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Basic information

Entry
Database: PDB / ID: 4ops
TitleCrystal structure of P domain from norovirus strain Farmington Hills 2004 in complex with HBGA type Leb (tetraglycan)
ComponentsMajor capsid protein
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 / Major capsid protein
Similarity search - Component
Biological speciesNorovirus Hu/GII.4/Farmington Hills/2004/USA
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.76 Å
AuthorsSingh, B.K. / Leuthold, M. / 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: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / 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 / 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_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,0753
Polymers67,3992
Non-polymers6761
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4660 Å2
ΔGint-2 kcal/mol
Surface area23510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.450, 90.110, 91.870
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: MET / End label comp-ID: MET / Auth seq-ID: 225 - 530 / Label seq-ID: 1 - 306

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB

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Components

#1: Protein Major capsid protein


Mass: 33699.574 Da / Num. of mol.: 2
Fragment: P domain Farmington Hills 2004 (residues 225 to 530)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/GII.4/Farmington Hills/2004/USA
Gene: JQ478408 / Plasmid: MBP-HTSHP / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: R4I4P2
#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.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.19 Å3/Da / Density % sol: 43.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: PEG 3350, Magnesium formate, 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: 0.9794 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jun 20, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.75→97.3449 Å / Num. obs: 59028 / % possible obs: 97.3 % / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 17.39 Å2 / Rmerge(I) obs: 0.112 / Net I/σ(I): 9.88
Reflection shell
Resolution (Å)Highest resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.75-1.795.70.5352.41195.1
1.79-1.840.4383.22199.8
1.84-1.90.7072.65197.9
1.9-1.950.6113.79183.5
1.95-2.020.3694.94199
2.02-2.090.3745.47197.2
2.09-2.170.2466.95199.4
2.17-2.260.2197.64196.1
2.26-2.360.1858.69198.2
2.36-2.470.13311.17199.7
2.47-2.610.11912.38199.8
2.61-2.760.11413.15199.2
2.76-2.960.08715.3199.4
2.96-3.190.07818.24199.6
3.19-3.50.07119.58198.9
3.5-3.910.07518.88196.7
3.91-4.510.05821.02198
4.51-5.530.05422.83199.2
5.53-7.820.05521.84199.2
7.820.04922.74197.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
PHASER2.5.3phasing
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.14data extraction
XDSdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→47.808 Å / SU ML: 0.18 / σ(F): 1.33 / Phase error: 21.06 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2164 2894 5 %
Rwork0.185 --
obs0.1866 57869 97.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.89 Å2
Refinement stepCycle: LAST / Resolution: 1.76→47.808 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4723 0 46 324 5093
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0134932
X-RAY DIFFRACTIONf_angle_d1.3626746
X-RAY DIFFRACTIONf_dihedral_angle_d13.3331770
X-RAY DIFFRACTIONf_chiral_restr0.058749
X-RAY DIFFRACTIONf_plane_restr0.008894
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2808X-RAY DIFFRACTION4.526TORSIONAL
12B2808X-RAY DIFFRACTION4.526TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.78890.27581400.20682653X-RAY DIFFRACTION100
1.7889-1.81970.22521390.17742652X-RAY DIFFRACTION100
1.8197-1.85280.24531390.18762633X-RAY DIFFRACTION100
1.8528-1.88840.28991390.25932636X-RAY DIFFRACTION98
1.8884-1.9270.53351120.51112102X-RAY DIFFRACTION80
1.927-1.96890.37941240.34192353X-RAY DIFFRACTION89
1.9689-2.01470.21971400.19712671X-RAY DIFFRACTION100
2.0147-2.06510.23851370.2172595X-RAY DIFFRACTION98
2.0651-2.12090.31731360.21892587X-RAY DIFFRACTION97
2.1209-2.18330.1891400.18542658X-RAY DIFFRACTION100
2.1833-2.25380.30981300.2562522X-RAY DIFFRACTION94
2.2538-2.33430.27041380.19722609X-RAY DIFFRACTION97
2.3343-2.42780.20241410.16792672X-RAY DIFFRACTION100
2.4278-2.53830.21341400.17062664X-RAY DIFFRACTION100
2.5383-2.67210.2031410.17022673X-RAY DIFFRACTION99
2.6721-2.83950.21581410.16772684X-RAY DIFFRACTION100
2.8395-3.05870.18931410.17662687X-RAY DIFFRACTION99
3.0587-3.36640.19911430.1772705X-RAY DIFFRACTION99
3.3664-3.85340.18861400.1632656X-RAY DIFFRACTION97
3.8534-4.85410.14411420.13262707X-RAY DIFFRACTION98
4.8541-47.82570.17661510.14692856X-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)
10.7991-0.0533-0.27831.79021.00581.60770.0101-0.08130.0038-0.0249-0.02840.0066-0.04020.00030.02270.08760.0038-0.00780.13330.01870.120911.0374104.113330.0678
21.1103-0.3856-0.7763.564-0.10011.4770.0583-0.16590.12370.2839-0.092-0.261-0.0830.09790.0080.1523-0.037-0.02670.1885-0.03010.136118.8502111.760841.8135
30.95680.19090.03951.20940.1541.05020.00760.0981-0.0707-0.1161-0.0466-0.06490.04830.04920.02740.12450.00720.00260.1222-0.00440.143813.724891.634420.2432
42.1792-0.53180.70950.3066-0.40960.7490.0405-0.0083-0.0586-0.0172-0.0008-0.00970.09840.0091-0.05080.17540.0080.00390.1325-0.0120.156617.2833118.711315.4723
52.6454-0.29580.17742.1355-1.65332.04650.09480.1688-0.1215-0.3278-0.1803-0.10950.3289-0.10110.07610.15960.02850.02860.1829-0.01920.17336.4284114.344318.5903
61.9555-1.4940.90075.2262-3.16943.32320.0526-0.1455-0.03790.1585-0.0476-0.0758-0.03370.11980.02380.1183-0.0206-0.01030.1866-0.02080.150132.2272113.992730.3129
71.8506-0.51250.57293.2104-1.34631.98520.0228-0.08820.04130.1803-0.1824-0.2931-0.05130.14060.19510.1080.0084-0.02020.2143-0.01740.18238.565117.484427.1944
82.3806-2.867-0.74734.2087-0.24951.811-0.0016-0.21810.36780.40970.0903-0.4377-0.3810.06-0.13510.1989-0.0309-0.02810.1789-0.03410.205425.8485127.284230.5314
91.6462-0.13770.50071.07770.04971.85070.03080.11370.214-0.0269-0.0476-0.0041-0.05880.06310.0190.13540.01690.00860.12620.01780.13718.6205125.300415.0811
102.4297-1.126-0.41692.87240.19483.43490.00470.0079-0.05280.06510.06140.1760.1024-0.3349-0.04220.1022-0.0146-0.01780.11110.01020.12441.619123.8199.6843
111.544-2.50460.94334.89590.58075.11310.02070.13720.1301-0.3746-0.1030.0585-0.2128-0.25120.030.1628-0.02-0.02150.2061-0.01120.19490.4968124.49662.886
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 225 through 323 )
2X-RAY DIFFRACTION2chain 'A' and (resid 324 through 399 )
3X-RAY DIFFRACTION3chain 'A' and (resid 400 through 530 )
4X-RAY DIFFRACTION4chain 'B' and (resid 225 through 292 )
5X-RAY DIFFRACTION5chain 'B' and (resid 293 through 323 )
6X-RAY DIFFRACTION6chain 'B' and (resid 324 through 352 )
7X-RAY DIFFRACTION7chain 'B' and (resid 353 through 380 )
8X-RAY DIFFRACTION8chain 'B' and (resid 381 through 399 )
9X-RAY DIFFRACTION9chain 'B' and (resid 400 through 464 )
10X-RAY DIFFRACTION10chain 'B' and (resid 465 through 513 )
11X-RAY DIFFRACTION11chain 'B' and (resid 514 through 530 )

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