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Yorodumi- EMDB-2056: Electron cryo-microscopy of the Hantaan virus glycoprotein spike -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2056 | |||||||||
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Title | Electron cryo-microscopy of the Hantaan virus glycoprotein spike | |||||||||
Map data | Reconstruction of the Hantaan virus Gn-Gc glycoprotein spike complex | |||||||||
Sample |
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Keywords | glycoprotein 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 / 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 | |||||||||
Biological species | Hantaan virus | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 25.0 Å | |||||||||
Authors | Battisti AJ / Chu YK / Chipman PR / Kaufmann B / Jonsson CB / Rossmann MG | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2056.map.gz | 1.3 MB | EMDB map data format | |
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Header (meta data) | emd-2056-v30.xml emd-2056.xml | 9.2 KB 9.2 KB | Display Display | EMDB header |
Images | emd_2056.tif | 255.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2056 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2056 | HTTPS FTP |
-Validation report
Summary document | emd_2056_validation.pdf.gz | 218.5 KB | Display | EMDB validaton report |
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Full document | emd_2056_full_validation.pdf.gz | 217.7 KB | Display | |
Data in XML | emd_2056_validation.xml.gz | 4.9 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2056 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2056 | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_2056.map.gz / Format: CCP4 / Size: 1.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Reconstruction of the Hantaan virus Gn-Gc glycoprotein spike complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 5.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Hantaan virus Gn-Gc glycoprotein spike complex
Entire | Name: Hantaan virus Gn-Gc glycoprotein spike complex |
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Components |
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-Supramolecule #1000: Hantaan virus Gn-Gc glycoprotein spike complex
Supramolecule | Name: Hantaan virus Gn-Gc glycoprotein spike complex / type: sample / ID: 1000 / Oligomeric state: tetramer of Gn-Gc heterodimers / Number unique components: 1 |
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Molecular weight | Theoretical: 392 KDa |
-Supramolecule #1: Hantaan virus
Supramolecule | Name: 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 |
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Host (natural) | Organism: Homo sapiens (human) / synonym: VERTEBRATES |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 / Details: 0.01 M Tris, 0.1 M NaCl, and 0.001 M EDTA |
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Grid | Details: 200 mesh holey carbon copper grids (R 2/2 Quantifoil; Micro Tools GmbH, Jena, Germany) |
Vitrification | Cryogen 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 |
-Electron microscopy
Microscope | FEI/PHILIPS CM300FEG/ST |
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Alignment procedure | Legacy - Astigmatism: Objective lens astigmatism was corrected at greater than 100,000 times magnification |
Date | Sep 13, 2008 |
Image recording | Category: 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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 55600 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 6.0 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 33000 |
Sample stage | Specimen holder model: GATAN LIQUID NITROGEN |
-Image processing
CTF correction | Details: phase reversals corrected using applyctf in EMAN |
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Final reconstruction | Applied 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 |
Final angle assignment | Details: SPIDER: theta 90 degrees, phi 90 degrees, delta theta for VO EA command=2.0 |
Final two d classification | Number classes: 412 |