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- PDB-5iyw: Protruding domain of GII.4 human norovirus CHDC2094 in complex wi... -

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Basic information

Entry
Database: PDB / ID: 5iyw
TitleProtruding domain of GII.4 human norovirus CHDC2094 in complex with 3-fucosyllactose (3FL)
ComponentsVP1
KeywordsVIRAL PROTEIN / Viral capsid protein / Protruding domain / Norovirus / Human milk oligosaccharides
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
Biological speciesNorovirus Hu/GII.4/CHDC2094/1974/US
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.41 Å
AuthorsSingh, B.K. / Hansman, G.S.
CitationJournal: To be published
Title: Structural basis for GII.4 norovirus inhibition by human milk oligosaccharides.
Authors: Singh, B.K. / Hansman, G.S.
History
DepositionMar 24, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Apr 5, 2017Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_struct_special_symmetry / pdbx_validate_close_contact / 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 / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_seq_id_1 / _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 2.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: VP1
B: VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7757
Polymers67,4852
Non-polymers1,2905
Water15,079837
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint10 kcal/mol
Surface area23670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.450, 107.110, 136.730
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-1045-

HOH

21A-1093-

HOH

31B-1140-

HOH

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Components

#1: Protein VP1


Mass: 33742.633 Da / Num. of mol.: 2 / Fragment: P DOMAIN (UNP residues 225-530)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus Hu/GII.4/CHDC2094/1974/US / Plasmid: MBP-HTSHP / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D0QJ68
#2: Polysaccharide alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]alpha-D-glucopyranose


Type: oligosaccharide / Mass: 488.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGalpb1-4]DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5][a1221m-1a_1-5][a2112h-1b_1-5]/1-2-3/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C2H6O2
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H5O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 837 / 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: 2.46 Å3/Da / Density % sol: 50.01 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: Sodium citrate, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.97625 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 23, 2015
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97625 Å / Relative weight: 1
ReflectionResolution: 1.4→43.67 Å / Num. obs: 128031 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 14.89 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.13
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.4-1.440.8651.41194
1.44-1.480.7441.71198.6
1.48-1.520.6142.06198.6
1.52-1.570.5162.48198.9
1.57-1.620.4233.06198.9
1.62-1.670.3413.74198.7
1.67-1.740.2824.41196.4
1.74-1.810.2155.95199.1
1.81-1.890.1757.23199.4
1.89-1.980.1558.6199.4
1.98-2.090.11311.78199.6
2.09-2.210.09913.28199.5
2.21-2.370.09214.49199.1
2.37-2.560.07716.3199.7
2.56-2.80.06618.34199.4
2.8-3.130.05620.56197.2
3.13-3.620.04625.3199.3
3.62-4.430.0427.12198.5
4.43-6.260.03729.2199.7
6.260.03728.73198

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.23 Å48.6 Å
Translation7.23 Å48.6 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
PHASER2.5.6phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IYN

5iyn


Resolution: 1.41→43.669 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.93
RfactorNum. reflection% reflection
Rfree0.1714 6294 5 %
Rwork0.1395 --
obs0.1411 125855 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.43 Å2 / Biso mean: 19.4323 Å2 / Biso min: 9.08 Å2
Refinement stepCycle: final / Resolution: 1.41→43.669 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4719 0 87 837 5643
Biso mean--34.92 29.31 -
Num. residues----609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085048
X-RAY DIFFRACTIONf_angle_d1.2216926
X-RAY DIFFRACTIONf_chiral_restr0.078781
X-RAY DIFFRACTIONf_plane_restr0.006911
X-RAY DIFFRACTIONf_dihedral_angle_d12.3681825
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.41-1.4260.30972080.23383947415599
1.426-1.44280.29792080.23863949415798
1.4428-1.46040.25352080.22223950415899
1.4604-1.47890.26582050.21783901410698
1.4789-1.49840.27212070.20083934414199
1.4984-1.51890.26552080.2123951415999
1.5189-1.54060.23552090.19613972418199
1.5406-1.56360.23892080.18993941414999
1.5636-1.5880.25112080.17523953416199
1.588-1.6140.22712090.16673980418999
1.614-1.64190.19542090.15483967417699
1.6419-1.67170.20022080.153948415699
1.6717-1.70390.19442040.14513878408297
1.7039-1.73870.17642040.13913868407296
1.7387-1.77650.18492090.12723982419199
1.7765-1.81780.16142100.12453985419599
1.8178-1.86330.1682090.12753965417499
1.8633-1.91360.15412110.1334017422899
1.9136-1.970.18672110.13813999421099
1.97-2.03350.14682100.126139894199100
2.0335-2.10620.17182110.127540224233100
2.1062-2.19050.13732120.124740154227100
2.1905-2.29020.17152100.12893990420099
2.2902-2.4110.15842120.1264045425799
2.411-2.5620.14082130.130540414254100
2.562-2.75980.16332120.136540214233100
2.7598-3.03750.17272110.13814009422098
3.0375-3.47680.16952120.13854034424699
3.4768-4.37980.15752140.12914061427599
4.3798-43.69030.1322240.12334247447199

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