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- PDB-3ast: Crystal structure of P domain Q389N mutant from Norovirus Funabas... -

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Basic information

Entry
Database: PDB / ID: 3ast
TitleCrystal structure of P domain Q389N mutant from Norovirus Funabashi258 stain in the complex with Lewis-b
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
Lewis B antigen, beta anomer / P-NITROPHENOL / Capsid protein
Similarity search - Component
Biological speciesNorwalk-like virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 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 / 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 / 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_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_label_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 2.1Nov 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 protein
B: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,1678
Polymers70,4912
Non-polymers1,6756
Water9,584532
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-19 kcal/mol
Surface area24740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.966, 74.966, 107.250
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31

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Components

#1: Protein Capsid protein


Mass: 35245.613 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)-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-beta-D-glucopyranose / Lewis B antigen / beta 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 B antigen, beta anomer
DescriptorTypeProgram
LFucpa1-2DGalpb1-3[LFucpa1-4]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_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
[][D-1-deoxy-GlcpNAc]{[(3+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}[(4+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-NPO / P-NITROPHENOL


Mass: 139.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 532 / 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: 2.47 Å3/Da / Density % sol: 50.17 % / Mosaicity: 0.697 °
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 315r / Detector: CCD / Date: Oct 27, 2010
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: 1.4→50 Å / Num. all: 131706 / Num. obs: 124888 / % possible obs: 94.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8 % / Rmerge(I) obs: 0.082 / Χ2: 2.451 / Net I/σ(I): 30.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.4-1.455.70.19129891.688198.2
1.45-1.516.40.162129811.852199
1.51-1.587.10.138130492.076199.1
1.58-1.667.70.119130782.274199.3
1.66-1.768.30.105130682.502199.4
1.76-1.98.90.091130872.705199.4
1.9-2.099.40.082130932.762199.5
2.09-2.399.80.074131342.665199.7
2.39-3.029.30.072129952.642198.7
3.02-506.70.07874142.996156.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 27.35 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å23.92 Å
Translation2.5 Å23.92 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
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
Starting model: 3ASS

3ass


Resolution: 1.4→23.92 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.931 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 0.848 / SU ML: 0.035 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.067 / ESU R Free: 0.066 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES
RfactorNum. reflection% reflectionSelection details
Rfree0.21201 6268 5 %RANDOM
Rwork0.19676 ---
obs0.19752 124868 94.81 %-
all-131706 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 54.43 Å2 / Biso mean: 16.733 Å2 / Biso min: 8.14 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å2-0 Å2
3----0 Å2
Refinement stepCycle: LAST / Resolution: 1.4→23.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4701 0 112 532 5345
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224986
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0541.9856841
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5055619
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.04624.516217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.97215695
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.3991522
X-RAY DIFFRACTIONr_chiral_restr0.0630.2762
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0223902
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4831.53084
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.92925028
X-RAY DIFFRACTIONr_scbond_it1.23331902
X-RAY DIFFRACTIONr_scangle_it2.0124.51809
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.404→1.44 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.235 462 -
Rwork0.235 8998 -
all-9460 -
obs--97.06 %

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