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- PDB-12pg: GII.3 P-domain in complex with M6 Nanobody -

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Basic information

Entry
Database: PDB / ID: 12pg
TitleGII.3 P-domain in complex with M6 Nanobody
Components
  • M6
  • VP1
KeywordsVIRAL PROTEIN / P-domain / nanobody / Norovirus
Function / homology:
Function and homology information
Biological speciesNorovirus Hu/Texas/TCH04-577/2004/US
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsApostol, C.V. / Anish, R. / Pham, S. / Sankaran, B. / 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 14, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 28, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
E: VP1
C: M6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9623
Polymers48,9262
Non-polymers351
Water3,279182
1
E: VP1
hetero molecules

E: VP1
hetero molecules

C: M6

C: M6


Theoretical massNumber of molelcules
Total (without water)97,9236
Polymers97,8524
Non-polymers712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_554-y,-x,-z-1/61
crystal symmetry operation5_444y-1,-x+y-1,z-1/61
crystal symmetry operation8_665x-y+1,-y+1,-z1
Unit cell
Length a, b, c (Å)87.300, 87.300, 225.830
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6
Components on special symmetry positions
IDModelComponents
11E-848-

HOH

21E-862-

HOH

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Components

#1: Protein VP1


Mass: 35617.637 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/Texas/TCH04-577/2004/US
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: B2DD27
#2: Antibody M6


Mass: 13308.611 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 182 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 300mM succinic acid 100mM citric acid NaOH, pH 3.5 22.5% PurePEGs cocktail 10mM phenol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.2 / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS3 S 2M / Detector: PIXEL / Date: Dec 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.2→45.24 Å / Num. obs: 26770 / % possible obs: 100 % / Redundancy: 30 % / Biso Wilson estimate: 33.23 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 14.8
Reflection shellResolution: 2.2→2.24 Å / Rmerge(I) obs: 0.785 / Num. unique obs: 1307

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→45.24 Å / SU ML: 0.2222 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.9052
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2301 1339 5 %
Rwork0.2016 25423 -
obs0.203 26762 99.99 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.45 Å2
Refinement stepCycle: LAST / Resolution: 2.2→45.24 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3300 0 1 182 3483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043386
X-RAY DIFFRACTIONf_angle_d0.65384613
X-RAY DIFFRACTIONf_chiral_restr0.0475498
X-RAY DIFFRACTIONf_plane_restr0.0052615
X-RAY DIFFRACTIONf_dihedral_angle_d13.01051222
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.280.25751300.23592467X-RAY DIFFRACTION99.96
2.28-2.370.25431320.22332498X-RAY DIFFRACTION100
2.37-2.480.28781300.22182467X-RAY DIFFRACTION100
2.48-2.610.2551300.21642492X-RAY DIFFRACTION100
2.61-2.770.261320.2212505X-RAY DIFFRACTION99.96
2.77-2.990.28851330.22332511X-RAY DIFFRACTION100
2.99-3.290.21921320.20832531X-RAY DIFFRACTION100
3.29-3.760.20091360.18712561X-RAY DIFFRACTION100
3.76-4.740.1731370.15982602X-RAY DIFFRACTION100
4.74-45.240.25811470.21612789X-RAY DIFFRACTION99.93

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