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- PDB-4p25: Structure of the P domain from a GI.7 Norovirus variant in comple... -

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Basic information

Entry
Database: PDB / ID: 4p25
TitleStructure of the P domain from a GI.7 Norovirus variant in complex with LeY HBGA.
ComponentsMajor capsid protein
KeywordsVIRAL PROTEIN / P domain / Capsid protein / Norovirus / HBGA / LeY / Lewis HBGA
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 / Viral coat protein subunit / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Lewis Y antigen, beta anomer / Major capsid protein
Similarity search - Component
Biological speciesNorovirus Hu/GI.7/TCH-060/USA/2003
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.4991 Å
AuthorsShanker, S. / Czako, R. / Sankaran, B. / Atmar, R. / Estes, M. / Prasad, B.V.V.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) United States
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: J.Virol. / Year: 2014
Title: Structural analysis of determinants of histo-blood group antigen binding specificity in genogroup I noroviruses.
Authors: Shanker, S. / Czako, R. / Sankaran, B. / Atmar, R.L. / Estes, M.K. / Prasad, B.V.
History
DepositionMar 1, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 2.0Nov 27, 2019Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / citation / entity / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_asym / struct_conn / struct_ref / struct_site_gen
Item: _atom_site.label_asym_id / _atom_site.label_entity_id ..._atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.type / _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_nonpoly_scheme.asym_id / _pdbx_nonpoly_scheme.entity_id / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_ref.biol_id / _struct_site_gen.label_asym_id
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description / 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 / refine_hist / struct_asym / struct_conn / 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.pdbx_value_order / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Dec 27, 2023Group: 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: Major capsid protein
B: Major capsid protein
C: Major capsid protein
D: Major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)133,4578
Polymers130,7544
Non-polymers2,7034
Water21,2221178
1
A: Major capsid protein
B: Major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7284
Polymers65,3772
Non-polymers1,3512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint19 kcal/mol
Surface area22140 Å2
MethodPISA
2
C: Major capsid protein
D: Major capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7284
Polymers65,3772
Non-polymers1,3512
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint17 kcal/mol
Surface area22640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.314, 63.124, 90.580
Angle α, β, γ (deg.)72.80, 82.18, 60.85
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Major capsid protein


Mass: 32688.531 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/GI.7/TCH-060/USA/2003 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: G8FL04
#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-beta-D-glucopyranose / Lewis Y antigen / beta anomer


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 675.630 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with branches / References: Lewis Y antigen, beta anomer
DescriptorTypeProgram
LFucpa1-2DGalpb1-4[LFucpa1-3]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_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
[][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1178 / 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: 2.28 Å3/Da / Density % sol: 45.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.2M Sodium Formate 0.1M Bis Tris Propane 20% PEG3350

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97939 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray / Wavelength: 0.97939 Å
Radiation wavelengthWavelength: 0.97939 Å / Relative weight: 1
ReflectionResolution: 1.499→40 Å / Num. obs: 176762 / % possible obs: 96.8 % / Redundancy: 3.9 % / Net I/σ(I): 28.5

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement
RefinementResolution: 1.4991→38.996 Å / SU ML: 0.13 / σ(F): 1.96 / Phase error: 17.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1745 8552 5.01 %
Rwork0.1342 --
obs0.1362 170635 92.34 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.4991→38.996 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8793 0 184 1178 10155
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0069244
X-RAY DIFFRACTIONf_angle_d1.16112669
X-RAY DIFFRACTIONf_dihedral_angle_d12.1323375
X-RAY DIFFRACTIONf_chiral_restr0.0711450
X-RAY DIFFRACTIONf_plane_restr0.0061648
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.4991-1.51610.2411130.1542303X-RAY DIFFRACTION39
1.5161-1.53390.23241960.15443633X-RAY DIFFRACTION63
1.5339-1.55260.22582460.14564810X-RAY DIFFRACTION82
1.5526-1.57230.22013200.14135330X-RAY DIFFRACTION92
1.5723-1.5930.21672860.13165535X-RAY DIFFRACTION94
1.593-1.61480.20292890.12835528X-RAY DIFFRACTION95
1.6148-1.63790.19813260.12825530X-RAY DIFFRACTION95
1.6379-1.66230.20162800.12735578X-RAY DIFFRACTION95
1.6623-1.68830.19032880.12375600X-RAY DIFFRACTION95
1.6883-1.7160.19473080.12615605X-RAY DIFFRACTION96
1.716-1.74560.19743080.12065564X-RAY DIFFRACTION96
1.7456-1.77730.18123060.12075619X-RAY DIFFRACTION96
1.7773-1.81150.1862940.11195615X-RAY DIFFRACTION96
1.8115-1.84850.1822890.10915615X-RAY DIFFRACTION96
1.8485-1.88870.16653030.10985631X-RAY DIFFRACTION96
1.8887-1.93260.1812920.12015630X-RAY DIFFRACTION96
1.9326-1.98090.18283020.11345656X-RAY DIFFRACTION97
1.9809-2.03450.16572720.11455686X-RAY DIFFRACTION97
2.0345-2.09430.19772640.12425704X-RAY DIFFRACTION97
2.0943-2.16190.15622910.1175723X-RAY DIFFRACTION97
2.1619-2.23920.18283050.12015666X-RAY DIFFRACTION97
2.2392-2.32880.18342790.1285721X-RAY DIFFRACTION97
2.3288-2.43480.17373070.13145698X-RAY DIFFRACTION98
2.4348-2.56320.17442750.14135713X-RAY DIFFRACTION98
2.5632-2.72370.17723340.14365725X-RAY DIFFRACTION98
2.7237-2.9340.17073080.14335706X-RAY DIFFRACTION98
2.934-3.22910.15913010.14055647X-RAY DIFFRACTION97
3.2291-3.6960.1642970.13955441X-RAY DIFFRACTION93
3.696-4.65540.14652660.13745280X-RAY DIFFRACTION90
4.6554-39.00920.16493070.16975591X-RAY DIFFRACTION96

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