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- PDB-7b09: Puumala virus glycoprotein (Gc) in complex with fab fragment P-4G2. -

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Basic information

Entry
Database: PDB / ID: 7b09
TitlePuumala virus glycoprotein (Gc) in complex with fab fragment P-4G2.
Components
  • (Envelope polyprotein) x 2
  • Heavy chain of fab fragment P-4G2
  • Light chain of fab fragment P-4G2
KeywordsVIRUS 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 / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / virion membrane ...symbiont-mediated suppression of host TRAF-mediated signal transduction / host cell Golgi membrane / host cell mitochondrion / host cell surface / symbiont-mediated suppression of host innate immune response / host cell endoplasmic reticulum membrane / fusion of virus membrane with host endosome membrane / symbiont entry into host cell / virion attachment to host cell / virion membrane / signal transduction / zinc ion binding / membrane
Similarity search - Function
Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / : / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / Hantavirus glycoprotein Gn, base / ITAM motif hantavirus type profile. / Hantavirus glycoprotein Gc / : ...Hantavirus glycoprotein Gn / ITAM motif, hantavirus type / Envelope glycoprotein precursor, Hantavirus / : / Hantavirus glycoprotein Gn, head / Hantavirus ITAM motif / Hantavirus glycoprotein Gn, base / ITAM motif hantavirus type profile. / Hantavirus glycoprotein Gc / : / Hantavirus glycoprotein Gc, N-terminal / Hantavirus glycoprotein Gc, C-terminal
Similarity search - Domain/homology
Envelopment polyprotein
Similarity search - Component
Biological speciesMyodes glareolus (Bank vole)
Puumala orthohantavirus
MethodELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 13.4 Å
AuthorsRissanen, I. / Stass, R. / Huiskonen, J.T. / Bowden, T.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
European Research Council (ERC)649053 United Kingdom
CitationJournal: 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
DepositionNov 19, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / em_admin / pdbx_entity_branch_descriptor / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_admin.last_update / _pdbx_entry_details.has_protein_modification

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Assembly

Deposited unit
H: Heavy chain of fab fragment P-4G2
L: Light chain of fab fragment P-4G2
A: Envelope polyprotein
B: Envelope polyprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)140,1837
Polymers138,7894
Non-polymers1,3943
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area8790 Å2
ΔGint-11 kcal/mol
Surface area53800 Å2
MethodPISA

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Components

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Protein , 2 types, 2 molecules AB

#3: Protein Envelope polyprotein / M polyprotein


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
#4: Protein Envelope polyprotein / M polyprotein


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

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Antibody , 2 types, 2 molecules HL

#1: Antibody Heavy chain of fab fragment P-4G2


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)
#2: Antibody Light chain of fab fragment P-4G2


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)

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Sugars , 3 types, 3 molecules

#5: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#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


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Details

Has ligand of interestN
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging

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Sample preparation

ComponentName: Puumala virus - Sotkamo / Type: VIRUS / Entity ID: #1-#3 / Source: RECOMBINANT
Source (natural)Organism: Puumala virus - Sotkamo
Source (recombinant)Organism: Homo sapiens (human)
Details of virusEmpty: YES / Enveloped: YES / Isolate: SPECIES / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Myodes glareolus
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid type: C-flat-2/1
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD
Image recordingElectron dose: 4.5 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM softwareName: Dynamo / Category: 3D reconstruction
CTF correctionType: PHASE FLIPPING ONLY
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 13.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1721 / Symmetry type: POINT
EM volume selectionNum. of tomograms: 56 / Num. of volumes extracted: 71216

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