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- PDB-7vs8: Crystal structure of P domain from norovirus GI.9 capsid protein ... -

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Basic information

Entry
Database: PDB / ID: 7vs8
TitleCrystal structure of P domain from norovirus GI.9 capsid protein in complex with Lewis b 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 B antigen, alpha anomer / VP1
Similarity search - Component
Biological speciesNorovirus Hu/GI/Vancouver730/2004/CAN
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.1Sep 7, 2022Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_vector_type / _entity_src_gen.plasmid_name
Revision 1.2Nov 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

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Assembly

Deposited unit
A: VP1
B: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,34617
Polymers67,5562
Non-polymers1,79015
Water6,738374
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7510 Å2
ΔGint-89 kcal/mol
Surface area23720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)183.749, 76.464, 103.281
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-(1-2)-beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-alpha-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 675.630 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with branches / References: Lewis B antigen, alpha anomer
DescriptorTypeProgram
LFucpa1-2DGalpb1-3[LFucpa1-4]DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3-3/a3-b1_a4-d1_b2-c1WURCSPDB2Glycan 1.1.0
#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.: 11 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 374 / 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: 4.44 Å3/Da / Density % sol: 72.31 %
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 20, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 45674 / % possible obs: 98.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.073 / Rrim(I) all: 0.086 / Net I/σ(I): 18.9
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.333 / Num. unique obs: 4263 / Rrim(I) all: 0.395

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Processing

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

7vp0


Resolution: 2.4→41.193 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 20.96 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1956 1995 4.37 %
Rwork0.1649 --
obs0.1663 45659 98.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.4→41.193 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4738 0 105 374 5217
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084982
X-RAY DIFFRACTIONf_angle_d0.9736858
X-RAY DIFFRACTIONf_dihedral_angle_d7.7712940
X-RAY DIFFRACTIONf_chiral_restr0.057790
X-RAY DIFFRACTIONf_plane_restr0.006902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4003-2.46030.25071210.22332795X-RAY DIFFRACTION88
2.4603-2.52680.28171410.21843087X-RAY DIFFRACTION97
2.5268-2.60120.25171430.20313081X-RAY DIFFRACTION98
2.6012-2.68510.23561420.20243122X-RAY DIFFRACTION98
2.6851-2.78110.25121430.20793064X-RAY DIFFRACTION98
2.7811-2.89240.24271410.18943130X-RAY DIFFRACTION99
2.8924-3.0240.20811420.18333130X-RAY DIFFRACTION99
3.024-3.18340.21491440.17823135X-RAY DIFFRACTION99
3.1834-3.38270.19981430.17783133X-RAY DIFFRACTION99
3.3827-3.64380.20491450.15943160X-RAY DIFFRACTION99
3.6438-4.01020.18381480.14943183X-RAY DIFFRACTION100
4.0102-4.58980.14541430.12353183X-RAY DIFFRACTION100
4.5898-5.78010.15131480.13373199X-RAY DIFFRACTION100

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