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- PDB-5jdb: Binding specificity of P[8] VP8* proteins of rotavirus vaccine st... -

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Basic information

Entry
Database: PDB / ID: 5jdb
TitleBinding specificity of P[8] VP8* proteins of rotavirus vaccine strains with histo-blood group antigens
ComponentsOuter capsid protein VP4
KeywordsVIRAL PROTEIN / rotavirus / VP8 / vaccine
Function / homology
Function and homology information


host cell rough endoplasmic reticulum / host cytoskeleton / viral outer capsid / permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / host cell endoplasmic reticulum-Golgi intermediate compartment / virion attachment to host cell / host cell plasma membrane / membrane
Similarity search - Function
Haemagglutinin outer capsid protein VP4, concanavalin-like domain / Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain / Rotavirus VP4 helical domain / Rotavirus VP4 helical domain / Outer capsid protein VP4 / Rotavirus VP4, membrane interaction domain superfamily / Rotavirus VP4, membrane interaction domain / Rotavirus VP4 membrane interaction domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily ...Haemagglutinin outer capsid protein VP4, concanavalin-like domain / Outer Capsid protein VP4 (Hemagglutinin) Concanavalin-like domain / Rotavirus VP4 helical domain / Rotavirus VP4 helical domain / Outer capsid protein VP4 / Rotavirus VP4, membrane interaction domain superfamily / Rotavirus VP4, membrane interaction domain / Rotavirus VP4 membrane interaction domain / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Outer capsid protein VP4
Similarity search - Component
Biological speciesRotavirus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsSun, X. / Guo, N. / Li, D. / Zhou, Y. / Jin, M. / Xie, G. / Pang, L. / Zhang, Q. / Cao, Y. / Duan, Z.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation31500139 China
National Natural Science Foundation81472003 China
CitationJournal: Virology / Year: 2016
Title: Binding specificity of P[8] VP8* proteins of rotavirus vaccine strains with histo-blood group antigens.
Authors: Sun, X. / Guo, N. / Li, D. / Jin, M. / Zhou, Y. / Xie, G. / Pang, L. / Zhang, Q. / Cao, Y. / Duan, Z.J.
History
DepositionApr 16, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 13, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_detector / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Outer capsid protein VP4
B: Outer capsid protein VP4
C: Outer capsid protein VP4
D: Outer capsid protein VP4
E: Outer capsid protein VP4
F: Outer capsid protein VP4


Theoretical massNumber of molelcules
Total (without water)110,9246
Polymers110,9246
Non-polymers00
Water8,701483
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.428, 114.931, 73.581
Angle α, β, γ (deg.)90.000, 96.050, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Outer capsid protein VP4


Mass: 18487.377 Da / Num. of mol.: 6 / Fragment: UNP RESIDUES 64-223
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rotavirus A / Production host: Escherichia coli K-12 (bacteria) / Strain (production host): K-12 / References: UniProt: E2EA82
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 483 / 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: 2.52 Å3/Da / Density % sol: 51.15 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.97944 Å
DetectorType: AGILENT EOS CCD / Detector: CCD / Date: Nov 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97944 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 83986 / % possible obs: 97.6 % / Redundancy: 3.9 % / Net I/σ(I): 17

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Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2DWR

2dwr


Resolution: 1.901→28.98 Å / SU ML: 0.21 / Cross valid method: NONE / σ(F): 1.35 / Phase error: 27.71
RfactorNum. reflection% reflection
Rfree0.2296 4086 4.87 %
Rwork0.2022 --
obs0.2036 83821 97.26 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 106.82 Å2 / Biso mean: 33.6432 Å2 / Biso min: 13.19 Å2
Refinement stepCycle: final / Resolution: 1.901→28.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7848 0 0 483 8331
Biso mean---39.48 -
Num. residues----960
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.41250.0546-0.0741.49740.57690.9518-0.08760.02460.1171-0.25470.01520.0903-0.157-0.0371-0.00160.21620.004-0.0310.18860.02940.249196.152326.55355.1688
20.2642-0.3864-0.15211.1703-0.07350.8055-0.0631-0.09520.14380.1341-0.0151-0.1237-0.07980.056-0.00010.1702-0.0278-0.04720.2331-0.03270.312966.001425.255732.932
30.5949-0.0678-0.08451.1135-0.25970.6986-0.00110.06170.1637-0.0954-0.096-0.11040.04790.0028-0.00050.19140.00130.01220.21570.05690.262560.127528.97051.1438
40.60630.0521-0.00571.37370.31171.03340.0044-0.06260.11610.1458-0.06970.0370.0324-0.011-0.0060.1843-0.00940.00850.2044-0.06560.1825102.211827.016637.0798
51.01180.43550.17891.0579-0.23321.0809-0.00460.0129-0.1729-0.0735-0.054-0.2230.09190.0186-0.00040.14150.01390.03260.15140.01020.247162.8616-0.897914.08
60.7312-0.13140.22480.8362-0.07311.10110.0136-0.0586-0.05890.0038-0.03940.11780.08990.0133-00.1547-0.01480.02050.15620.00070.17699.2497-1.289821.5478
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA1 - 160
2X-RAY DIFFRACTION2chain BB1 - 160
3X-RAY DIFFRACTION3chain CC1 - 160
4X-RAY DIFFRACTION4chain DD1 - 160
5X-RAY DIFFRACTION5chain EE1 - 160
6X-RAY DIFFRACTION6chain FF1 - 160

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