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- PDB-5zv7: P domain of GII.17-2014/15 complexed with B-trisaccharide -

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Basic information

Entry
Database: PDB / ID: 5zv7
TitleP domain of GII.17-2014/15 complexed with B-trisaccharide
ComponentsVP1
KeywordsVIRAL PROTEIN / capsid / protruding domain / dimer / HBGA recognition
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
Capsid protein / VP1
Similarity search - Component
Biological speciesNorovirus GII.17
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsChen, Y. / Li, X.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31670752 China
CitationJournal: J. Virol. / Year: 2019
Title: Structural Adaptations of Norovirus GII.17/13/21 Lineage through Two Distinct Evolutionary Paths.
Authors: Qian, Y. / Song, M. / Jiang, X. / Xia, M. / Meller, J. / Tan, M. / Chen, Y. / Li, X. / Rao, Z.
History
DepositionMay 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Dec 25, 2019Group: Data collection / Category: chem_comp / reflns_shell / Item: _chem_comp.type / _reflns_shell.Rmerge_I_obs
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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _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 2.1Nov 22, 2023Group: 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)69,9264
Polymers68,9492
Non-polymers9772
Water8,287460
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5010 Å2
ΔGint12 kcal/mol
Surface area24740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.699, 86.851, 97.431
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein VP1


Mass: 34474.414 Da / Num. of mol.: 2 / Fragment: P domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Norovirus GII.17 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A1C9I7R1, UniProt: A0A0E3X5I8*PLUS
#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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / 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: 2.32 Å3/Da / Density % sol: 47.04 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 11% (w/v) polyethylene glycol (PEG) 3350, 4%(v/v) Tacsimate (pH7.0)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 47017 / % possible obs: 99.1 % / Redundancy: 10.4 % / Rmerge(I) obs: 0.113 / Net I/σ(I): 44.1
Reflection shellResolution: 1.95→1.98 Å / Rmerge(I) obs: 0.414 / Mean I/σ(I) obs: 12.7 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.7_650refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5ZUS

5zus


Resolution: 1.95→40.966 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.98 / Phase error: 26.14
RfactorNum. reflection% reflection
Rfree0.234 2384 5.09 %
Rwork0.205 --
obs0.2065 46842 98.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Bsol: 39.522 Å2 / ksol: 0.299 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.2888 Å2-0 Å20 Å2
2---12.5182 Å20 Å2
3---10.2294 Å2
Refinement stepCycle: LAST / Resolution: 1.95→40.966 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4815 0 66 460 5341
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075027
X-RAY DIFFRACTIONf_angle_d1.2876882
X-RAY DIFFRACTIONf_dihedral_angle_d14.1821799
X-RAY DIFFRACTIONf_chiral_restr0.088753
X-RAY DIFFRACTIONf_plane_restr0.006918
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9504-1.99030.24421450.23732474X-RAY DIFFRACTION95
1.9903-2.03350.26671320.23332590X-RAY DIFFRACTION99
2.0335-2.08080.30461450.23392577X-RAY DIFFRACTION99
2.0808-2.13290.25381520.21772611X-RAY DIFFRACTION100
2.1329-2.19050.26211500.21642583X-RAY DIFFRACTION100
2.1905-2.2550.24121470.2242609X-RAY DIFFRACTION99
2.255-2.32780.3011480.22282596X-RAY DIFFRACTION99
2.3278-2.41090.27981340.20822613X-RAY DIFFRACTION100
2.4109-2.50750.24231480.23292625X-RAY DIFFRACTION100
2.5075-2.62160.27121130.22942674X-RAY DIFFRACTION100
2.6216-2.75980.26091260.22882631X-RAY DIFFRACTION100
2.7598-2.93260.26731440.22812647X-RAY DIFFRACTION100
2.9326-3.1590.28431370.2172651X-RAY DIFFRACTION99
3.159-3.47670.23451390.20552638X-RAY DIFFRACTION99
3.4767-3.97940.2461350.22551X-RAY DIFFRACTION95
3.9794-5.01230.19231380.17472600X-RAY DIFFRACTION96
5.0123-40.97470.17311510.18332788X-RAY DIFFRACTION98

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