+Open data
-Basic information
Entry | Database: PDB / ID: 6odf | |||||||||
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Title | EEEV glycoproteins bound with heparan sulfate | |||||||||
Components |
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Keywords | VIRUS / EEEV | |||||||||
Function / homology | Function and homology information togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host gene expression / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell ...togavirin / T=4 icosahedral viral capsid / symbiont-mediated suppression of host gene expression / symbiont-mediated suppression of host toll-like receptor signaling pathway / host cell cytoplasm / symbiont entry into host cell / serine-type endopeptidase activity / fusion of virus membrane with host endosome membrane / host cell nucleus / virion attachment to host cell / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / RNA binding / membrane / plasma membrane / cytoplasm Similarity search - Function | |||||||||
Biological species | Eastern equine encephalitis virus | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 5.8 Å | |||||||||
Authors | Rossmann, M.G. / Chen, C.L. | |||||||||
Funding support | United States, 1items
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Citation | Journal: Proc Natl Acad Sci U S A / Year: 2020 Title: Cryo-EM structure of eastern equine encephalitis virus in complex with heparan sulfate analogues. Authors: Chun-Liang Chen / S Saif Hasan / Thomas Klose / Yingyuan Sun / Geeta Buda / Chengqun Sun / William B Klimstra / Michael G Rossmann / Abstract: Eastern equine encephalitis virus (EEEV), a mosquito-borne icosahedral alphavirus found mainly in North America, causes human and equine neurotropic infections. EEEV neurovirulence is influenced by ...Eastern equine encephalitis virus (EEEV), a mosquito-borne icosahedral alphavirus found mainly in North America, causes human and equine neurotropic infections. EEEV neurovirulence is influenced by the interaction of the viral envelope protein E2 with heparan sulfate (HS) proteoglycans from the host's plasma membrane during virus entry. Here, we present a 5.8-Å cryoelectron microscopy (cryo-EM) structure of EEEV complexed with the HS analog heparin. "Peripheral" HS binding sites were found to be associated with the base of each of the E2 glycoproteins that form the 60 quasi-threefold spikes (q3) and the 20 sites associated with the icosahedral threefold axes (i3). In addition, there is one HS site at the vertex of each q3 and i3 spike (the "axial" sites). Both the axial and peripheral sites are surrounded by basic residues, suggesting an electrostatic mechanism for HS binding. These residues are highly conserved among EEEV strains, and therefore a change in these residues might be linked to EEEV neurovirulence. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6odf.cif.gz | 648.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6odf.ent.gz | 536.8 KB | Display | PDB format |
PDBx/mmJSON format | 6odf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6odf_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 6odf_full_validation.pdf.gz | 1.4 MB | Display | |
Data in XML | 6odf_validation.xml.gz | 102.5 KB | Display | |
Data in CIF | 6odf_validation.cif.gz | 158.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/6odf ftp://data.pdbj.org/pub/pdb/validation_reports/od/6odf | HTTPS FTP |
-Related structure data
Related structure data | 20019MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Symmetry | Point symmetry: (Schoenflies symbol: I (icosahedral)) |
-Components
#1: Protein | Mass: 47938.141 Da / Num. of mol.: 4 / Fragment: UNP residues 802-1242 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Eastern equine encephalitis virus / Cell line (production host): BHK-15 / Production host: Cricetinae gen. sp. (mammal) References: UniProt: E9KXM2, UniProt: Q4QXJ7*PLUS, togavirin #2: Protein | Mass: 47046.953 Da / Num. of mol.: 4 / Fragment: UNP residues 325-744 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Eastern equine encephalitis virus / Cell line (production host): BHK-15 / Production host: Cricetinae gen. sp. (mammal) References: UniProt: E9KXL2, UniProt: Q4QXJ7*PLUS, togavirin #3: Polysaccharide | 2-O-sulfo-beta-L-galactopyranuronic acid-(1-4)-[(2R,3R,4R,5R,6R)-2,4,5-trihydroxy-6-(sulfooxy) ...2-O-sulfo-beta-L-galactopyranuronic acid-(1-4)-[(2R,3R,4R,5R,6R)-2,4,5-trihydroxy-6-(sulfooxy)tetrahydro-2H-pyran-3-yl]sulfamic acid Type: oligosaccharide / Mass: 581.459 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: EEEV glycoproteins bound with heparan / Type: VIRUS / Entity ID: #1-#2 / Source: RECOMBINANT | ||||||||||||||||||||
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Molecular weight | Experimental value: NO | ||||||||||||||||||||
Source (natural) | Organism: Eastern equine encephalitis virus | ||||||||||||||||||||
Source (recombinant) | Organism: Cricetinae gen. sp. (mammal) / Cell: BHK-15 | ||||||||||||||||||||
Details of virus | Empty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRION | ||||||||||||||||||||
Buffer solution | pH: 8 / Details: Tris | ||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. | ||||||||||||||||||||
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE / Humidity: 80 % / Chamber temperature: 298 K |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 32 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 17022 | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: I (icosahedral) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 5.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 17022 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6MX4 |