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

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Basic information

Entry
Database: PDB / ID: 6jyn
TitleGII.13/21 noroviruses recognize glycans with a terminal beta-galactose via an unconventional glycan binding site
Componentshuman norovirus P domain protein
KeywordsVIRAL PROTEIN / Human noroviruses
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
human norovirus P domain protein
Similarity search - Component
Biological speciesHuman norovirus - Alphatron
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.599 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 26, 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: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / 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 / 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 / _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 / _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 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)136,9728
Polymers135,4394
Non-polymers1,5334
Water28,1031560
1
A: human norovirus P domain protein
B: human norovirus P domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4864
Polymers67,7192
Non-polymers7672
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint7 kcal/mol
Surface area23950 Å2
MethodPISA
2
C: human norovirus P domain protein
D: human norovirus P domain protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,4864
Polymers67,7192
Non-polymers7672
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4730 Å2
ΔGint-9 kcal/mol
Surface area23700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.936, 122.935, 83.280
Angle α, β, γ (deg.)90.000, 90.070, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
human norovirus P domain protein


Mass: 33859.688 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: A0A509GV45*PLUS
#2: Polysaccharide
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1560 / 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: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium citrate tribasic dehydrate, 20 percent 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: 0.97774 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Sep 16, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97774 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.47
ReflectionResolution: 1.599→50 Å / Num. obs: 184076 / % possible obs: 99.5 % / Redundancy: 6.8 % / Net I/σ(I): 18.333
Reflection shellResolution: 1.6→1.66 Å / Num. unique obs: 184076 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PDB_EXTRACT3.24data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.599→49.455 Å / Cross valid method: THROUGHOUT / σ(F): 95.38 / Phase error: 22.6 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2007 8591 5.02 %
Rwork0.1808 162530 -
obs0.1864 171051 92.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 107.42 Å2 / Biso mean: 16.1865 Å2 / Biso min: 6.88 Å2
Refinement stepCycle: final / Resolution: 1.599→49.455 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9568 0 104 1560 11232
Biso mean--33.91 23.71 -
Num. residues----1232
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5998-1.62740.29212770.25375981625865
1.6274-1.6570.27052990.24496389668869
1.657-1.68880.24413750.2456657703273
1.6888-1.72330.24153470.23787006735376
1.7233-1.76080.25454260.23037255768179
1.7608-1.80170.24024070.22537485789281
1.8017-1.84680.24994550.21447960841586
1.8468-1.89670.21954540.21438455890992
1.8967-1.95250.23294570.20628749920695
1.9525-2.01550.20554100.20378777918795
2.0155-2.08750.20434480.19798788923695
2.0875-2.1710.21274460.19698730917694
2.171-2.26980.20264700.19348740921095
2.2698-2.38940.21184470.19078786923395
2.3894-2.53890.22634590.1878770922995
2.5389-2.73480.20934340.18778827926195
2.7348-3.00960.19624820.18338734921694
3.0096-3.44430.18514560.16558790924695
3.4443-4.33630.16724400.14788814925495
4.3363-26.18230.18424730.15068837931094
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)
10.41540.0222-0.05540.5247-0.23390.42250.01850.0631-0.0046-0.0070.00050.0272-0.0239-0.0097-0.02170.06880.0057-0.00480.093-0.00320.0626-53.1842-18.52864.5467
20.5237-0.1137-0.05880.53850.25880.53190.0141-0.02720.01380.00040.0165-0.0341-0.01090.0468-0.03440.0633-0.0072-0.00240.09610.00470.0547-38.1955-18.455623.9124
30.33920.05270.07760.48610.20440.58690.00670.0827-0.0075-0.01120.0213-0.03550.00120.0799-0.02730.05920.00420.00460.1294-0.00250.0627-73.1853-11.768446.1755
40.3858-0.05680.10080.531-0.28850.61440.0139-0.0210.0006-0.00080.01490.0367-0.0022-0.0596-0.02610.0583-0.00140.00460.10350.00060.0662-88.224-12.02365.5852
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA3 - 602
2X-RAY DIFFRACTION2chain BB3 - 602
3X-RAY DIFFRACTION3chain CC3 - 602
4X-RAY DIFFRACTION4chain DD3 - 602

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