface. Large cytoplasmic extensions associated with each Gn-Gc spike also form a lattice on the inner surface of the viral membrane. Rod-shaped ribonucleoprotein complexes are arranged into nearly parallel pairs and triplets within virions. Our results differ from the T=12 icosahedral organization found for some bunyaviruses. However, a comparison of our results with the previous tomographic studies of the nonpathogenic Tula hantavirus indicates a common structural organization for hantaviruses.
History
DepositionMar 20, 2012-
Header (metadata) releaseMar 22, 2012-
Map releaseMar 22, 2012-
UpdateMar 22, 2012-
Current statusMar 22, 2012Processing site: PDBe / Status: Released

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Structure visualization

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

image2056.tif

Downloads & links

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Map

FileDownload / File: emd_2056.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the Hantaan virus Gn-Gc glycoprotein spike complex
Voxel sizeX=Y=Z: 5.4 Å
Density
Contour LevelBy AUTHOR: 1.0 / Movie #1: 1
Minimum - Maximum-7.12656021 - 8.03274822
Average (Standard dev.)0.0 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions808080
Spacing808080
CellA=B=C: 432.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z5.45.45.4
M x/y/z808080
origin x/y/z0.0000.0000.000
length x/y/z432.000432.000432.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS808080
D min/max/mean-7.1278.033-0.000

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Supplemental data

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Sample components

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Entire : Hantaan virus Gn-Gc glycoprotein spike complex

EntireName: Hantaan virus Gn-Gc glycoprotein spike complex
Components
  • Sample: Hantaan virus Gn-Gc glycoprotein spike complex
  • Virus: Hantaan virus

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Supramolecule #1000: Hantaan virus Gn-Gc glycoprotein spike complex

SupramoleculeName: Hantaan virus Gn-Gc glycoprotein spike complex / type: sample / ID: 1000 / Oligomeric state: tetramer of Gn-Gc heterodimers / Number unique components: 1
Molecular weightTheoretical: 392 KDa

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Supramolecule #1: Hantaan virus

SupramoleculeName: Hantaan virus / type: virus / ID: 1
Details: The Gn-Gc spike was reconstructed from projection images of virions.
NCBI-ID: 11599 / Sci species name: Hantaan virus / Virus type: VIRION / Virus isolate: STRAIN / Virus enveloped: Yes / Virus empty: No
Host (natural)Organism: Homo sapiens (human) / synonym: VERTEBRATES

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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: 0.01 M Tris, 0.1 M NaCl, and 0.001 M EDTA
GridDetails: 200 mesh holey carbon copper grids (R 2/2 Quantifoil; Micro Tools GmbH, Jena, Germany)
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER
Method: Small aliquots (3.5 microliters) of purified Hantaan virus particles were applied to holey carbon grids and vitrified in liquid ethane under BSL-3 conditions

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/ST
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 55600 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 33000
Sample stageSpecimen holder model: GATAN LIQUID NITROGEN
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at greater than 100,000 times magnification
DateSep 13, 2008
Image recordingCategory: CCD / Film or detector model: GENERIC TVIPS (4k x 4k) / Digitization - Sampling interval: 15.0 µm / Number real images: 105 / Average electron dose: 20 e/Å2 / Bits/pixel: 8

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Image processing

CTF correctionDetails: phase reversals corrected using applyctf in EMAN
Final two d classificationNumber classes: 412
Final angle assignmentDetails: SPIDER: theta 90 degrees, phi 90 degrees, delta theta for VO EA command=2.0
Final reconstructionApplied symmetry - Point group: C4 (4 fold cyclic) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 25.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: EMAN, SPIDER
Details: The Gn-Gc glycoprotein spike complex was reconstructed from projection images of intact virions. Four-fold symmetry was enforced in the final cycles of reconstruction.
Number images used: 9806

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