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

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Basic information

Entry
Database: PDB / ID: 5iyp
TitleProtruding domain of GII.4 human norovirus CHDC2094 in complex with HBGA type A (triglycan)
ComponentsVP1
KeywordsVIRAL PROTEIN / Norovirus / Virus capsid / Protruding domain / 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: 1.27 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: 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)69,16812
Polymers67,4852
Non-polymers1,68310
Water15,511861
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7180 Å2
ΔGint35 kcal/mol
Surface area22950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.710, 106.120, 135.920
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-1053-

HOH

21B-1144-

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-(1-2)-[2-acetamido-2-deoxy-alpha-D-galactopyranose-(1-3)]alpha-D-galactopyranose


Type: oligosaccharide / Mass: 529.490 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-2[DGalpNAca1-3]DGalpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2112h-1a_1-5][a1221m-1a_1-5][a2112h-1a_1-5_2*NCC/3=O]/1-2-3/a2-b1_a3-c1WURCSPDB2Glycan 1.1.0
[][a-D-Galp]{[(2+1)][a-L-Fucp]{}[(3+1)][a-D-GalpNAc]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 7 / 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.: 861 / 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: 2.4 Å3/Da / Density % sol: 48.83 %
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: 1.25→48.25 Å / Num. obs: 175960 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 12.32 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.057 / Net I/σ(I): 12.8
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.25-1.280.6871.69197.1
1.28-1.320.6051.94199.2
1.32-1.360.5132.28199
1.36-1.40.4412.62198.2
1.4-1.440.3513.5199.3
1.44-1.490.2754.44199.4
1.49-1.550.2245.39199.7
1.55-1.610.1686.98199.6
1.61-1.690.1348.44198.7
1.69-1.770.10710.67198.6
1.77-1.860.08214.2199.5
1.86-1.980.06617.55199.6
1.98-2.110.05221.75199.3
2.11-2.280.04424.93199
2.28-2.50.03927.09197.4
2.5-2.80.03432.87199.2
2.8-3.230.02938.38199
3.23-3.950.02444.17198.4
3.95-5.590.02246.37196.9
5.590.02648.26198.1

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.28 Å48.25 Å
Translation7.28 Å48.25 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: 1.27→48.248 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 15.53
RfactorNum. reflection% reflection
Rfree0.1594 8405 5 %
Rwork0.1349 --
obs0.1361 168078 98.98 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 88.98 Å2 / Biso mean: 16.9017 Å2 / Biso min: 7.93 Å2
Refinement stepCycle: final / Resolution: 1.27→48.248 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4719 0 113 861 5693
Biso mean--38.56 26.26 -
Num. residues----609
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0085119
X-RAY DIFFRACTIONf_angle_d1.2467023
X-RAY DIFFRACTIONf_chiral_restr0.076792
X-RAY DIFFRACTIONf_plane_restr0.006923
X-RAY DIFFRACTIONf_dihedral_angle_d12.1871837
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.27-1.28440.27182770.23125250X-RAY DIFFRACTION99
1.2844-1.29950.27982800.24065334X-RAY DIFFRACTION99
1.2995-1.31540.2782790.23575294X-RAY DIFFRACTION99
1.3154-1.3320.25292780.22145286X-RAY DIFFRACTION99
1.332-1.34960.24512770.20895265X-RAY DIFFRACTION99
1.3496-1.36810.23912790.20575287X-RAY DIFFRACTION99
1.3681-1.38760.22692740.19155201X-RAY DIFFRACTION97
1.3876-1.40830.20982770.17235277X-RAY DIFFRACTION99
1.4083-1.43030.21492800.1675324X-RAY DIFFRACTION99
1.4303-1.45380.21082800.1575314X-RAY DIFFRACTION99
1.4538-1.47890.19562780.15385279X-RAY DIFFRACTION99
1.4789-1.50570.18432790.15155306X-RAY DIFFRACTION100
1.5057-1.53470.20632810.15155344X-RAY DIFFRACTION100
1.5347-1.5660.17222830.12955372X-RAY DIFFRACTION100
1.566-1.60010.14292790.11525304X-RAY DIFFRACTION100
1.6001-1.63730.15872800.11565317X-RAY DIFFRACTION99
1.6373-1.67830.15972790.11715290X-RAY DIFFRACTION99
1.6783-1.72360.15972760.11415242X-RAY DIFFRACTION98
1.7236-1.77440.13652800.11115330X-RAY DIFFRACTION99
1.7744-1.83160.14962820.10985348X-RAY DIFFRACTION99
1.8316-1.89710.13632800.11385332X-RAY DIFFRACTION100
1.8971-1.97310.1432830.11675367X-RAY DIFFRACTION100
1.9731-2.06290.14782810.12075342X-RAY DIFFRACTION99
2.0629-2.17160.13612820.12295356X-RAY DIFFRACTION99
2.1716-2.30770.15712800.12325334X-RAY DIFFRACTION99
2.3077-2.48580.17452780.13085270X-RAY DIFFRACTION97
2.4858-2.7360.16022820.13475365X-RAY DIFFRACTION99
2.736-3.13180.1462850.13945421X-RAY DIFFRACTION99
3.1318-3.94550.14632840.13575390X-RAY DIFFRACTION98
3.9455-48.2480.12082920.12185532X-RAY DIFFRACTION97

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