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- PDB-5n7m: Protruding domain of GI.1 norovirus in complex with 2-fucosyllact... -

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Basic information

Entry
Database: PDB / ID: 5n7m
TitleProtruding domain of GI.1 norovirus in complex with 2-fucosyllactose (2FL)
ComponentsCapsid protein VP1
KeywordsVIRAL PROTEIN / Norovirus / Protruding domain / human milk oligosaccharides / 2FL
Function / homology
Function and homology information


T=3 icosahedral viral capsid / host cell cytoplasm / identical protein binding
Similarity search - Function
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 speciesNorwalk virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.73 Å
AuthorsHansman, G.S. / Koromyslova, A.D.
CitationJournal: Virology / Year: 2017
Title: Human norovirus inhibition by a human milk oligosaccharide.
Authors: Koromyslova, A. / Tripathi, S. / Morozov, V. / Schroten, H. / Hansman, G.S.
History
DepositionFeb 20, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 24, 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_conn_angle / struct_asym / struct_conn / struct_conn_type / 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_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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.ptnr1_label_seq_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 / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Jan 17, 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 VP1
B: Capsid protein VP1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,60415
Polymers63,0232
Non-polymers1,58113
Water9,494527
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6150 Å2
ΔGint-6 kcal/mol
Surface area21980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.070, 84.070, 165.120
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Capsid protein VP1 / CP / p59


Mass: 31511.262 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Sequence maps to GenBank entry M87661.1, protein id AAB50466.1, residues 224 to 530
Source: (gene. exp.) Norwalk virus / Gene: ORF2 / Plasmid: pMBP / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: Q83884
#2: Polysaccharide alpha-L-fucopyranose-(1-2)-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
LFucpa1-2DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5][a2112h-1b_1-5][a1221m-1a_1-5]/1-2-3/a4-b1_b2-c1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{[(2+1)][a-L-Fucp]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Na
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / 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: 2.67 Å3/Da / Density % sol: 53.98 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4.2 / Details: 0.1 M phosphate citrate, 0.2 M NaCl, 20% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 24, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 1.73→43.906 Å / Num. obs: 71336 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 7.355 % / Biso Wilson estimate: 23.8 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.08 / Rrim(I) all: 0.086 / Χ2: 1.163 / Net I/σ(I): 15.88
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.73-1.837.5210.7782.12111010.8430.83597.1
1.83-1.967.6460.4773.9107880.9330.512100
1.96-2.117.5570.2786.97100250.9730.29999.9
2.11-2.317.3740.17111.3692700.9880.18599.9
2.31-2.596.8230.11315.9584070.9930.12299.9
2.59-2.996.8230.07223.7474840.9970.07899.9
2.99-3.657.6810.0543663720.9980.058100
3.65-5.157.4170.04144.149970.9990.044100
5.15-43.9066.9690.03644.429470.9980.0499.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
XSCALEdata scaling
PHASERphasing
PDB_EXTRACT3.22data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BY1

3by1


Resolution: 1.73→43.906 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 18.41
RfactorNum. reflection% reflection
Rfree0.1913 3565 5 %
Rwork0.1604 --
obs0.1619 71324 99.46 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 83.9 Å2 / Biso mean: 27.7776 Å2 / Biso min: 12.88 Å2
Refinement stepCycle: final / Resolution: 1.73→43.906 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4299 0 104 528 4931
Biso mean--35.05 36.06 -
Num. residues----576
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074681
X-RAY DIFFRACTIONf_angle_d0.8826462
X-RAY DIFFRACTIONf_chiral_restr0.06735
X-RAY DIFFRACTIONf_plane_restr0.007849
X-RAY DIFFRACTIONf_dihedral_angle_d9.3542786
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7265-1.75010.32621260.3042395252188
1.7501-1.77510.2971410.253626812822100
1.7751-1.80160.281400.229126552795100
1.8016-1.82980.24931410.216127012842100
1.8298-1.85980.24441430.206227122855100
1.8598-1.89180.23571390.187626472786100
1.8918-1.92630.22781430.18927102853100
1.9263-1.96330.24031410.19426972838100
1.9633-2.00340.21531430.199127102853100
2.0034-2.04690.22321410.170226782819100
2.0469-2.09460.19781430.163827152858100
2.0946-2.14690.17991420.158627002842100
2.1469-2.2050.20861430.156927132856100
2.205-2.26990.1781430.165127112854100
2.2699-2.34310.22051420.164226962838100
2.3431-2.42690.20331420.169427042846100
2.4269-2.5240.2331430.172327262869100
2.524-2.63890.19311440.162627152859100
2.6389-2.7780.2021420.163627132855100
2.778-2.9520.20211450.168827462891100
2.952-3.17990.18191450.161927472892100
3.1799-3.49970.17511440.153827652909100
3.4997-4.00590.18081470.141727742921100
4.0059-5.04580.13771470.118128022949100
5.0458-43.920.1671550.147129463101100

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