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- PDB-5hza: Crystal structure of GII.10 P domain in complex with 3-fucosyllac... -

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Basic information

Entry
Database: PDB / ID: 5hza
TitleCrystal structure of GII.10 P domain in complex with 3-fucosyllactose (3 FL)
ComponentsCapsid proteinCapsid
KeywordsVIRAL PROTEIN / Norovirus / P domain / HMO / 3-fucosyllactose / human milk / Virus
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 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit ...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 / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesNorovirus GII.10
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.35 Å
AuthorsHansman, G.S. / Koromyslova, A.D. / Singh, B.K.
CitationJournal: J.Virol. / Year: 2016
Title: Structural Basis for Norovirus Inhibition by Human Milk Oligosaccharides.
Authors: Weichert, S. / Koromyslova, A. / Singh, B.K. / Hansman, S. / Jennewein, S. / Schroten, H. / Hansman, G.S.
History
DepositionFeb 2, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Mar 2, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2016Group: Database references
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 / 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 / _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: Capsid protein
B: Capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,18514
Polymers69,0132
Non-polymers1,17112
Water14,376798
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint28 kcal/mol
Surface area23760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)65.710, 78.170, 71.840
Angle α, β, γ (deg.)90.00, 102.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Capsid protein / Capsid


Mass: 34506.660 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus GII.10 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q5F4T5
#2: Polysaccharide alpha-L-fucopyranose-(1-3)-[beta-D-galactopyranose-(1-4)]beta-D-glucopyranose


Type: oligosaccharide / Mass: 488.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
LFucpa1-3[DGalpb1-4]DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5][a1221m-1a_1-5][a2112h-1b_1-5]/1-2-3/a3-b1_a4-c1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(3+1)][a-L-Fucp]{}[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 798 / 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: 2.61 Å3/Da / Density % sol: 52.91 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: sodium nitrate, bis-tris propane, PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.35→49.61 Å / Num. obs: 142746 / % possible obs: 91.7 % / Observed criterion σ(I): -3 / Redundancy: 2.3 % / Biso Wilson estimate: 12.25 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.05 / Rsym value: 0.06 / Net I/σ(I): 9.84
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.35-1.430.3442.23189.5
1.43-1.530.2213.47190
1.53-1.650.1425.43191.8
1.65-1.810.0957.95191.3
1.81-2.020.06611.75193
2.02-2.340.05215.31191.6
2.34-2.860.04218.53194.8
2.86-4.040.03422.23193.5
4.04-49.6120.02924.11194.4

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation7.05 Å49.61 Å
Translation7.05 Å49.61 Å

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XSCALEdata scaling
PHASER2.5.6phasing
PDB_EXTRACT3.2data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ONU

3onu


Resolution: 1.35→49.61 Å / SU ML: 0.11 / Cross valid method: FREE R-VALUE / σ(F): 1.24 / Phase error: 18.05
RfactorNum. reflection% reflection
Rfree0.1789 11575 5 %
Rwork0.1608 --
obs0.1617 142739 75.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.35→49.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4769 0 77 798 5644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065095
X-RAY DIFFRACTIONf_angle_d1.0636975
X-RAY DIFFRACTIONf_dihedral_angle_d11.5641834
X-RAY DIFFRACTIONf_chiral_restr0.043783
X-RAY DIFFRACTIONf_plane_restr0.005920
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3495-1.36480.25773300.26356238X-RAY DIFFRACTION64
1.3648-1.38080.25373760.2447043X-RAY DIFFRACTION73
1.3808-1.39770.27223690.24487152X-RAY DIFFRACTION73
1.3977-1.41540.26333580.23887049X-RAY DIFFRACTION73
1.4154-1.4340.25133670.22867058X-RAY DIFFRACTION72
1.434-1.45370.24063590.22716998X-RAY DIFFRACTION72
1.4537-1.47440.24133480.21526685X-RAY DIFFRACTION68
1.4744-1.49640.2333880.20037105X-RAY DIFFRACTION73
1.4964-1.51980.20393730.19637068X-RAY DIFFRACTION73
1.5198-1.54470.20413780.18747257X-RAY DIFFRACTION75
1.5447-1.57140.21144060.17757277X-RAY DIFFRACTION75
1.5714-1.59990.1923730.17557356X-RAY DIFFRACTION75
1.5999-1.63070.1863840.1737292X-RAY DIFFRACTION75
1.6307-1.6640.21133800.17427263X-RAY DIFFRACTION75
1.664-1.70020.20413850.16787212X-RAY DIFFRACTION74
1.7002-1.73970.1883670.16586915X-RAY DIFFRACTION71
1.7397-1.78330.19433820.15937308X-RAY DIFFRACTION76
1.7833-1.83150.16824010.1597419X-RAY DIFFRACTION76
1.8315-1.88540.18214070.15867510X-RAY DIFFRACTION77
1.8854-1.94620.18583920.16237552X-RAY DIFFRACTION77
1.9462-2.01580.17314050.15677504X-RAY DIFFRACTION77
2.0158-2.09650.17943900.15757449X-RAY DIFFRACTION77
2.0965-2.19190.16133760.1587119X-RAY DIFFRACTION73
2.1919-2.30750.17533930.15747509X-RAY DIFFRACTION77
2.3075-2.4520.15864110.15037888X-RAY DIFFRACTION81
2.452-2.64140.17094250.15437984X-RAY DIFFRACTION82
2.6414-2.90710.1964100.16257879X-RAY DIFFRACTION81
2.9071-3.32770.1684000.15337688X-RAY DIFFRACTION79
3.3277-4.19230.15284210.13548090X-RAY DIFFRACTION83
4.1923-49.64690.14294210.13278124X-RAY DIFFRACTION83

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