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- PDB-7kjp: Disulfide Stabilized Norovirus GI.1 VLP Shell Region -

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Basic information

Entry
Database: PDB / ID: 7kjp
TitleDisulfide Stabilized Norovirus GI.1 VLP Shell Region
ComponentsCapsid protein VP1
KeywordsVIRUS LIKE PARTICLE / Norovirus / Stabilized / VLP / Shell
Function / homology
Function and homology information


T=3 icosahedral viral capsid / host cell cytoplasm / identical protein binding
Similarity search - Function
Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Biological speciesNorwalk virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.86 Å
AuthorsGorman, J. / Kwong, P.D.
Funding support United States, 4items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM103310 United States
Other privateSF349247 (Simons Foundation) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)S10 OD019994-01 United States
Other privateF00316 (Agouron Institute) United States
CitationJournal: NPJ Vaccines / Year: 2020
Title: Disulfide stabilization of human norovirus GI.1 virus-like particles focuses immune response toward blockade epitopes.
Authors: Raffaello Verardi / Lisa C Lindesmith / Yaroslav Tsybovsky / Jason Gorman / Gwo-Yu Chuang / Caitlin E Edwards / Paul D Brewer-Jensen / Michael L Mallory / Li Ou / Arne Schön / Wei Shi / Ena ...Authors: Raffaello Verardi / Lisa C Lindesmith / Yaroslav Tsybovsky / Jason Gorman / Gwo-Yu Chuang / Caitlin E Edwards / Paul D Brewer-Jensen / Michael L Mallory / Li Ou / Arne Schön / Wei Shi / Ena S Tully / George Georgiou / Ralph S Baric / Peter D Kwong /
Abstract: Human noroviruses are non-enveloped, single-strand RNA viruses that cause pandemic outbreaks of acute gastroenteritis. A bivalent vaccine containing GI.1 and GII.4 virus-like particles (VLPs) has ...Human noroviruses are non-enveloped, single-strand RNA viruses that cause pandemic outbreaks of acute gastroenteritis. A bivalent vaccine containing GI.1 and GII.4 virus-like particles (VLPs) has been shown to be safe and highly immunogenic, but its efficacy and durability have been limited. Here, we show that norovirus GI.1 VLPs are unstable and contain a substantial fraction of dissociated VLP components. Broadly reactive, non-neutralizing antibodies isolated from vaccinated donors bound to the dissociated components, but not to the intact VLPs. Engineering of interprotomer disulfide bonds within the shell domain prevented disassembly of the VLPs, while preserving antibody accessibility to blockade epitopes. Without adjuvant, mice immunized with stabilized GI.1 VLPs developed faster blockade antibody titers compared to immunization with wild-type GI.1 VLPs. In addition, immunization with stabilized particles focused immune responses toward surface-exposed epitopes and away from occluded epitopes. Overall, disulfide-stabilized norovirus GI.1 VLPs elicited improved responses over the non-disulfide-stabilized version, suggesting their promise as candidate vaccines.
History
DepositionOct 26, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 2, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_ISSN / _citation.journal_volume ..._citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / em_3d_fitting_list / em_admin / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_struct_oper_list
Item: _citation.country / _database_2.pdbx_DOI ..._citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: Capsid protein VP1
B: Capsid protein VP1
C: Capsid protein VP1


Theoretical massNumber of molelcules
Total (without water)169,9953
Polymers169,9953
Non-polymers00
Water00
1
A: Capsid protein VP1
B: Capsid protein VP1
C: Capsid protein VP1
x 60


Theoretical massNumber of molelcules
Total (without water)10,199,693180
Polymers10,199,693180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Capsid protein VP1
B: Capsid protein VP1
C: Capsid protein VP1
x 5


  • icosahedral pentamer
  • 850 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)849,97415
Polymers849,97415
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein VP1
B: Capsid protein VP1
C: Capsid protein VP1
x 6


  • icosahedral 23 hexamer
  • 1.02 MDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)1,019,96918
Polymers1,019,96918
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein Capsid protein VP1 / CP / p59


Mass: 56664.961 Da / Num. of mol.: 3 / Fragment: shell region
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norwalk virus (strain GI/Human/United States/Norwalk/1968)
Strain: GI/Human/United States/Norwalk/1968 / Gene: ORF2 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q83884
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Norovirus Hu/1968/US / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Norovirus Hu/1968/US
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Details of virusEmpty: YES / Enveloped: NO / Isolate: OTHER / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Homo sapiens
Buffer solutionpH: 7.4
Buffer componentName: PBS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid type: C-flat-1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE

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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 / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 70.48 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 777

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Processing

SoftwareName: PHENIX / Version: 1.18.2_3874: / Classification: refinement
EM software
IDNameCategory
2Leginonimage acquisition
4CTFFINDCTF correction
7UCSF Chimeramodel fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
11cryoSPARCclassification
12cryoSPARC3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionResolution: 3.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 23476 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingProtocol: FLEXIBLE FIT / Space: REAL
Atomic model buildingPDB-ID: 1IHM

1ihm


Accession code: 1IHM / Source name: PDB / Type: experimental model
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0024089
ELECTRON MICROSCOPYf_angle_d0.4855601
ELECTRON MICROSCOPYf_dihedral_angle_d12.9431470
ELECTRON MICROSCOPYf_chiral_restr0.045644
ELECTRON MICROSCOPYf_plane_restr0.003737

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