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

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Basic information

Entry
Database: PDB / ID: 11hb
TitleCrystal structure of a GII.4 norovirus capsid P domain in complex with neutralizing antibody 17A5
Components
  • 17A5 Heavy Chain
  • 17A5 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: 3.36 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
L: 17A5 Light Chain
H: 17A5 Heavy Chain
B: Major capsid protein VP1
C: 17A5 Light Chain
D: 17A5 Heavy Chain
E: Major capsid protein VP1
K: 17A5 Light Chain
G: 17A5 Heavy Chain


Theoretical massNumber of molelcules
Total (without water)251,8969
Polymers251,8969
Non-polymers00
Water00
1
A: Major capsid protein VP1
L: 17A5 Light Chain
H: 17A5 Heavy Chain

E: Major capsid protein VP1
K: 17A5 Light Chain
G: 17A5 Heavy Chain


Theoretical massNumber of molelcules
Total (without water)167,9316
Polymers167,9316
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x+1/2,y-1/2,-z1
2
B: Major capsid protein VP1
C: 17A5 Light Chain
D: 17A5 Heavy Chain

B: Major capsid protein VP1
C: 17A5 Light Chain
D: 17A5 Heavy Chain


Theoretical massNumber of molelcules
Total (without water)167,9316
Polymers167,9316
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Unit cell
Length a, b, c (Å)271.954, 134.910, 133.913
Angle α, β, γ (deg.)90.000, 91.753, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z

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Components

#1: Protein Major capsid protein VP1


Mass: 34560.484 Da / Num. of mol.: 3
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 17A5 Light Chain


Mass: 24786.473 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Cricetulus griseus (Chinese hamster)
#3: Antibody 17A5 Heavy Chain


Mass: 24618.529 Da / Num. of mol.: 3
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: 4.87 Å3/Da / Density % sol: 74.76 %
Crystal growTemperature: 297.15 K / Method: vapor diffusion, hanging drop / pH: 4.6 / Details: 0.1M Sodium Acetate, 2M Sodium formate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.97648 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 15, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97648 Å / Relative weight: 1
ReflectionResolution: 3.36→48.43 Å / Num. obs: 68516 / % possible obs: 98.4 % / Redundancy: 6.9 % / CC1/2: 0.982 / Net I/σ(I): 7.4
Reflection shellResolution: 3.36→3.44 Å / Num. unique obs: 68516 / CC1/2: 0.415

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Processing

Software
NameVersionClassification
PHENIX1.21.1_5286refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.36→48.43 Å / SU ML: 0.6874 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 33.8374
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2996 6683 5.01 %
Rwork0.2577 126663 -
obs0.2598 68516 98.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 104.89 Å2
Refinement stepCycle: LAST / Resolution: 3.36→48.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16393 0 0 0 16393
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.002216836
X-RAY DIFFRACTIONf_angle_d0.504322976
X-RAY DIFFRACTIONf_chiral_restr0.04042573
X-RAY DIFFRACTIONf_plane_restr0.00372957
X-RAY DIFFRACTIONf_dihedral_angle_d9.37375978
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.36-3.40.46432230.39214080X-RAY DIFFRACTION96.65
3.4-3.440.45412180.38824102X-RAY DIFFRACTION94.72
3.44-3.480.43782290.38464043X-RAY DIFFRACTION95.34
3.48-3.520.40882460.36344236X-RAY DIFFRACTION97.37
3.52-3.570.40312500.36214134X-RAY DIFFRACTION98.23
3.57-3.620.36992030.34434264X-RAY DIFFRACTION97.94
3.62-3.670.41112200.37483916X-RAY DIFFRACTION93.15
3.67-3.730.39211770.36714256X-RAY DIFFRACTION96.54
3.73-3.780.38852060.33644243X-RAY DIFFRACTION99.55
3.78-3.850.38422190.32734305X-RAY DIFFRACTION99.78
3.85-3.910.40052010.36934213X-RAY DIFFRACTION98.09
3.91-3.980.3792290.32274277X-RAY DIFFRACTION99.51
3.98-4.060.35962060.29374341X-RAY DIFFRACTION99.45
4.06-4.140.32432470.25844163X-RAY DIFFRACTION99.64
4.14-4.230.29732190.25634327X-RAY DIFFRACTION99.67
4.23-4.330.27062070.24524321X-RAY DIFFRACTION99.65
4.33-4.440.27512210.22934281X-RAY DIFFRACTION99.56
4.44-4.560.25482780.20764159X-RAY DIFFRACTION99.44
4.56-4.690.29182350.22454258X-RAY DIFFRACTION99.51
4.69-4.840.25172060.20864301X-RAY DIFFRACTION99.34
4.85-5.020.23612420.20994260X-RAY DIFFRACTION99.25
5.02-5.220.25792710.22334198X-RAY DIFFRACTION99.13
5.22-5.460.30852550.22414103X-RAY DIFFRACTION96.69
5.46-5.740.27512320.23984273X-RAY DIFFRACTION99.49
5.74-6.10.24042280.22324291X-RAY DIFFRACTION99.63
6.1-6.570.28682260.2294260X-RAY DIFFRACTION99.42
6.57-7.230.27422080.23614270X-RAY DIFFRACTION99.25
7.23-8.270.28181880.21914283X-RAY DIFFRACTION99.05
8.27-10.410.21722140.19334246X-RAY DIFFRACTION98.48
10.41-48.430.22811790.22444259X-RAY DIFFRACTION98.27

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