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- PDB-4p3i: Structure of the P domain from a GI.7 Norovirus variant in comple... -

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Basic information

Entry
Database: PDB / ID: 4p3i
TitleStructure of the P domain from a GI.7 Norovirus variant in complex with LeA HBGA.
ComponentsP domain of VP1
KeywordsVIRAL PROTEIN / P domain / Capsid protein / Norovirus / HBGA / LeA / Lewis HBGA / nonsecretor
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 A antigen, beta anomer / Major capsid protein
Similarity search - Component
Biological speciesNorovirus Hu/GI.7/TCH-060/USA/2003
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.6941 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 7, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 2.0Mar 21, 2018Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / diffrn_detector / entity / entity_src_gen / pdbx_database_status / pdbx_entity_nonpoly / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_asym / struct_conn / struct_site_gen
Item: _atom_site.label_asym_id / _atom_site.label_entity_id ..._atom_site.label_asym_id / _atom_site.label_entity_id / _citation.journal_id_CSD / _diffrn_detector.pdbx_collection_date / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _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_site_gen.label_asym_id
Revision 2.1Nov 27, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support / Item: _chem_comp.type
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 / 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 / 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 3.1Aug 5, 2020Group: Structure summary / Category: pdbx_molecule_features
Revision 3.2Dec 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: P domain of VP1
B: P domain of VP1
C: P domain of VP1
D: P domain of VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)132,5888
Polymers130,4704
Non-polymers2,1184
Water22,2851237
1
A: P domain of VP1
B: P domain of VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2944
Polymers65,2352
Non-polymers1,0592
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4830 Å2
ΔGint0 kcal/mol
Surface area22090 Å2
MethodPISA
2
C: P domain of VP1
D: P domain of VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,2944
Polymers65,2352
Non-polymers1,0592
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint0 kcal/mol
Surface area22430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.168, 63.277, 90.400
Angle α, β, γ (deg.)72.77, 82.20, 60.31
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
P domain of VP1


Mass: 32617.451 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
beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 529.490 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with branches / References: Lewis A antigen, beta anomer
DescriptorTypeProgram
DGalpb1-3[LFucpa1-4]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{}[(4+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1237 / 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: 2.26 Å3/Da / Density % sol: 45.61 %
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: 0.97935 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 17, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.694→40 Å / Num. obs: 122863 / % possible obs: 97.5 % / Redundancy: 3.6 % / Net I/σ(I): 17.3

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement
RefinementResolution: 1.6941→38.92 Å / SU ML: 0.15 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 17.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1774 6146 5.03 %Random
Rwork0.1551 ---
obs0.1562 122269 96.19 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.6941→38.92 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8686 0 144 1237 10067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0119096
X-RAY DIFFRACTIONf_angle_d1.46112466
X-RAY DIFFRACTIONf_dihedral_angle_d11.8523297
X-RAY DIFFRACTIONf_chiral_restr0.0921418
X-RAY DIFFRACTIONf_plane_restr0.0071628
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6941-1.71340.26061380.21522741X-RAY DIFFRACTION67
1.7134-1.73350.23371770.21053698X-RAY DIFFRACTION92
1.7335-1.75470.24381970.20023753X-RAY DIFFRACTION93
1.7547-1.77690.24051830.20263898X-RAY DIFFRACTION96
1.7769-1.80030.2392070.18583859X-RAY DIFFRACTION95
1.8003-1.82490.21442080.17593788X-RAY DIFFRACTION96
1.8249-1.8510.19062130.16633886X-RAY DIFFRACTION97
1.851-1.87860.18772050.16723862X-RAY DIFFRACTION96
1.8786-1.9080.20762180.16383885X-RAY DIFFRACTION97
1.908-1.93930.18432090.16063870X-RAY DIFFRACTION96
1.9393-1.97270.19232140.16023935X-RAY DIFFRACTION97
1.9727-2.00860.18542170.16033909X-RAY DIFFRACTION97
2.0086-2.04720.19932050.1563868X-RAY DIFFRACTION97
2.0472-2.0890.18881960.14913879X-RAY DIFFRACTION97
2.089-2.13440.17831990.14973930X-RAY DIFFRACTION98
2.1344-2.18410.17842120.14813926X-RAY DIFFRACTION97
2.1841-2.23870.15842260.14323892X-RAY DIFFRACTION98
2.2387-2.29920.17552000.15213963X-RAY DIFFRACTION98
2.2992-2.36680.17722100.15093922X-RAY DIFFRACTION98
2.3668-2.44320.20282190.15683933X-RAY DIFFRACTION97
2.4432-2.53050.17371990.16593934X-RAY DIFFRACTION98
2.5305-2.63180.18162320.16083938X-RAY DIFFRACTION98
2.6318-2.75160.20321930.16773985X-RAY DIFFRACTION98
2.7516-2.89660.18892030.16463939X-RAY DIFFRACTION99
2.8966-3.0780.17982000.15813987X-RAY DIFFRACTION99
3.078-3.31550.14432050.14124013X-RAY DIFFRACTION99
3.3155-3.6490.15392090.13713967X-RAY DIFFRACTION99
3.649-4.17650.14362280.13273981X-RAY DIFFRACTION99
4.1765-5.25980.14921920.13084014X-RAY DIFFRACTION99
5.2598-38.93060.18492320.1773968X-RAY DIFFRACTION99
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)
12.0303-0.19690.22681.09290.38821.46550.00710.0666-0.00980.0224-0.0114-0.045-0.01160.03780.01210.1092-0.02430.00710.08720.00590.079199.086963.4804-28.4556
22.2678-0.52660.02570.8108-0.04841.2111-0.0314-0.2818-0.070.1210.05860.0995-0.0235-0.30020.030.1486-0.02650.02820.18680.00190.100979.007863.1104-21.3153
31.8788-0.20840.41211.4846-0.00611.6465-0.0314-0.16010.15180.06150.00860.1184-0.1404-0.23150.01970.11860.01560.02970.1369-0.01610.112877.606472.9355-28.2088
41.6393-0.36380.38070.57380.02350.2972-0.099-0.17130.15160.08880.0643-0.0874-0.097-0.0820.03940.149-0.0165-0.00650.1241-0.02440.129696.383770.401-24.0061
53.04250.05250.08741.9320.03271.36090.0226-0.1256-0.41080.14140.0113-0.03770.25420.1031-0.01890.1602-0.0002-0.01240.09380.00890.1325101.975651.9309-24.0243
63.00630.3221-0.12032.5288-0.2722.62830.04390.0062-0.0883-0.1144-0.0467-0.13580.01380.2885-0.02660.1132-0.0022-0.0150.088-0.00950.1326110.715659.7802-28.5474
72.70780.24090.75352.7665-0.75413.3521-0.0074-0.0657-0.0090.20870.0131-0.21450.00010.3187-0.01680.11530.00340.00020.1149-0.02480.1553111.84658.3011-26.7912
80.78650.1771-0.07290.99-0.29040.88910.00180.0784-0.0269-0.0425-0.00270.04210.042-0.0882-0.00350.0832-0.0184-0.00590.1039-0.01230.084381.850156.1131-46.8455
90.3523-0.6225-0.32676.7223-0.66420.45860.02120.1946-0.1465-0.17160.1590.70480.008-0.3664-0.14310.1248-0.0249-0.00350.18140.0260.183571.492251.1556-39.1438
100.9938-0.0116-0.18521.2543-0.43821.2427-0.0093-0.0273-0.19490.0434-0.0327-0.08880.11630.04020.05830.1545-0.0293-0.0130.0920.0150.167883.54838.4169-32.1275
114.5451-0.7824-0.17922.5859-0.29340.40460.0130.1185-0.4442-0.0124-0.07710.10890.1585-0.04420.04330.1917-0.0493-0.00740.1370.0350.167580.041833.1803-30.169
121.78660.2937-0.06940.8482-0.09470.6236-0.0242-0.03860.0657-0.01870.04320.0585-0.03340.0207-0.030.07090.00760.00080.06150.0070.067881.494850.41358.3935
133.38841.12650.67421.30170.35230.71140.04030.15870.151-0.30210.1002-0.5202-0.1480.14260.10150.1343-0.00910.06090.1238-0.0020.1704102.714753.74013.487
142.0015-0.03760.54151.186-0.48741.66160.01210.04370.0291-0.0214-0.0748-0.15220.04390.23340.0220.0541-0.0080.01360.0981-0.00760.082100.932452.018613.3524
151.6650.25710.28050.6511-0.29080.8028-0.0076-0.07910.1448-0.02620.03890.0585-0.0949-0.0144-0.01050.06310.00880.01450.0601-0.00720.089482.388554.479412.4457
161.7235-0.3621-0.04761.9684-0.36672.62580.0176-0.04990.0224-0.0780.05770.2801-0.0497-0.228-0.05840.06910.0134-0.02280.09760.01290.125163.327949.75487.5625
170.4674-0.1429-0.21610.5630.36031.5744-0.0008-0.0491-0.0631-0.0173-0.00780.01830.00720.01220.00660.0731-0.00030.0020.05620.00780.071486.318129.091912.8236
181.05080.09550.17310.96090.41571.1529-0.0131-0.22020.01760.106-0.0113-0.0680.02880.0185-0.0050.09640.0059-0.00350.13690.0180.078793.425434.288527.9762
190.503-0.1650.16680.93120.70591.24930.024-0.048-0.09860.08080.011-0.03630.18410.0892-0.01850.08690.01690.00290.09140.01960.081293.648224.237211.7798
201.27940.08570.51642.35731.33441.8366-0.03930.0713-0.2002-0.2173-0.10090.3004-0.1463-0.30940.16290.11530.007-0.0260.1442-0.03970.09175.53828.9351-0.3806
211.25420.31880.69052.6488-0.09391.33770.010.0710.0567-0.2185-0.0303-0.0918-0.00330.24530.02890.12320.01870.00490.0977-0.01770.070488.382526.9371-10.8058
221.94270.31970.29441.32280.74311.27440.16450.1446-0.1671-0.241-0.1591-0.07040.0230.0018-0.01870.16990.0447-0.00330.0847-0.01070.057487.371324.8999-11.4719
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 231 through 270 )
2X-RAY DIFFRACTION2chain 'A' and (resid 271 through 317 )
3X-RAY DIFFRACTION3chain 'A' and (resid 318 through 397 )
4X-RAY DIFFRACTION4chain 'A' and (resid 398 through 448 )
5X-RAY DIFFRACTION5chain 'A' and (resid 449 through 473 )
6X-RAY DIFFRACTION6chain 'A' and (resid 474 through 500 )
7X-RAY DIFFRACTION7chain 'A' and (resid 501 through 525 )
8X-RAY DIFFRACTION8chain 'B' and (resid 232 through 425 )
9X-RAY DIFFRACTION9chain 'B' and (resid 426 through 441 )
10X-RAY DIFFRACTION10chain 'B' and (resid 442 through 500 )
11X-RAY DIFFRACTION11chain 'B' and (resid 501 through 525 )
12X-RAY DIFFRACTION12chain 'C' and (resid 232 through 297 )
13X-RAY DIFFRACTION13chain 'C' and (resid 298 through 319 )
14X-RAY DIFFRACTION14chain 'C' and (resid 320 through 377 )
15X-RAY DIFFRACTION15chain 'C' and (resid 378 through 458 )
16X-RAY DIFFRACTION16chain 'C' and (resid 459 through 526 )
17X-RAY DIFFRACTION17chain 'D' and (resid 232 through 331 )
18X-RAY DIFFRACTION18chain 'D' and (resid 332 through 377 )
19X-RAY DIFFRACTION19chain 'D' and (resid 378 through 448 )
20X-RAY DIFFRACTION20chain 'D' and (resid 449 through 465 )
21X-RAY DIFFRACTION21chain 'D' and (resid 466 through 500 )
22X-RAY DIFFRACTION22chain 'D' and (resid 501 through 526 )

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