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- PDB-12tr: 2 molecules of Fab NORO-320 bound to C-D VP1 dimer of GII.4 Syd V... -

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Basic information

Entry
Database: PDB / ID: 12tr
Title2 molecules of Fab NORO-320 bound to C-D VP1 dimer of GII.4 Syd VLP (T=4)
Components
  • Fab NORO-320 Heavy Chain
  • Fab NORO-320 Light Chain
  • VP1
KeywordsVIRUS LIKE PARTICLE / Norovirus / Sydney / VLP / Capsid / Antibody
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 / host cell cytoplasm / VP1
Function and homology information
Biological speciesNorovirus Hu/GII.4/Sydney/NSW0514/2012/AU
Homo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.28 Å
AuthorsApostol, C.V. / Anish, R. / Pham, S. / Prasad, B.V.V.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)P01 AI057788 United States
CitationJournal: Res Sq / Year: 2026
Title: Symmetry-breaking antibody binding reveals extensive capsid malleability in pandemic human norovirus.
Authors: Carmen V Apostol / Ramakrishnan Anish / Son Pham / Khalil Ettayebi / Janam Dave / Frederick H Neill / Marina Bok / Banumathi Sankaran / Sue Crawford / Robert L Atmar / James E Crowe / ...Authors: Carmen V Apostol / Ramakrishnan Anish / Son Pham / Khalil Ettayebi / Janam Dave / Frederick H Neill / Marina Bok / Banumathi Sankaran / Sue Crawford / Robert L Atmar / James E Crowe / Viviana Parreño / Mary K Estes / B V Venkataram Prasad /
Abstract: Virus capsids are metastable assemblies with an exquisite balance between stability and flexibility, obligatory for entry, infectivity, and immune escape. Yet, the extent to which human viruses ...Virus capsids are metastable assemblies with an exquisite balance between stability and flexibility, obligatory for entry, infectivity, and immune escape. Yet, the extent to which human viruses exploit capsid plasticity and how that consequently shapes antigenic landscapes remains poorly understood. Human noroviruses (HuNoVs) are the leading cause of acute viral gastroenteritis worldwide. GII.4 HuNoVs have been evolving epochally, driving most global pandemics, and since 2012, GII.4 Sydney has been the dominant variant. The major capsid protein VP1 is central to infectivity and immune recognition, and VP1-based virus-like particles (VLPs) are considered promising vaccine candidates. Yet, how the icosahedral HuNoV capsid responds to antibody pressure at the atomic level is still unclear. Here, we present the first atomic structure of GII.4 Sydney capsid determined by cryo-EM, revealing the structural features that likely contribute to its sustained dominance. Using focused refinement, we uncovered the remarkable capsid plasticity in response to symmetry-breaking binding of neutralizing and non-neutralizing antibodies. VP1 adopts 11 distinct conformational modalities to accommodate asymmetric antibody binding, and antibody-disrupted VLPs reassemble into smaller particles with five additional VP1 states. This previously unrecognized extent of conformational adaptability provides key insights for designing next-generation VLP- or mRNA-based vaccines targeting HuNoV infections.
History
DepositionApr 18, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2026Provider: repository / Type: Initial release
Revision 1.0Oct 28, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
C: VP1
D: VP1
E: Fab NORO-320 Heavy Chain
F: Fab NORO-320 Light Chain
G: Fab NORO-320 Heavy Chain
H: Fab NORO-320 Light Chain


Theoretical massNumber of molelcules
Total (without water)216,5306
Polymers216,5306
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein VP1


Mass: 59157.246 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/GII.4/Sydney/NSW0514/2012/AU
Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: K4LM89
#2: Antibody Fab NORO-320 Heavy Chain


Mass: 25202.338 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody Fab NORO-320 Light Chain


Mass: 23905.609 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster)
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 / Type: VIRUS / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Norovirus
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Details of virusEmpty: YES / Enveloped: YES / Isolate: STRAIN / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Norovirus Hu/GII.4/Sydney/NSW0514/2012/AU
Virus shellName: VP1 / Diameter: 420 nm / Triangulation number (T number): 3
Buffer solutionpH: 6 / Details: 1X PBS
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 291 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 130000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm
Specimen holderCryogen: NITROGEN
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3290
Details: Images were collected in movie mode at 35 frames per second
EM imaging opticsEnergyfilter name: GIF Bioquantum

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Processing

EM software
IDNameVersionCategory
1cryoSPARCv4.7.0particle selection
2PHENIX2.0_5824model refinement
3EPU3.14image acquisition
5cryoSPARCv4.7.0CTF correction
10cryoSPARCv4.7.0initial Euler assignment
11cryoSPARCv4.7.0final Euler assignment
13cryoSPARCv4.7.03D reconstruction
CTF correctionType: NONE
3D reconstructionResolution: 6.28 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 22827 / Symmetry type: POINT
RefinementHighest resolution: 6.28 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00314603
ELECTRON MICROSCOPYf_angle_d0.69619946
ELECTRON MICROSCOPYf_dihedral_angle_d5.9011985
ELECTRON MICROSCOPYf_chiral_restr0.0482229
ELECTRON MICROSCOPYf_plane_restr0.0072609

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