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- PDB-7vs9: Crystal structure of P domain from norovirus GI.9 capsid protein ... -

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Basic information

Entry
Database: PDB / ID: 7vs9
TitleCrystal structure of P domain from norovirus GI.9 capsid protein in complex with Lewis x antigen.
ComponentsVP1
KeywordsVIRAL PROTEIN / norovirus / p-domain / capsid / histo blood group antigen
Function / homology
Function and homology information


virion component / host cell cytoplasm / metal ion binding
Similarity search - Function
Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit
Similarity search - Domain/homology
Lewis X antigen, alpha anomer / VP1
Similarity search - Component
Biological speciesNorovirus Hu/GI/Vancouver730/2004/CAN
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.26 Å
AuthorsMurayama, K. / Kato-Murayama, M. / Shirouzu, M.
Funding support Japan, 1items
OrganizationGrant numberCountry
Japan Agency for Medical Research and Development (AMED) Japan
CitationJournal: Febs Open Bio / Year: 2022
Title: Lewis fucose is a key moiety for the recognition of histo-blood group antigens by GI.9 norovirus, as revealed by structural analysis.
Authors: Kimura-Someya, T. / Kato-Murayama, M. / Katsura, K. / Sakai, N. / Murayama, K. / Hanada, K. / Shirouzu, M. / Someya, Y.
History
DepositionOct 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 31, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: VP1
B: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,23122
Polymers67,5562
Non-polymers1,67520
Water9,422523
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7280 Å2
ΔGint-147 kcal/mol
Surface area23880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.200, 77.244, 103.526
Angle α, β, γ (deg.)90.00, 124.20, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein VP1 / capsid protein


Mass: 33777.852 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/GI/Vancouver730/2004/CAN / Details (production host): Cell-free protein synthesis / Production host: Escherichia coli (E. coli) / References: UniProt: F2XMU3
#2: Polysaccharide alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 529.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with branches / References: Lewis X antigen, alpha anomer
DescriptorTypeProgram
LFucpa1-3[DGalpb1-4]DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5]/1-2-3/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 523 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 4.51 Å3/Da / Density % sol: 72.72 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 9 / Details: magnesium chloride, Bicine, pH 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E SUPERBRIGHT / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Feb 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 56256 / % possible obs: 99.6 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.088 / Rrim(I) all: 0.103 / Net I/σ(I): 15.3
Reflection shellResolution: 2.26→2.34 Å / Rmerge(I) obs: 0.349 / Num. unique obs: 5539 / Rrim(I) all: 0.411

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7VP0

7vp0


Resolution: 2.26→35.207 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1945 2010 3.57 %
Rwork0.165 --
obs0.1661 56237 99.53 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.26→35.207 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4738 0 90 523 5351
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084960
X-RAY DIFFRACTIONf_angle_d0.9316824
X-RAY DIFFRACTIONf_dihedral_angle_d7.8732922
X-RAY DIFFRACTIONf_chiral_restr0.057780
X-RAY DIFFRACTIONf_plane_restr0.006902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.26-2.31630.24731430.20373777X-RAY DIFFRACTION98
2.3163-2.37890.29751410.1963863X-RAY DIFFRACTION99
2.3789-2.44890.20991410.19423800X-RAY DIFFRACTION99
2.4489-2.5280.2721410.1953845X-RAY DIFFRACTION99
2.528-2.61830.23131420.19093835X-RAY DIFFRACTION100
2.6183-2.72310.2171430.19763872X-RAY DIFFRACTION100
2.7231-2.8470.25761430.19123900X-RAY DIFFRACTION100
2.847-2.9970.21241470.18233829X-RAY DIFFRACTION100
2.997-3.18460.19271450.17543881X-RAY DIFFRACTION100
3.1846-3.43030.18571430.16963893X-RAY DIFFRACTION100
3.4303-3.77520.1821410.15543887X-RAY DIFFRACTION100
3.7752-4.32060.20371460.13493939X-RAY DIFFRACTION100
4.3206-5.44030.12931440.12733915X-RAY DIFFRACTION100

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