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- PDB-4p2n: Structure of the P domain from a GI.7 Norovirus variant in comple... -

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Basic information

Entry
Database: PDB / ID: 4p2n
TitleStructure of the P domain from a GI.7 Norovirus variant in complex with LeX HBGA
ComponentsMajor capsid protein
KeywordsVIRAL PROTEIN / P domain / Capsid protein / Norovirus / HBGA / LeY / 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 X antigen, beta anomer / Major capsid protein
Similarity search - Component
Biological speciesNorovirus Hu/GI.7/TCH-060/USA/2003
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.7 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 Cancer Institute (NIH/NCI) United States
National Institutes of Health/National Institute of Diabetes and Digestive and Kidney Disease (NIH/NIDDK) 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 4, 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_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 / _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_oper_list.symmetry_operation / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_label_asym_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)132,5888
Polymers130,4704
Non-polymers2,1184
Water21,3841187
1
A: Major capsid protein
B: Major capsid protein
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 area4770 Å2
ΔGint2 kcal/mol
Surface area22400 Å2
MethodPISA
2
C: Major capsid protein
D: Major capsid protein
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 area4720 Å2
ΔGint5 kcal/mol
Surface area22190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.267, 63.031, 90.278
Angle α, β, γ (deg.)99.02, 98.16, 119.51
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Major capsid protein


Mass: 32617.451 Da / Num. of mol.: 4 / Fragment: UNP residues 226-526
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-(1-3)-[beta-D-galactopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose / Lewis X antigen / beta anomer


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 X antigen, beta anomer
DescriptorTypeProgram
LFucpa1-3[DGalpb1-4]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5][a2112h-1b_1-5]/1-2-3/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1187 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.26 Å3/Da / Density % sol: 45.5 %
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 / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 122585 / % possible obs: 97.5 % / Redundancy: 3.9 % / Net I/σ(I): 16.84

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement
RefinementResolution: 1.7→45.954 Å / SU ML: 0.12 / σ(F): 1.99 / Phase error: 16.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1714 6140 5.02 %
Rwork0.1553 --
obs0.1561 122288 96.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→45.954 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8731 0 144 1187 10062
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089169
X-RAY DIFFRACTIONf_angle_d1.23812568
X-RAY DIFFRACTIONf_dihedral_angle_d11.873326
X-RAY DIFFRACTIONf_chiral_restr0.0761429
X-RAY DIFFRACTIONf_plane_restr0.0061643
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71620.20411700.18883271X-RAY DIFFRACTION82
1.7162-1.73640.21181950.18533735X-RAY DIFFRACTION94
1.7364-1.75750.21181970.18563836X-RAY DIFFRACTION95
1.7575-1.77980.21592020.17983845X-RAY DIFFRACTION96
1.7798-1.80320.19052130.17533835X-RAY DIFFRACTION95
1.8032-1.82790.19552110.173825X-RAY DIFFRACTION97
1.8279-1.8540.20321900.16683903X-RAY DIFFRACTION96
1.854-1.88170.17552110.15763833X-RAY DIFFRACTION97
1.8817-1.91110.18822130.15423837X-RAY DIFFRACTION96
1.9111-1.94240.17552170.15643832X-RAY DIFFRACTION97
1.9424-1.97590.17572060.15563911X-RAY DIFFRACTION97
1.9759-2.01180.18712010.15993825X-RAY DIFFRACTION97
2.0118-2.05050.2161940.15573890X-RAY DIFFRACTION97
2.0505-2.09240.18442010.15313897X-RAY DIFFRACTION97
2.0924-2.13790.18022050.14933869X-RAY DIFFRACTION97
2.1379-2.18760.15462210.14973897X-RAY DIFFRACTION97
2.1876-2.24230.16612330.14643867X-RAY DIFFRACTION98
2.2423-2.3030.17012250.1533929X-RAY DIFFRACTION98
2.303-2.37070.17111950.15463863X-RAY DIFFRACTION98
2.3707-2.44720.19081990.16023923X-RAY DIFFRACTION98
2.4472-2.53470.19812290.16453906X-RAY DIFFRACTION98
2.5347-2.63620.181790.16463953X-RAY DIFFRACTION98
2.6362-2.75610.17342220.17013926X-RAY DIFFRACTION98
2.7561-2.90140.15881880.1663939X-RAY DIFFRACTION99
2.9014-3.08320.16942040.15823957X-RAY DIFFRACTION99
3.0832-3.32120.16051960.14433980X-RAY DIFFRACTION99
3.3212-3.65530.13092030.14223942X-RAY DIFFRACTION99
3.6553-4.18390.1641980.13633994X-RAY DIFFRACTION99
4.1839-5.270.13781990.13053973X-RAY DIFFRACTION99
5.27-45.97040.17352230.17793955X-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)
11.40.06740.23370.82960.08220.6641-0.0222-0.0595-0.0403-0.02940.023-0.0557-0.01120.00720.00490.05820.00630.0050.0498-0.0020.050617.07220.967511.6263
23.19860.6778-0.49911.9902-0.10053.0786-0.02850.197-0.2234-0.16960.10610.3670.241-0.14220.06220.1063-0.006-0.06330.0892-0.00690.1462-4.6446-2.55097.3108
31.6805-0.3028-0.43221.08420.31821.2651-0.00230.0036-0.0576-0.0028-0.05590.1508-0.0205-0.18710.02730.0461-0.0097-0.01390.0886-0.00110.0726-2.8341-0.90517.1465
41.44070.1314-0.20850.6910.37410.6617-0.0274-0.1827-0.19870.04920.0248-0.06960.16430.0210.03660.090.0134-0.01130.08350.030.089514.0312-5.919.7025
52.3394-0.0624-0.24782.10320.15633.27470.03280.0930.1035-0.1171-0.0507-0.0406-0.17710.18740.03920.05130.0017-0.00180.0664-0.00890.088520.56034.19648.9086
62.1136-0.12030.01232.10640.14432.43830.02440.0282-0.04260.00430.0549-0.26160.01120.2459-0.01740.0770.01380.03690.0963-0.00850.119933.98451.875710.7513
71.2929-0.45520.07361.690.1221.1824-0.0044-0.129-0.0665-0.11560.025-0.25850.06410.2293-0.02040.05980.01250.01890.1016-0.00210.113735.80110.670912.1547
80.5717-0.16860.27910.5978-0.46761.45080.0032-0.03890.0539-0.016-0.0004-0.0113-0.0129-0.0291-0.00060.0702-0.0022-0.0010.0548-0.01160.067911.78321.605315.8569
91.13720.6264-0.46022.2392-0.52851.48020.0072-0.0949-0.05670.0986-0.0365-0.06080.01740.0280.05280.06870.0014-0.00830.0927-0.01910.05028.096716.105226.7331
100.98230.3068-0.07680.9072-0.28531.45550.0209-0.13710.10750.083-0.01710.1241-0.114-0.10670.00360.06750.01390.00980.1089-0.02120.07882.005120.355329.0718
110.7348-0.3578-0.14650.7601-0.5061.18360.0218-0.0320.08440.0167-0.0181-0.0281-0.1326-0.05130.00570.09650.001-0.00920.0754-0.00880.06238.834927.186111.2035
121.35120.0138-0.42272.1719-0.28011.7750.00710.1022-0.0163-0.2456-0.09160.0343-0.0388-0.11020.07210.11380.01610.01220.07660.02170.055312.526424.9359-5.9403
132.34920.4419-0.42641.8961-1.16231.5930.07690.14380.1461-0.1715-0.04790.0113-0.0215-0.0313-0.01040.16080.0372-0.01140.07710.00140.040811.138626.2668-7.5996
140.76930.50980.33621.21350.55791.32840.01720.05430.05930.00020.0137-0.028-0.04090.0566-0.01590.0692-0.01370.01230.08080.00760.081813.471-1.4288-39.7287
151.1843-0.2518-0.05661.7265-0.01230.86410.02390.1122-0.0533-0.1147-0.0037-0.08770.05840.0984-0.0180.0904-0.00120.00440.1067-0.01210.077418.8828-13.1514-46.1978
161.13230.3361-0.12132.30510.48481.3812-0.03510.2210.1842-0.25880.06390.0677-0.25310.06580.02480.1207-0.04390.0090.1290.01730.136320.23625.77-43.4355
172.39750.16610.55571.9382-0.05171.350.034-0.24240.16880.1191-0.02840.0991-0.1025-0.0289-0.00020.1415-0.02890.00650.096-0.02920.111711.44934.574-32.1138
181.06070.0501-0.10581.35490.14681.2567-0.0535-0.05180.17840.02510.00140.0707-0.18840.03120.070.1587-0.02570.01730.0854-0.03140.196516.167316.2042-26.5161
193.921-0.67810.26512.7559-0.00290.60620.04560.08430.41670.0203-0.0418-0.0731-0.18940.02990.05070.1758-0.05120.02590.1281-0.04030.17218.201517.9216-26.2051
201.12130.76360.43450.93240.05681.03750.03210.11320.14630.035-0.10440.1021-0.1438-0.02660.06970.1221-0.01870.00260.10450.01810.09990.7948-5.6177-27.9038
211.8066-0.0237-0.23540.6210.00681.0279-0.0045-0.17960.00470.08960.0144-0.03850.0390.19820.00540.1246-0.0072-0.01210.13050.00610.066212.7797-14.1192-18.1457
221.8671-0.0579-0.85191.4202-0.3132.20690.0149-0.1156-0.0350.0315-0.0099-0.07910.02460.2007-0.02080.09690.0074-0.02290.13290.00810.089720.516-18.6564-24.8676
230.67210.4145-0.69540.77160.01951.8837-0.0492-0.3932-0.22450.14510.0552-0.27060.22230.43220.01350.13450.042-0.03020.23090.04320.154824.4894-24.1915-19.9909
242.0504-0.4393-0.6230.35310.05290.6601-0.0636-0.0437-0.17210.07660.01770.04990.13080.01690.05660.134-0.0191-0.00160.08930.01620.11465.1689-20.9873-22.6647
253.58110.0573-0.05221.6762-0.09281.17660.016-0.16790.38470.1721-0.01290.0688-0.2497-0.0876-0.03170.16180.00290.02430.0922-0.01060.1319-3.7257-0.8486-20.1343
262.85520.3161-0.1292.17270.48712.51240.06480.12650.0846-0.0936-0.04960.17920.0022-0.2574-0.05140.1073-0.00170.0230.09650.01520.1286-12.4496-8.6948-24.7864
271.90140.3744-1.04752.75630.67173.27960.0041-0.05410.05330.20480.03440.2515-0.0034-0.2992-0.04160.10010.015-0.01090.12410.02330.1451-13.6421-7.4539-23.1506
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 231 through 297 )
2X-RAY DIFFRACTION2chain 'A' and (resid 298 through 319 )
3X-RAY DIFFRACTION3chain 'A' and (resid 320 through 377 )
4X-RAY DIFFRACTION4chain 'A' and (resid 378 through 441 )
5X-RAY DIFFRACTION5chain 'A' and (resid 442 through 458 )
6X-RAY DIFFRACTION6chain 'A' and (resid 459 through 500 )
7X-RAY DIFFRACTION7chain 'A' and (resid 501 through 525 )
8X-RAY DIFFRACTION8chain 'B' and (resid 232 through 317 )
9X-RAY DIFFRACTION9chain 'B' and (resid 318 through 348 )
10X-RAY DIFFRACTION10chain 'B' and (resid 349 through 397 )
11X-RAY DIFFRACTION11chain 'B' and (resid 398 through 458 )
12X-RAY DIFFRACTION12chain 'B' and (resid 459 through 500 )
13X-RAY DIFFRACTION13chain 'B' and (resid 501 through 525 )
14X-RAY DIFFRACTION14chain 'C' and (resid 232 through 317 )
15X-RAY DIFFRACTION15chain 'C' and (resid 318 through 397 )
16X-RAY DIFFRACTION16chain 'C' and (resid 398 through 441 )
17X-RAY DIFFRACTION17chain 'C' and (resid 442 through 458 )
18X-RAY DIFFRACTION18chain 'C' and (resid 459 through 500 )
19X-RAY DIFFRACTION19chain 'C' and (resid 501 through 525 )
20X-RAY DIFFRACTION20chain 'D' and (resid 230 through 252 )
21X-RAY DIFFRACTION21chain 'D' and (resid 253 through 317 )
22X-RAY DIFFRACTION22chain 'D' and (resid 318 through 354 )
23X-RAY DIFFRACTION23chain 'D' and (resid 355 through 377 )
24X-RAY DIFFRACTION24chain 'D' and (resid 378 through 448 )
25X-RAY DIFFRACTION25chain 'D' and (resid 449 through 473 )
26X-RAY DIFFRACTION26chain 'D' and (resid 474 through 500 )
27X-RAY DIFFRACTION27chain 'D' and (resid 501 through 526 )

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Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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