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- PDB-11ha: Crystal structure of a GII.4 norovirus capsid P domain in complex... -

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Basic information

Entry
Database: PDB / ID: 11ha
TitleCrystal structure of a GII.4 norovirus capsid P domain in complex with neutralizing antibody 24C10
Components
  • 24C10 Heavy Chain
  • 24C10 Light Chain
  • Major capsid protein VP1
KeywordsVIRAL PROTEIN / Norovirus GII.4 / P domain / Capsid protein / Antibody
Function / homologyCalicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / virion component / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / host cell cytoplasm / Major capsid protein VP1
Function and homology information
Biological speciesNorovirus GII.4 Sydney 2012
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGhosh, A. / DuBois, R.M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)R21AI180523 United States
CitationJournal: Res Sq / Year: 2026
Title: Structural and genetic analysis of neutralizing antibodies reveals mechanisms of GII.4 norovirus antigenic evolution.
Authors: Parra, G. / Pilewski, K. / Ghosh, A. / Tohma, K. / Ford-Siltz, L. / Hernandez, A. / Pajuelo, M. / Landivar, M. / DuBois, R.
History
DepositionFeb 23, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major capsid protein VP1
B: Major capsid protein VP1
L: 24C10 Light Chain
H: 24C10 Heavy Chain
K: 24C10 Light Chain
G: 24C10 Heavy Chain


Theoretical massNumber of molelcules
Total (without water)165,1496
Polymers165,1496
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.117, 56.428, 182.117
Angle α, β, γ (deg.)90.000, 99.574, 90.000
Int Tables number4
Space group name H-MP1211
Space group name HallP2yb
Symmetry operation#1: x,y,z
#2: -x,y+1/2,-z

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Components

#1: Protein Major capsid protein VP1


Mass: 34560.484 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus GII.4 Sydney 2012 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A1P8DD09
#2: Antibody 24C10 Light Chain


Mass: 23352.721 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody 24C10 Heavy Chain


Mass: 24661.506 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
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: 2.7 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 297.15 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.2 M HEPES: NaOH, pH 7.5, 8 % (w/v) PEG 8000, 8 % (v/v) Ethylene Glycol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 16, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.7→47.78 Å / Num. obs: 49114 / % possible obs: 99.8 % / Redundancy: 13.6 % / Biso Wilson estimate: 53.6 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.1463 / Net I/σ(I): 12.22
Reflection shellResolution: 2.7→2.77 Å / Num. unique obs: 3474 / CC1/2: 0.723

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
DIALSdata reduction
DIALSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→47.78 Å / SU ML: 0.3518 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.5415
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2455 1992 4.06 %
Rwork0.2084 47115 -
obs0.2099 49107 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 59.52 Å2
Refinement stepCycle: LAST / Resolution: 2.7→47.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11181 0 0 0 11181
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003711502
X-RAY DIFFRACTIONf_angle_d0.683715703
X-RAY DIFFRACTIONf_chiral_restr0.04771736
X-RAY DIFFRACTIONf_plane_restr0.00552029
X-RAY DIFFRACTIONf_dihedral_angle_d13.71674088
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.770.32961360.28243338X-RAY DIFFRACTION100
2.77-2.840.33621450.27013342X-RAY DIFFRACTION99.18
2.84-2.930.30891360.27373309X-RAY DIFFRACTION100
2.93-3.020.3171420.26273303X-RAY DIFFRACTION99.37
3.02-3.130.32251390.25213373X-RAY DIFFRACTION99.89
3.13-3.250.31591430.25053325X-RAY DIFFRACTION99.71
3.25-3.40.2751480.23473329X-RAY DIFFRACTION99.71
3.4-3.580.2581360.23033354X-RAY DIFFRACTION99.8
3.58-3.810.28811400.21763345X-RAY DIFFRACTION99.89
3.81-4.10.23261390.20833383X-RAY DIFFRACTION99.94
4.1-4.510.21961400.17023367X-RAY DIFFRACTION100
4.51-5.160.1891500.16363424X-RAY DIFFRACTION99.97
5.16-6.50.20011420.18793398X-RAY DIFFRACTION100
6.5-47.780.19961560.18053525X-RAY DIFFRACTION99.81

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