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- PDB-6jys: GII.13/21 noroviruses recognize glycans with a terminal beta-gala... -

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Basic information

Entry
Database: PDB / ID: 6jys
TitleGII.13/21 noroviruses recognize glycans with a terminal beta-galactose via an unconventional glycan binding site
Componentshuman norovirus P protein
KeywordsVIRAL PROTEIN / human noroviruses / histo-blood group antigens / glycan / receptor
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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Thomsen-Friedenreich antigen / THREONINE / human norovirus P protein
Similarity search - Component
Biological speciesHuman norovirus - Alphatron
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.697 Å
AuthorsDuan, Z. / Xin, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Science Foundation (China)no.2018ZA10711-001 and no.2017ZX10104001 China
CitationJournal: J.Virol. / Year: 2019
Title: GII.13/21 Noroviruses Recognize Glycans with a Terminal beta-Galactose via an Unconventional Glycan Binding Site.
Authors: Cong, X. / Sun, X.M. / Qi, J.X. / Li, H.B. / Chai, W.G. / Zhang, Q. / Wang, H. / Kong, X.Y. / Song, J. / Pang, L.L. / Jin, M. / Li, D.D. / Tan, M. / Duan, Z.J.
History
DepositionApr 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 22, 2019Provider: repository / Type: Initial release
Revision 1.1Jun 5, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 31, 2019Group: Data collection / Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_unobs_or_zero_occ_atoms / 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.pdbx_formal_charge / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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 2.1Mar 6, 2024Group: 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
Revision 2.2May 1, 2024Group: Derived calculations / Category: struct_conn / Item: _struct_conn.pdbx_role

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: human norovirus P protein
B: human norovirus P protein
C: human norovirus P protein
D: human norovirus P protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)137,4799
Polymers135,6234
Non-polymers1,8565
Water29,4371634
1
A: human norovirus P protein
D: human norovirus P protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,5784
Polymers67,8122
Non-polymers7672
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-3 kcal/mol
Surface area23590 Å2
MethodPISA
2
B: human norovirus P protein
hetero molecules

C: human norovirus P protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9015
Polymers67,8122
Non-polymers1,0893
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_445-x-1,y-1/2,-z+1/21
Buried area5790 Å2
ΔGint3 kcal/mol
Surface area24140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.728, 99.695, 221.824
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
human norovirus P protein


Mass: 33905.820 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human norovirus - Alphatron
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: A0A509GV48*PLUS
#2: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose / Thomsen-Friedenreich antigen


Type: oligosaccharide, Oligosaccharide / Class: Antigen / Mass: 383.349 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: Thomsen-Friedenreich antigen
DescriptorTypeProgram
DGalpb1-3DGalpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2112h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GalpNAc]{[(3+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Polysaccharide beta-D-galactopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)]2-acetamido-2-deoxy- ...beta-D-galactopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)]2-acetamido-2-deoxy-alpha-D-galactopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3[DGlcpNAcb1-6]DGalpNAca1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2112h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2-3/a3-b1_a6-c1WURCSPDB2Glycan 1.1.0
[]{[(3+1)][a-D-GalpNAc]{[(3+1)][b-D-Galp]{}[(6+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#4: Chemical ChemComp-THR / THREONINE


Type: L-peptide linking / Mass: 119.119 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H9NO3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1634 / 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: 2.48 Å3/Da / Density % sol: 50.32 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M ammonium acetate, 0.1 M HEPES pH 7.5, 5% polyethylene glycol 3350

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Data collection

DiffractionMean temperature: 113 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97917 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 2, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97917 Å / Relative weight: 1
ReflectionResolution: 1.697→50 Å / Num. obs: 144550 / % possible obs: 96.8 % / Redundancy: 11.6 % / Biso Wilson estimate: 14.16 Å2 / Net I/σ(I): 19.652
Reflection shellResolution: 1.7→1.76 Å

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.697→48.635 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.08
RfactorNum. reflection% reflection
Rfree0.1876 7153 4.97 %
Rwork0.1649 --
obs0.166 143826 96.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.92 Å2 / Biso mean: 18.9656 Å2 / Biso min: 4.53 Å2
Refinement stepCycle: final / Resolution: 1.697→48.635 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9584 0 114 1634 11332
Biso mean--25.65 27.49 -
Num. residues----1233
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6966-1.71590.29031990.22773853405283
1.7159-1.73610.26142330.21754284451791
1.7361-1.75720.27571980.21714328452693
1.7572-1.77950.2342230.20444420464393
1.7795-1.80290.23922340.18614356459093
1.8029-1.82760.23172320.18174427465994
1.8276-1.85370.2222320.17954409464194
1.8537-1.88140.20362340.18894415464995
1.8814-1.91080.2122280.18934452468094
1.9108-1.94210.20872280.18984435466395
1.9421-1.97560.20812080.18354542475096
1.9756-2.01150.21112460.17794458470495
2.0115-2.05020.20142160.1684474469095
2.0502-2.0920.222340.17024526476095
2.092-2.13750.19112640.17044451471596
2.1375-2.18730.1842620.16784533479596
2.1873-2.2420.19412440.1654586483097
2.242-2.30260.192620.17184551481397
2.3026-2.37030.20822130.16914633484697
2.3703-2.44680.19592620.16874636489898
2.4468-2.53430.20282390.17114694493399
2.5343-2.63570.16682160.17084722493899
2.6357-2.75570.18612570.16764714497199
2.7557-2.9010.17012710.16934694496599
2.901-3.08270.20382490.16584723497299
3.0827-3.32060.17762680.156547605028100
3.3206-3.65470.16882550.149647935048100
3.6547-4.18330.1412440.139148495093100
4.1833-5.26950.1542380.126748885126100
5.2695-48.65460.172640.16015067533199
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)
10.2972-0.1518-0.02830.24280.12650.4445-0.0229-0.01170.01860.00040.02190.0059-0.0226-0.0297-0.0070.0488-0.00420.00690.0617-0.00260.0607-34.01371.17866.4819
20.31430.12220.12050.0602-0.06310.75730.02040.01110.01250.0204-0.0238-0.0087-0.1210.01-0.0060.1028-0.0011-0.00130.03470.01170.0671-44.4097-32.054548.7912
30.3439-0.0478-0.13250.18560.21010.67020.01160.0085-0.0050.0041-0.00520.00630.11450.06240.01830.09740.00840.00810.04820.0030.0692-5.4543-3.456657.6426
40.3374-0.0099-0.00460.4321-0.17470.2996-0.008-0.02050.04810.01590.0264-0.0540.00510.05850.07040.0332-00.01290.0692-0.01290.0716-12.4499-9.73279.6999
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B
3X-RAY DIFFRACTION3chain C
4X-RAY DIFFRACTION4chain D

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