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- PDB-4opo: Crystal structure of P domain from norovirus strain Saga4 in comp... -

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Basic information

Entry
Database: PDB / ID: 4opo
TitleCrystal structure of P domain from norovirus strain Saga4 in complex with HBGA type Leb (tetraglycan)
ComponentsVP1
KeywordsVIRAL PROTEIN / Norovirus / Viral Capsid Protein / Histo Blood Group Antigen (HBGA) / Protruding Domain
Function / homology
Function and homology information


virion component / host cell cytoplasm
Similarity search - Function
Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / 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 ...Nucleoplasmin-like/VP (viral coat and capsid proteins) / Positive stranded ssRNA viruses / 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 / ACETATE ION / VP1
Similarity search - Component
Biological speciesNorovirus Hu/GII-4/Kumamoto5/2006/JP
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.4 Å
AuthorsSingh, B.K. / Hansman, G.S.
CitationJournal: J.Virol. / Year: 2015
Title: Human noroviruses' fondness for histo-blood group antigens.
Authors: Singh, B.K. / Leuthold, M.M. / Hansman, G.S.
History
DepositionFeb 6, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 17, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 11, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_special_symmetry / pdbx_validate_close_contact / 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 / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_atom_id_1 / _pdbx_validate_close_contact.auth_atom_id_2 / _pdbx_validate_close_contact.auth_comp_id_1 / _pdbx_validate_close_contact.auth_comp_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 2.1Feb 28, 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: VP1
B: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,86211
Polymers68,0822
Non-polymers1,7809
Water14,628812
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7020 Å2
ΔGint21 kcal/mol
Surface area23270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.660, 58.600, 97.170
Angle α, β, γ (deg.)90.00, 107.15, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-817-

HOH

21B-1087-

HOH

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Components

#1: Protein VP1


Mass: 34041.059 Da / Num. of mol.: 2 / Fragment: P domain Saga4 (UNP residues 225-530)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/GII-4/Kumamoto5/2006/JP / Gene: AB447457 / Plasmid: MBP-HTSHP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: B5BTT5
#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
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}[(4+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 812 / 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: 2.27 Å3/Da / Density % sol: 45.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: Sodium acetate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.979701 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Feb 23, 2013
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979701 Å / Relative weight: 1
ReflectionResolution: 1.38→46.42 Å / Num. obs: 124462 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 11.6 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 12.76
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.38-1.423.60.931.71196.1
1.42-1.450.7982.13199.5
1.45-1.50.6412.81199.6
1.5-1.540.5353.42199.6
1.54-1.590.4254.34199.7
1.59-1.650.3425.31199.7
1.65-1.710.2776.43199.7
1.71-1.780.2148.09199.6
1.78-1.860.1610.19199.7
1.86-1.950.12711.97199.8
1.95-2.060.08916.04199.8
2.06-2.180.0719199.6
2.18-2.330.05721.91199.7
2.33-2.520.04923.82199.8
2.52-2.760.04126.76199.7
2.76-3.090.03530199.8
3.09-3.560.02936.11199.5
3.56-4.360.02839.09198.8
4.36-6.170.02739.07197.3
6.170.02934.72189.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.14 Å46.42 Å
Translation7.14 Å46.42 Å

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.2phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.14data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→46.42 Å / SU ML: 0.13 / σ(F): 1.99 / Phase error: 17.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1854 5975 5 %
Rwork0.1508 --
obs0.1525 119485 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.25 Å2
Refinement stepCycle: LAST / Resolution: 1.4→46.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4770 0 120 812 5702
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075122
X-RAY DIFFRACTIONf_angle_d1.2027004
X-RAY DIFFRACTIONf_dihedral_angle_d12.31863
X-RAY DIFFRACTIONf_chiral_restr0.072794
X-RAY DIFFRACTIONf_plane_restr0.006913
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4-1.41590.28561980.24913760X-RAY DIFFRACTION99
1.4159-1.43260.27091980.22993762X-RAY DIFFRACTION99
1.4326-1.45010.26962000.21733789X-RAY DIFFRACTION100
1.4501-1.46840.25031970.19613750X-RAY DIFFRACTION100
1.4684-1.48770.23712000.19433800X-RAY DIFFRACTION100
1.4877-1.50810.2511960.19013737X-RAY DIFFRACTION100
1.5081-1.52970.22431970.18743743X-RAY DIFFRACTION99
1.5297-1.55250.22541990.17773791X-RAY DIFFRACTION100
1.5525-1.57680.20652000.16313793X-RAY DIFFRACTION100
1.5768-1.60260.19061980.15623759X-RAY DIFFRACTION100
1.6026-1.63020.19561990.15483792X-RAY DIFFRACTION100
1.6302-1.65990.19291990.15233770X-RAY DIFFRACTION100
1.6599-1.69180.19352000.15563795X-RAY DIFFRACTION100
1.6918-1.72640.2032000.15143801X-RAY DIFFRACTION100
1.7264-1.76390.19171960.14353735X-RAY DIFFRACTION100
1.7639-1.80490.1781990.13433783X-RAY DIFFRACTION100
1.8049-1.85010.16522000.13643784X-RAY DIFFRACTION100
1.8501-1.90010.16431990.13713794X-RAY DIFFRACTION100
1.9001-1.9560.18582020.13543830X-RAY DIFFRACTION100
1.956-2.01910.16081990.1283776X-RAY DIFFRACTION100
2.0191-2.09130.15491990.12943780X-RAY DIFFRACTION100
2.0913-2.1750.18041990.13413792X-RAY DIFFRACTION100
2.175-2.2740.1772000.12973804X-RAY DIFFRACTION100
2.274-2.39390.17892000.13893786X-RAY DIFFRACTION100
2.3939-2.54390.18612010.14793826X-RAY DIFFRACTION100
2.5439-2.74030.1822000.15093790X-RAY DIFFRACTION100
2.7403-3.0160.17092010.15353831X-RAY DIFFRACTION100
3.016-3.45230.18582020.14263831X-RAY DIFFRACTION100
3.4523-4.3490.15372010.13883816X-RAY DIFFRACTION99
4.349-46.450.18891960.16593710X-RAY DIFFRACTION94
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.0299-0.01150.02860.0035-0.01090.0141-0.03890.04050.1178-0.0875-0.06490.0768-0.0618-0.1749-0.01730.64280.4112-0.05780.0119-0.19440.3489132.6933.88624.246
20.01020.0040.01180.00610.00420.0042-0.0554-0.05610.14410.1125-0.1722-0.0137-0.14160.214-0.00370.2887-0.095-0.01730.22280.01840.1926149.822-2.59620.954
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(CHAIN B AND RESID 607:610 )B607 - 610
2X-RAY DIFFRACTION2(CHAIN B AND RESID 603:606 )B603 - 606

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