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- PDB-4p26: Structure of the P domain from a GI.7 Norovirus variant in comple... -

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Basic information

Entry
Database: PDB / ID: 4p26
TitleStructure of the P domain from a GI.7 Norovirus variant in complex with A-type 2 HBGA
ComponentsP domain of VP1
KeywordsVIRAL PROTEIN / P domain / Capsid protein / Norovirus / HBGA / A type 2 / Type 2 HBGA / Secretor
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 / Viral coat protein subunit / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Blood group A H type 2 antigen, beta anomer / Major capsid protein
Similarity search - Component
Biological speciesNorovirus Hu/GI.7/TCH-060/USA/2003
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_unobs_or_zero_occ_atoms / 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 / _atom_site_anisotrop.pdbx_label_asym_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_site_gen.label_asym_id
Revision 3.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_validate_symm_contact / 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.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_2 / _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: Derived calculations / Structure summary / Category: pdbx_molecule_features / struct_conn / Item: _struct_conn.pdbx_leaving_atom_flag
Revision 3.2Sep 27, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
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)132,6687
Polymers130,4704
Non-polymers2,1983
Water17,529973
1
A: P domain of VP1
B: P domain of VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,7004
Polymers65,2352
Non-polymers1,4652
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5250 Å2
ΔGint17 kcal/mol
Surface area22830 Å2
MethodPISA
2
C: P domain of VP1
D: P domain of VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9683
Polymers65,2352
Non-polymers7331
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-1 kcal/mol
Surface area22560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.580, 63.260, 90.430
Angle α, β, γ (deg.)99.25, 97.82, 119.62
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 alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D- ...alpha-L-fucopyranose-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 732.682 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide with branches / References: Blood group A H type 2 antigen, beta anomer
DescriptorTypeProgram
LFucpa1-2[DGalpNAca1-3]DGalpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/4,4,3/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5][a1221m-1a_1-5][a2112h-1a_1-5_2*NCC/3=O]/1-2-3-4/a4-b1_b2-c1_b3-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}[(3+1)][a-D-GalpNAc]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 973 / 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: 2.28 Å3/Da / Density % sol: 46.03 %
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: Jan 28, 2013
RadiationProtocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.9→34.024 Å / Num. obs: 87902 / % possible obs: 96.8 % / Redundancy: 3.4 % / Net I/σ(I): 9.1

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4P12

4p12


Resolution: 1.9→34.024 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 18.48 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.189 4403 5.01 %Random
Rwork0.1597 ---
obs0.1612 87893 96.81 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→34.024 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8743 0 150 973 9866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.019151
X-RAY DIFFRACTIONf_angle_d1.31512541
X-RAY DIFFRACTIONf_dihedral_angle_d12.5633326
X-RAY DIFFRACTIONf_chiral_restr0.0851419
X-RAY DIFFRACTIONf_plane_restr0.0061645
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.92160.24961500.19312776X-RAY DIFFRACTION95
1.9216-1.94420.24191320.18682723X-RAY DIFFRACTION95
1.9442-1.96790.23031730.18232736X-RAY DIFFRACTION96
1.9679-1.99280.22071400.17862736X-RAY DIFFRACTION96
1.9928-2.0190.24981570.17642772X-RAY DIFFRACTION96
2.019-2.04670.23311400.17722781X-RAY DIFFRACTION96
2.0467-2.07590.22971220.17512764X-RAY DIFFRACTION96
2.0759-2.10690.22321570.17142774X-RAY DIFFRACTION96
2.1069-2.13980.18361380.16832735X-RAY DIFFRACTION96
2.1398-2.17490.20591300.1612777X-RAY DIFFRACTION96
2.1749-2.21240.21031410.1632760X-RAY DIFFRACTION97
2.2124-2.25260.20271450.16292793X-RAY DIFFRACTION96
2.2526-2.2960.19071420.16982741X-RAY DIFFRACTION97
2.296-2.34280.19171580.16782853X-RAY DIFFRACTION97
2.3428-2.39370.22571400.16932721X-RAY DIFFRACTION97
2.3937-2.44940.22931530.16932801X-RAY DIFFRACTION97
2.4494-2.51060.21821720.17322774X-RAY DIFFRACTION97
2.5106-2.57850.20721440.17352743X-RAY DIFFRACTION97
2.5785-2.65430.22341440.16892828X-RAY DIFFRACTION97
2.6543-2.740.20421350.17332818X-RAY DIFFRACTION97
2.74-2.83790.20431320.16552772X-RAY DIFFRACTION97
2.8379-2.95140.21231580.16672781X-RAY DIFFRACTION98
2.9514-3.08570.20751360.16592821X-RAY DIFFRACTION97
3.0857-3.24820.18161480.14972807X-RAY DIFFRACTION98
3.2482-3.45160.16481540.14372800X-RAY DIFFRACTION98
3.4516-3.71780.16411660.14482827X-RAY DIFFRACTION98
3.7178-4.09130.13581650.13692781X-RAY DIFFRACTION98
4.0913-4.6820.1231550.12222799X-RAY DIFFRACTION98
4.682-5.89390.15891310.14352851X-RAY DIFFRACTION98
5.8939-34.02950.1881450.1772845X-RAY DIFFRACTION98
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)
12.6657-0.07120.38582.465-0.07891.6320.03670.08090.13480.0161-0.06740.1208-0.2153-0.0197-0.00160.1149-0.02130.01450.10440.02340.079218.736227.360257.9715
22.266-0.3468-0.38381.02290.0941.2111-0.002-0.32580.02160.15530.0097-0.08490.03320.1911-0.00460.1502-0.0169-0.01980.13290.01170.062430.922418.15467.7657
31.9902-0.0766-0.21111.49360.09022.1541-0.0069-0.1774-0.17660.0663-0.0241-0.18370.13550.23650.00890.08660.0217-0.02520.11210.02410.116839.99059.983960.059
41.8273-0.3327-0.98451.30370.24690.6812-0.0552-0.1823-0.14220.15060.03460.02190.05560.10220.03350.1158-0.0122-0.00060.10740.02130.08920.156413.371265.786
53.25420.46540.06491.94270.00622.42150.0462-0.06420.33050.0159-0.06170.1812-0.1517-0.24980.02040.12760.01190.02710.0740.00530.11879.816528.057363.3036
62.65740.278-1.48373.28941.74534.80270.0402-0.05420.02210.1522-0.05970.27450.024-0.4160.00990.10.0263-0.01080.13780.0170.13884.217425.396362.6548
70.78610.56270.29951.68820.78021.46330.00290.03220.0773-0.0149-0.0064-0.0125-0.08470.04040.00180.0714-0.01280.01040.08470.01250.070931.538431.178544.9923
81.6289-0.61540.292.4905-1.09992.60120.01190.1301-0.214-0.148-0.0311-0.01750.22880.05130.06660.0726-0.00010.00670.1023-0.03330.094935.101715.051638.7819
90.55650.2469-0.16042.15960.22650.9854-0.00150.07020.0773-0.22130.0017-0.153-0.15130.1261-0.00370.0903-0.02210.01040.13070.00680.107940.174533.807742.6574
100.67750.07630.1653.26110.23661.7067-0.0152-0.13370.33110.15950.01720.0293-0.1081-0.0240.0160.1414-0.0490.00190.0882-0.0220.092831.21837.914252.3054
110.93420.1277-0.23551.0806-0.13610.7097-0.0013-0.09690.15560.1438-0.0042-0.0422-0.06270.03850.00790.1516-0.0365-0.00140.1024-0.0160.167238.085947.371161.0227
124.5788-0.34070.78712.01450.34050.7949-0.0150.03750.6725-0.0389-0.0503-0.0012-0.21980.03770.05930.2-0.01820.01950.1295-0.02730.202333.814754.04658.5576
130.7628-0.07620.15380.8774-0.43962.0892-0-0.00440.0503-0.089-0.0105-0.0140.0262-0.01260.01180.08560.0150.00120.072-0.00890.081630.070154.4287101.467
141.79120.5215-0.46081.9496-0.63352.00490.0232-0.21560.07490.1117-0.03180.0848-0.079-0.01810.0140.07470.0105-0.00650.1209-0.02290.069723.693151.2849114.6612
153.3475-0.2885-1.18061.8783-0.61422.39510.0083-0.11230.45250.33820.12430.4426-0.4395-0.56420.02250.18550.06970.01560.19640.00980.159117.432262.7329107.234
161.0181-0.2085-0.27381.3667-0.76011.98760.03080.01190.0988-0.0084-0.0391-0.0608-0.11040.06290.00260.11730.0055-0.0080.0887-0.00330.076229.697159.218293.5255
171.52720.4508-0.41182.55880.05642.1553-0.0510.20250.0376-0.2136-0.01090.1658-0.0021-0.22520.06490.1410.0192-0.01190.13090.01640.105527.762156.973878.757
182.41220.7175-0.46651.9649-1.0841.7490.03320.15390.1804-0.2101-0.03860.12080.043-0.0665-0.01360.20180.0434-0.0160.12670.00150.083428.75959.020178.0353
192.4150.33510.03281.90530.35351.19180.0101-0.0841-0.0925-0.00950.0178-0.11620.03180.06770.00760.0860.0127-0.00270.0858-0.00450.081138.28633.608697.8237
203.52290.4876-0.20642.92450.13313.42150.02980.2631-0.1944-0.19410.08630.32580.1162-0.2087-0.08590.11720.0089-0.05650.1303-0.0050.15513.42931.449594.2955
213.1569-0.8285-1.14562.41440.56342.6343-0.0671-0.0824-0.0479-0.0619-0.03330.04990.02370.00870.07950.0813-0.0197-0.0230.0845-0.0110.092121.156331.2125101.7771
222.29890.5884-1.212.12231.84732.95940.22950.1990.3985-0.2154-0.43580.6904-0.4339-0.3264-0.13030.11670.0538-0.03910.1989-0.03040.274810.393941.3593105.2833
232.3767-0.4354-0.26072.4206-0.26031.5533-0.0415-0.0984-0.18340.0765-0.0570.08950.1171-0.12080.08480.0898-0.00960.0030.1294-0.00750.09817.439827.8346105.6645
243.04-0.6717-0.04991.16770.17621.66850.15780.0877-0.5199-0.0194-0.0326-0.16780.237-0.0618-0.11720.16170.0246-0.00180.12180.00290.166938.41723.493599.2221
252.81260.0881-0.64431.39940.04033.40590.0373-0.1724-0.01740.0337-0.0673-0.0734-0.18980.33830.04180.07130.0088-0.0220.0858-0.02230.094136.394835.943299.36
263.03860.14520.25543.05550.44973.6980.05030.04860.0329-0.05780.0426-0.1942-0.00690.2837-0.05630.11260.01650.04140.1262-0.01290.122252.171734.543696.2577
271.8765-0.47630.0232.49060.36542.43880.0161-0.1101-0.0512-0.13450.0502-0.29370.09030.2813-0.10210.10250.01550.01420.1362-0.00610.170854.192533.481198.1641
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 230 through 252 )
2X-RAY DIFFRACTION2chain 'A' and (resid 253 through 331 )
3X-RAY DIFFRACTION3chain 'A' and (resid 332 through 397 )
4X-RAY DIFFRACTION4chain 'A' and (resid 398 through 448 )
5X-RAY DIFFRACTION5chain 'A' and (resid 449 through 500 )
6X-RAY DIFFRACTION6chain 'A' and (resid 501 through 526 )
7X-RAY DIFFRACTION7chain 'B' and (resid 232 through 331 )
8X-RAY DIFFRACTION8chain 'B' and (resid 332 through 377 )
9X-RAY DIFFRACTION9chain 'B' and (resid 378 through 431 )
10X-RAY DIFFRACTION10chain 'B' and (resid 432 through 465 )
11X-RAY DIFFRACTION11chain 'B' and (resid 466 through 508 )
12X-RAY DIFFRACTION12chain 'B' and (resid 509 through 526 )
13X-RAY DIFFRACTION13chain 'C' and (resid 231 through 317 )
14X-RAY DIFFRACTION14chain 'C' and (resid 318 through 387 )
15X-RAY DIFFRACTION15chain 'C' and (resid 388 through 407 )
16X-RAY DIFFRACTION16chain 'C' and (resid 408 through 465 )
17X-RAY DIFFRACTION17chain 'C' and (resid 466 through 500 )
18X-RAY DIFFRACTION18chain 'C' and (resid 501 through 526 )
19X-RAY DIFFRACTION19chain 'D' and (resid 231 through 289 )
20X-RAY DIFFRACTION20chain 'D' and (resid 290 through 319 )
21X-RAY DIFFRACTION21chain 'D' and (resid 320 through 339 )
22X-RAY DIFFRACTION22chain 'D' and (resid 340 through 354 )
23X-RAY DIFFRACTION23chain 'D' and (resid 355 through 397 )
24X-RAY DIFFRACTION24chain 'D' and (resid 398 through 431 )
25X-RAY DIFFRACTION25chain 'D' and (resid 432 through 458 )
26X-RAY DIFFRACTION26chain 'D' and (resid 459 through 500 )
27X-RAY DIFFRACTION27chain 'D' and (resid 501 through 526 )

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