+Open data
-Basic information
Entry | Database: PDB / ID: 5fyn | |||||||||
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Title | Sub-tomogram averaging of Tula virus glycoprotein spike | |||||||||
Components | PUUMALA VIRUS GN GLYCOPROTEIN | |||||||||
Keywords | VIRAL PROTEIN / TULA 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 | |||||||||
Biological species | PUUMALA VIRUS | |||||||||
Method | ELECTRON MICROSCOPY / electron tomography / cryo EM / Resolution: 15.6 Å | |||||||||
Authors | Li, S. / Rissanen, I. / Zeltina, A. / Hepojoki, J. / Raghwani, J. / Harlos, K. / Pybus, O.G. / Huiskonen, J.T. / Bowden, T.A. | |||||||||
Citation | Journal: 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5fyn.cif.gz | 136.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5fyn.ent.gz | 109.1 KB | Display | PDB format |
PDBx/mmJSON format | 5fyn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5fyn_validation.pdf.gz | 934.4 KB | Display | wwPDB validaton report |
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Full document | 5fyn_full_validation.pdf.gz | 940.6 KB | Display | |
Data in XML | 5fyn_validation.xml.gz | 28 KB | Display | |
Data in CIF | 5fyn_validation.cif.gz | 41.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fy/5fyn ftp://data.pdbj.org/pub/pdb/validation_reports/fy/5fyn | HTTPS FTP |
-Related structure data
Related structure data | 3364MC 5fxuC 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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-Components
#1: Protein | Mass: 38945.363 Da / Num. of mol.: 2 / Fragment: ECTODOMAIN, UNP RESIDUES 29-383 Source method: isolated from a genetically manipulated source Source: (gene. exp.) PUUMALA VIRUS / Plasmid: PHLSEC / Cell line (production host): HEK293 / Production host: HOMO SAPIENS (human) / References: UniProt: Q9WJ31 #2: Polysaccharide | alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | 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: electron tomography |
-Sample preparation
Component | Name: GLYCOPROTEIN SPIKE OF TULA HANTAVIRUS / Type: VIRUS |
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Buffer solution | Name: 25 MM TRIS, 75 MM NACL / pH: 8 / Details: 25 MM TRIS, 75 MM NACL |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: HOLEY CARBON |
Vitrification | Instrument: GATAN CRYOPLUNGE 3 / Cryogen name: ETHANE-PROPANE / Details: LIQUID ETHANE-PROPANE |
-Electron microscopy imaging
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
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Microscopy | Model: FEI POLARA 300 / Date: Aug 14, 2014 |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 160000 X / Calibrated magnification: 37037 X / Nominal defocus max: 3800 nm / Nominal defocus min: 2000 nm / Cs: 2 mm |
Specimen holder | Temperature: 100 K / Tilt angle max: 45 ° / Tilt angle min: -45 ° |
Image recording | Electron dose: 60 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
Image scans | Num. digital images: 30 |
-Processing
EM software |
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CTF correction | Details: EACH TILTED IMAGE | ||||||||||||||||||||
Symmetry | Point symmetry: C2 (2 fold cyclic) | ||||||||||||||||||||
3D reconstruction | Method: SUBTOMOGRAM AVERAGING / Resolution: 15.6 Å / Num. of particles: 5449 / Actual pixel size: 2.7 Å / Magnification calibration: KNOWN ATOMIC MODEL Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-3364. (DEPOSITION ID: 14310). Symmetry type: POINT | ||||||||||||||||||||
Atomic model building | Protocol: OTHER / Space: REAL / Target criteria: Cross-correlation coefficient Details: METHOD--LOCAL CORRELATION REFINEMENT PROTOCOL--X-RAY | ||||||||||||||||||||
Atomic model building | PDB-ID: 5FXU | ||||||||||||||||||||
Refinement | Highest resolution: 15.6 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 15.6 Å
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