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Yorodumi- PDB-7b09: Puumala virus glycoprotein (Gc) in complex with fab fragment P-4G2. -
+Open data
-Basic information
Entry | Database: PDB / ID: 7b09 | ||||||
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Title | Puumala virus glycoprotein (Gc) in complex with fab fragment P-4G2. | ||||||
Components |
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Keywords | VIRUS LIKE PARTICLE / VLP / virus-like particle / Puumala / PUUV / glycoprotein / spike / fab / P-4G2 / antibody / epitope | ||||||
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 | Myodes glareolus (Bank vole) Puumala orthohantavirus | ||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 13.4 Å | ||||||
Authors | Rissanen, I. / Stass, R. / Huiskonen, J.T. / Bowden, T.A. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: Elife / Year: 2020 Title: Molecular rationale for antibody-mediated targeting of the hantavirus fusion glycoprotein. Authors: Ilona Rissanen / Robert Stass / Stefanie A Krumm / Jeffrey Seow / Ruben Jg Hulswit / Guido C Paesen / Jussi Hepojoki / Olli Vapalahti / Åke Lundkvist / Olivier Reynard / Viktor Volchkov / ...Authors: Ilona Rissanen / Robert Stass / Stefanie A Krumm / Jeffrey Seow / Ruben Jg Hulswit / Guido C Paesen / Jussi Hepojoki / Olli Vapalahti / Åke Lundkvist / Olivier Reynard / Viktor Volchkov / Katie J Doores / Juha T Huiskonen / Thomas A Bowden / Abstract: The intricate lattice of Gn and Gc glycoprotein spike complexes on the hantavirus envelope facilitates host-cell entry and is the primary target of the neutralizing antibody-mediated immune response. ...The intricate lattice of Gn and Gc glycoprotein spike complexes on the hantavirus envelope facilitates host-cell entry and is the primary target of the neutralizing antibody-mediated immune response. Through study of a neutralizing monoclonal antibody termed mAb P-4G2, which neutralizes the zoonotic pathogen Puumala virus (PUUV), we provide a molecular-level basis for antibody-mediated targeting of the hantaviral glycoprotein lattice. Crystallographic analysis demonstrates that P-4G2 binds to a multi-domain site on PUUV Gc and may preclude fusogenic rearrangements of the glycoprotein that are required for host-cell entry. Furthermore, cryo-electron microscopy of PUUV-like particles in the presence of P-4G2 reveals a lattice-independent configuration of the Gc, demonstrating that P-4G2 perturbs the (Gn-Gc) lattice. This work provides a structure-based blueprint for rationalizing antibody-mediated targeting of 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 | 7b09.cif.gz | 461.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7b09.ent.gz | 388.7 KB | Display | PDB format |
PDBx/mmJSON format | 7b09.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7b09_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7b09_full_validation.pdf.gz | 1.2 MB | Display | |
Data in XML | 7b09_validation.xml.gz | 41.9 KB | Display | |
Data in CIF | 7b09_validation.cif.gz | 63.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b0/7b09 ftp://data.pdbj.org/pub/pdb/validation_reports/b0/7b09 | HTTPS FTP |
-Related structure data
Related structure data | 11964MC 6z06C 7b0aC 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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1 |
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-Components
-Protein , 2 types, 2 molecules AB
#3: Protein | Mass: 49827.898 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Puumala orthohantavirus / Gene: gpc / Production host: Homo sapiens (human) / References: UniProt: Q9WJ31 |
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#4: Protein | Mass: 40061.566 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Puumala orthohantavirus / Gene: gpc / Production host: Homo sapiens (human) / References: UniProt: Q9WJ31 |
-Antibody , 2 types, 2 molecules HL
#1: Antibody | Mass: 25018.047 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myodes glareolus (Bank vole) / Production host: Homo sapiens (human) |
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#2: Antibody | Mass: 23881.582 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Myodes glareolus (Bank vole) / Production host: Homo sapiens (human) |
-Sugars , 3 types, 3 molecules
#5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose |
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#6: 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 |
#7: Sugar | ChemComp-NAG / |
-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging |
-Sample preparation
Component | Name: Puumala virus - Sotkamo / Type: VIRUS / Entity ID: #1-#3 / Source: RECOMBINANT |
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Source (natural) | Organism: Puumala virus - Sotkamo |
Source (recombinant) | Organism: Homo sapiens (human) |
Details of virus | Empty: YES / Enveloped: YES / Isolate: SPECIES / Type: VIRUS-LIKE PARTICLE |
Natural host | Organism: Myodes glareolus |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid type: C-flat-2/1 |
Vitrification | Cryogen name: ETHANE-PROPANE |
-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 |
Image recording | Electron dose: 4.5 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software | Name: Dynamo / Category: 3D reconstruction |
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CTF correction | Type: PHASE FLIPPING ONLY |
Symmetry | Point symmetry: C4 (4 fold cyclic) |
3D reconstruction | Resolution: 13.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1721 / Symmetry type: POINT |
EM volume selection | Num. of tomograms: 56 / Num. of volumes extracted: 71216 |