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- PDB-7mry: Norovirus T=3 GII.4 HOV VLP -

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Basic information

Entry
Database: PDB / ID: 7mry
TitleNorovirus T=3 GII.4 HOV VLP
ComponentsVP1
KeywordsVIRUS / T=3 Capsid GII.4 HOV Norovirus
Function / homologyCalicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / VP1
Function and homology information
Biological speciesNorovirus GII.4
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsSalmen, W. / Hu, L. / Prasad, B.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI057788 United States
CitationJournal: Nat Commun / Year: 2022
Title: Atomic structure of the predominant GII.4 human norovirus capsid reveals novel stability and plasticity.
Authors: Liya Hu / Wilhelm Salmen / Rong Chen / Yi Zhou / Frederick Neill / James E Crowe / Robert L Atmar / Mary K Estes / B V Venkataram Prasad /
Abstract: Human noroviruses (HuNoVs) cause sporadic and epidemic viral gastroenteritis worldwide. The GII.4 variants are responsible for most HuNoV infections, and GII.4 virus-like particles (VLPs) are being ...Human noroviruses (HuNoVs) cause sporadic and epidemic viral gastroenteritis worldwide. The GII.4 variants are responsible for most HuNoV infections, and GII.4 virus-like particles (VLPs) are being used in vaccine development. The atomic structure of the GII.4 capsid in the native T = 3 state has not been determined. Here we present the GII.4 VLP structure with T = 3 symmetry determined using X-ray crystallography and cryo-EM at 3.0 Å and 3.8 Å resolution, respectively, which reveals unanticipated novel features. A novel aspect in the crystal structure determined without imposing icosahedral symmetry is the remarkable adaptability of the capsid protein VP1 driven by the flexible hinge between the shell and the protruding domains. In both crystal and cryo-EM structures, VP1 adopts a stable conformation with the protruding domain resting on the shell domain, in contrast to the 'rising' conformation observed in recent cryo-EM structures of other GII.4 VLPs. Our studies further revealed that the resting state of VP1 dimer is stabilized by a divalent ion, and chelation using EDTA increases capsid diameter, exposing new hydrophobic and antigenic sites and suggesting a transition to the rising conformation. These novel insights into GII.4 capsid structure, stability, and antigen presentation may be useful for ongoing vaccine development.
History
DepositionMay 10, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Mar 15, 2023Group: 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.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Movie
  • 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
  • EMDB-23960
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  • Superimposition on EM map
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Structure viewerMolecule:
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Assembly

Deposited unit
A: VP1
B: VP1
C: VP1


Theoretical massNumber of molelcules
Total (without water)176,2833
Polymers176,2833
Non-polymers00
Water905
1
A: VP1
B: VP1
C: VP1
x 60


Theoretical massNumber of molelcules
Total (without water)10,576,961180
Polymers10,576,961180
Non-polymers00
Water3,243180
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: VP1
B: VP1
C: VP1
x 5


  • icosahedral pentamer
  • 881 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)881,41315
Polymers881,41315
Non-polymers00
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: VP1
B: VP1
C: VP1
x 6


  • icosahedral 23 hexamer
  • 1.06 MDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)1,057,69618
Polymers1,057,69618
Non-polymers00
Water32418
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 VP1


Mass: 58760.895 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus GII.4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: A9YYE4
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: H2O

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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 GII.4 / Type: VIRUS / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Norovirus GII.4
Source (recombinant)Organism: Trichoplusia ni (cabbage looper)
Details of virusEmpty: YES / Enveloped: NO / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Buffer solutionpH: 6
SpecimenConc.: 0.96 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: JEOL 3200FSC
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: SPOT SCAN
Electron lensMode: BRIGHT FIELDBright-field microscopy
Image recordingAverage exposure time: 10 sec. / Electron dose: 55.96 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

Software
NameVersionClassificationNB
phenix.real_space_refine1.19.2_4158refinement
PHENIX1.19.2_4158refinement
EM software
IDNameVersionCategory
9cryoSPARC2.15.0initial Euler assignment
10cryoSPARC2.15.0final Euler assignment
12cryoSPARC2.15.03D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 51913
Details: Using Cryosparc GSFSC, resolution calculated: No Mask = 4.2 A, Spherical = 4 A, Loose = 3.9 A, Tight = 3.8 A, corrected = 3.8 A
Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 76.67 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002411680
ELECTRON MICROSCOPYf_angle_d0.534416028
ELECTRON MICROSCOPYf_chiral_restr0.04351781
ELECTRON MICROSCOPYf_plane_restr0.00442138
ELECTRON MICROSCOPYf_dihedral_angle_d3.99351559

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