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- PDB-8vkx: VX22 bound to GII.4 P domain -

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Basic information

Entry
Database: PDB / ID: 8vkx
TitleVX22 bound to GII.4 P domain
Components
  • VP1
  • VX22 heavy chain
  • VX22 light chain
KeywordsVIRAL PROTEIN/IMMUNE SYSTEM / norovirus / VP1 / monoclonal antibody / VIRAL PROTEIN / VIRAL PROTEIN-IMMUNE SYSTEM complex
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 / VP1
Function and homology information
Biological speciesHomo sapiens (human)
Norovirus Hu/GII.4/Sydney/NSW0514/2012/AU
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.35 Å
AuthorsOlia, A.S. / Park, J. / Lindesmith, L.C. / Kwong, P.D.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: To Be Published
Title: Mapping of molecular pathways to broadly protective human antibodies to GII.4 variants and GII genotypes of human norovirus.
Authors: Lindesmith, L.C. / Park, J. / Olia, A.S. / Kwong, P.D. / Georgiou, G. / Baric, R.S.
History
DepositionJan 10, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: VX22 heavy chain
L: VX22 light chain
A: VP1


Theoretical massNumber of molelcules
Total (without water)81,7713
Polymers81,7713
Non-polymers00
Water50428
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)114.326, 148.980, 148.872
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody VX22 heavy chain


Mass: 24892.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody VX22 light chain


Mass: 22904.469 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein VP1


Mass: 33973.883 Da / Num. of mol.: 1
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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / Source method: isolated from a natural source / Formula: H2O
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: 3.88 Å3/Da / Density % sol: 68.27 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1M LiSO4 15% PEG 8,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Mar 27, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.35→50 Å / Num. obs: 18184 / % possible obs: 96.5 % / Redundancy: 3.9 % / CC1/2: 0.933 / Rmerge(I) obs: 0.198 / Rpim(I) all: 0.114 / Rrim(I) all: 0.23 / Net I/σ(I): 4.1
Reflection shellResolution: 3.35→3.41 Å / Rmerge(I) obs: 0.628 / Mean I/σ(I) obs: 1 / Num. unique obs: 907 / CC1/2: 0.629 / Rpim(I) all: 0.372 / Rrim(I) all: 0.735

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.35→50 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2715 --
Rwork0.2447 --
obs-17791 94.43 %
Displacement parametersBiso mean: 59.92 Å2
Refinement stepCycle: LAST / Resolution: 3.35→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5640 0 0 28 5668
LS refinement shellResolution: 3.35→3.43 Å
RfactorNum. reflection% reflection
Rfree0.3356 130 -
Rwork0.3168 1176 -
obs--93 %

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