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- PDB-3asp: Crystal structure of P domain from Norovirus Funabashi258 stain i... -

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Basic information

Entry
Database: PDB / ID: 3asp
TitleCrystal structure of P domain from Norovirus Funabashi258 stain in the complex with A-antigen
ComponentsCapsid protein
KeywordsVIRAL PROTEIN / protein-sugar complex / Histo-blood group antigen / capsid protein / Lectin-like protein
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
Blood group A H type 1 antigen, beta anomer / Capsid protein
Similarity search - Component
Biological speciesNorwalk-like virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.6 Å
AuthorsKubota, T. / Kumagai, A. / Itoh, H. / Furukawa, S. / Narimatsu, H. / Wakita, T. / Ishii, K. / Takeda, N. / Someya, Y. / Shirato, H.
CitationJournal: J.Virol. / Year: 2012
Title: Structural basis for the recognition of Lewis antigens by genogroup I norovirus
Authors: Kubota, T. / Kumagai, A. / Ito, H. / Furukawa, S. / Someya, Y. / Takeda, N. / Ishii, K. / Wakita, T. / Narimatsu, H. / Shirato, H.
History
DepositionDec 17, 2010Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 20, 2013Group: Database references
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 / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _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.ptnr1_label_seq_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 2.1Aug 5, 2020Group: Structure summary / Category: pdbx_molecule_features
Revision 2.2Mar 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
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 protein
B: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,0316
Polymers70,5192
Non-polymers1,5114
Water7,332407
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-19 kcal/mol
Surface area24650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.624, 74.624, 106.996
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Capsid protein


Mass: 35259.641 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 221-541
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norwalk-like virus / Strain: GI/2 Funabashi 258 / Gene: capsid, ORF2 / Plasmid: pGEX-6P-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8JW44
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D- ...alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 732.682 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with branches / References: Blood group A H type 1 antigen, beta anomer
DescriptorTypeProgram
LFucpa1-2[DGalpNAca1-3]DGalpb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5][a2112h-1a_1-5_2*NCC/3=O]/1-2-3-4/a3-b1_b2-c1_b3-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}[(3+1)][a-D-GalpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / 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: 2.44 Å3/Da / Density % sol: 49.57 %
Crystal growTemperature: 298 K / Method: hanging drop / pH: 4.6
Details: PEG 6000, hexanediol, pH 4.6, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 10, 2008
RadiationMonochromator: Numerical link type Si(111) double crystal monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→50 Å / Num. all: 87958 / Num. obs: 87885 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.5 % / Rmerge(I) obs: 0.067 / Χ2: 1.723 / Net I/σ(I): 12.7
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.6-1.6311.10.68744301.5871100
1.63-1.6611.30.60843711.5321100
1.66-1.6911.30.52644201.5941100
1.69-1.7211.30.44943791.5781100
1.72-1.7611.40.35843731.5771100
1.76-1.811.40.29244031.5831100
1.8-1.8511.40.24543911.6181100
1.85-1.911.40.19943661.6041100
1.9-1.9511.40.16644771.6851100
1.95-2.0211.50.13144091.6331100
2.02-2.0911.50.11543291.7511100
2.09-2.1711.50.09244371.7091100
2.17-2.2711.50.08544161.7851100
2.27-2.3911.60.07443951.731100
2.39-2.5411.60.06843831.7971100
2.54-2.7411.60.05844061.8111100
2.74-3.0111.60.0544091.8631100
3.01-3.4511.60.04343931.9661100
3.45-4.3411.60.03844032.0371100
4.34-5011.40.03643951.985199.7

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 33.89 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å35.23 Å
Translation2.5 Å35.23 Å

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Processing

Software
NameVersionClassificationNB
PHASER2.1.4phasing
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.6→35.23 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.952 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 1.393 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.082 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.2007 4406 5 %RANDOM
Rwork0.1824 ---
all0.1833 87958 --
obs0.1833 87885 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 46.46 Å2 / Biso mean: 18.0736 Å2 / Biso min: 9.32 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.6→35.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4703 0 102 407 5212
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224973
X-RAY DIFFRACTIONr_angle_refined_deg1.0771.9846827
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6685619
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.59324.562217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.46315697
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3711522
X-RAY DIFFRACTIONr_chiral_restr0.0640.2764
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0223886
X-RAY DIFFRACTIONr_mcbond_it0.5291.53084
X-RAY DIFFRACTIONr_mcangle_it125028
X-RAY DIFFRACTIONr_scbond_it1.30331889
X-RAY DIFFRACTIONr_scangle_it2.2424.51795
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 324 -
Rwork0.256 6132 -
all-6456 -
obs--99.8 %

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