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

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Basic information

Entry
Database: PDB / ID: 5iyq
TitleProtruding domain of GII.4 human norovirus CHDC2094 in complex with HBGA type B (triglycan)
ComponentsProtruding domain of GII.4 norovirus CHDC2094 capsid
KeywordsVIRAL PROTEIN / Viral capsid protein / Protruding domain / Norovirus / HBGA
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: Four decades of structural evolution of GII.4 norovirus
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: Atomic model / Data collection ...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 / 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_alt_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 / _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: Protruding domain of GII.4 norovirus CHDC2094 capsid
B: Protruding domain of GII.4 norovirus CHDC2094 capsid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,22217
Polymers67,3112
Non-polymers1,91115
Water14,700816
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8060 Å2
ΔGint47 kcal/mol
Surface area22770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.810, 105.930, 135.480
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
11B-1111-

HOH

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Components

#1: Protein Protruding domain of GII.4 norovirus CHDC2094 capsid


Mass: 33655.559 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-(1-2)-[alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose


Type: oligosaccharide / Mass: 488.438 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2[DGalpa1-3]DGalpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2112h-1a_1-5][a1221m-1a_1-5]/1-2-1/a2-b1_a3-c1WURCSPDB2Glycan 1.1.0
[][a-D-Galp]{[(2+1)][a-L-Fucp]{}[(3+1)][a-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 816 / 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: 2.39 Å3/Da / Density % sol: 48.61 %
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: ID23-1 / Wavelength: 0.97625 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 27, 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→48.17 Å / Num. obs: 126435 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 5.9 % / Biso Wilson estimate: 13.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.072 / Net I/σ(I): 15.47
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.4-1.440.8931.91198.9
1.44-1.470.7152.39199.9
1.47-1.520.5932.89199.9
1.52-1.560.4753.52199.7
1.56-1.620.3724.47199.5
1.62-1.670.2995.761100
1.67-1.740.2436.951100
1.74-1.810.1829.11199.9
1.81-1.890.1411.6199.9
1.89-1.980.10913.97199.3
1.98-2.090.08418.82199.8
2.09-2.210.07222.13199.9
2.21-2.370.06225.381100
2.37-2.550.05727.3199.9
2.55-2.80.04830.15199.7
2.8-3.130.03937.87199.5
3.13-3.610.03147.37199.7
3.61-4.420.02553.38198.7
4.42-6.260.02451.64199.6
6.260.02756.27197.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.26 Å48.17 Å
Translation7.26 Å48.17 Å

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Processing

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

5iyn


Resolution: 1.41→48.167 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 14.27
RfactorNum. reflection% reflection
Rfree0.1559 6182 5 %
Rwork0.1262 --
obs0.1277 123646 99.75 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 101.47 Å2 / Biso mean: 16.8018 Å2 / Biso min: 7.84 Å2
Refinement stepCycle: final / Resolution: 1.41→48.167 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4707 0 131 816 5654
Biso mean--28.84 27.22 -
Num. residues----608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075065
X-RAY DIFFRACTIONf_angle_d1.2356929
X-RAY DIFFRACTIONf_chiral_restr0.075765
X-RAY DIFFRACTIONf_plane_restr0.006908
X-RAY DIFFRACTIONf_dihedral_angle_d12.1881897
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 (%)
1.41-1.4260.24652060.217339154121100
1.426-1.44280.26342030.202438514054100
1.4428-1.46040.26972030.201938604063100
1.4604-1.47890.21712060.174739254131100
1.4789-1.49830.22282040.16838644068100
1.4983-1.51890.17582050.162839074112100
1.5189-1.54060.21072050.155838964101100
1.5406-1.56360.17912050.149138854090100
1.5636-1.5880.2132020.14823844404699
1.588-1.6140.17572050.138738994104100
1.614-1.64190.18922040.124638774081100
1.6419-1.67170.17822070.119539274134100
1.6717-1.70390.16452050.114238934098100
1.7039-1.73870.16012050.11438974102100
1.7387-1.77650.15892040.110938754079100
1.7765-1.81780.14312070.107639224129100
1.8178-1.86330.15442060.108939314137100
1.8633-1.91360.1482040.112338754079100
1.9136-1.970.15562060.11243907411399
1.97-2.03350.132050.109938924097100
2.0335-2.10620.14332080.114539504158100
2.1062-2.19060.14592050.113439064111100
2.1906-2.29020.13912070.112139234130100
2.2902-2.4110.13022070.114139284135100
2.411-2.5620.12782080.120439554163100
2.562-2.75980.16872070.127639464153100
2.7598-3.03750.15622080.13293944415299
3.0375-3.4770.16052090.129839764185100
3.477-4.38010.13542090.12423971418099
4.3801-48.19510.14312170.12764123434099

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