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- PDB-3pun: Crystal structure of P domain dimer of Norovirus VA207 with Lewis... -

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Basic information

Entry
Database: PDB / ID: 3pun
TitleCrystal structure of P domain dimer of Norovirus VA207 with Lewis y tetrasaccharide
ComponentsCapsid
KeywordsVIRAL PROTEIN / Greek Key / Mixed alpha/beta Structure / Receptor Binding / Carbohydrate/Sugar Binding / Capsid
Function / homology
Function and homology information


Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit ...Positive stranded ssRNA viruses / Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / Calicivirus coat protein C-terminal / Calicivirus coat protein C-terminal / Calicivirus coat protein / Calicivirus coat protein / Elongation Factor Tu (Ef-tu); domain 3 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Lewis Y antigen, alpha anomer / Capsid
Similarity search - Component
Biological speciesHuman calicivirus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsChen, Y. / Tan, M. / Xia, M. / Hao, N. / Zhang, X.C. / Huang, P. / Jiang, X. / Li, X. / Rao, Z.
CitationJournal: Plos Pathog. / Year: 2011
Title: Crystallography of a Lewis-binding norovirus, elucidation of strain-specificity to the polymorphic human histo-blood group antigens
Authors: Chen, Y. / Tan, M. / Xia, M. / Hao, N. / Zhang, X.C. / Huang, P. / Jiang, X. / Li, X. / Rao, Z.
History
DepositionDec 6, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 3, 2011Provider: repository / Type: Initial release
Revision 1.1Apr 11, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Capsid
B: Capsid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,7014
Polymers69,3492
Non-polymers1,3512
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3130 Å2
ΔGint-9 kcal/mol
Surface area23470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.168, 96.123, 101.981
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Capsid /


Mass: 34674.652 Da / Num. of mol.: 2 / Fragment: P DOMAIN, UNP residues 222-537 / Mutation: T289N, N374D, R425G, Q466R, V482A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human calicivirus / Strain: VA97207 / Gene: CAPSID / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q91H09
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2- ...alpha-L-fucopyranose-(1-2)-beta-D-galactopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-alpha-D-glucopyranose / Lewis Y antigen / alpha anomer


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 Y antigen, alpha anomer
DescriptorTypeProgram
LFucpa1-2DGalpb1-4[LFucpa1-3]DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1a_1-5_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5]/1-2-3-2/a3-b1_a4-c1_c2-d1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O

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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: 2.37 Å3/Da / Density % sol: 48.18 % / Mosaicity: 0.977 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 10% (w/v) PEG 3350, 50mM magnesium formate, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Nov 24, 2007 / Details: Rigaku Osmic Varimax Confocal optics
RadiationMonochromator: Rigaku Osmic Varimax Confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.05→50 Å / Num. obs: 42294 / % possible obs: 99.9 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.076 / Χ2: 1.571 / Net I/σ(I): 15.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.05-2.1260.5341351.1361100
2.12-2.216.20.42541621.2391100
2.21-2.316.40.31542101.3491100
2.31-2.436.40.24741771.4551100
2.43-2.586.50.241761.5541100
2.58-2.786.50.14742191.7811100
2.78-3.066.50.10442391.9161100
3.06-3.516.50.07442361.8061100
3.51-4.426.50.05542911.6821100
4.42-506.30.04344491.704198.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.5 Å21.81 Å
Translation3.5 Å21.81 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.3phasing
PHENIXrefinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3PUM

3pum


Resolution: 2.05→21.806 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 1.58 / σ(F): 0.1 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2038 2031 5.01 %RANDOM
Rwork0.1847 ---
obs0.1857 40540 95.91 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.703 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso max: 80.93 Å2 / Biso mean: 36.994 Å2 / Biso min: 20.7 Å2
Baniso -1Baniso -2Baniso -3
1--1.2098 Å2-0 Å20 Å2
2---5.9787 Å2-0 Å2
3---7.3607 Å2
Refinement stepCycle: LAST / Resolution: 2.05→21.806 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4680 0 92 333 5105
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084908
X-RAY DIFFRACTIONf_angle_d1.0696698
X-RAY DIFFRACTIONf_chiral_restr0.249740
X-RAY DIFFRACTIONf_plane_restr0.005890
X-RAY DIFFRACTIONf_dihedral_angle_d16.7551774
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 15

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0469-2.09450.25261340.2212342247690
2.0945-2.14680.2591270.21682411253892
2.1468-2.20480.23991160.20422438255492
2.2048-2.26960.22031390.20132506264595
2.2696-2.34280.24691250.19132489261493
2.3428-2.42640.26411040.19752545264995
2.4264-2.52340.19871260.20512513263995
2.5234-2.63810.22481440.20892565270997
2.6381-2.77690.26541150.21462606272197
2.7769-2.95050.23421460.22282579272597
2.9505-3.17770.23771560.21152624278098
3.1777-3.49630.23131310.19422670280199
3.4963-3.99950.17571490.16512678282799
3.9995-5.02870.14681620.13822694285699
5.0287-21.80690.171570.159928493006100

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