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- PDB-3tb0: Crystal structure of Rhesus Rotavirus VP8* in complex with N-Glyc... -

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Basic information

Entry
Database: PDB / ID: 3tb0
TitleCrystal structure of Rhesus Rotavirus VP8* in complex with N-Glycolylneuraminic acid
ComponentsOuter capsid protein VP4
KeywordsSUGAR BINDING PROTEIN / VIRAL PROTEIN / BETA SANDWICH / LECTIN / Neu5Gc
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
Chem-MN0 / Outer capsid protein VP4
Similarity search - Component
Biological speciesRhesus rotavirus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYu, X. / Blanchard, H.
CitationJournal: J.Virol. / Year: 2012
Title: Structural Basis of Rotavirus Strain Preference toward N-Acetyl- or N-Glycolylneuraminic Acid-Containing Receptors.
Authors: Yu, X. / Dang, V.T. / Fleming, F.E. / von Itzstein, M. / Coulson, B.S. / Blanchard, H.
History
DepositionAug 4, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 5, 2012Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,9185
Polymers18,1561
Non-polymers7624
Water3,891216
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.420, 48.420, 130.910
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-495-

HOH

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Components

#1: Protein Outer capsid protein VP4 / Hemagglutinin / Outer capsid protein VP8* / Outer capsid protein VP5*


Mass: 18156.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhesus rotavirus
Strain: Monkey/United States/RRV/1980 G3-P5B[3]-I2-R2-C3-M3-A9-Nx-T3-E3-H6
Plasmid: P-GEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P12473
#2: Sugar ChemComp-MN0 / methyl 3,5-dideoxy-5-[(hydroxyacetyl)amino]-D-glycero-alpha-D-galacto-non-2-ulopyranosidonic acid / methyl 3,5-dideoxy-5-[(hydroxyacetyl)amino]-D-glycero-alpha-D-galacto-non-2-ulosidonic acid / methyl 3,5-dideoxy-5-[(hydroxyacetyl)amino]-D-glycero-D-galacto-non-2-ulosidonic acid / methyl 3,5-dideoxy-5-[(hydroxyacetyl)amino]-D-glycero-galacto-non-2-ulosidonic acid / Methyl group


Type: D-saccharide / Mass: 339.296 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C12H21NO10
IdentifierTypeProgram
2-O-methyl-5-N-glycolyl-a-D-neuraminic acidIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PREDICTED AMINO ACID SEQUENCE OF PGEXRRV-VP8* AT POSITION 73 WAS IDENTICAL WITH THAT OF THE ...THE PREDICTED AMINO ACID SEQUENCE OF PGEXRRV-VP8* AT POSITION 73 WAS IDENTICAL WITH THAT OF THE PUBLISHED RRV VP4 SEQUENCE (ACCESSION NUMBER AY033150, ENTREZ DATABASE).

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.11 Å3/Da / Density % sol: 41.79 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: OTHER
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2→65.78 Å / Num. obs: 10639

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Processing

SoftwareName: REFMAC / Version: 5.5.0110 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→38.93 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.88 / SU B: 4.397 / SU ML: 0.125 / Cross valid method: THROUGHOUT / ESU R: 0.223 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: FLEXIBILITY OF THE TYR 155 CARBONYL IS OBSERVED. DENSITY FOR THIS CARBONYL GROUP IS AMBIGUOUS AND DOES NOT CLEARLY INDICATE ITS EXACT ORIENTATION. A PARTIALLY OCCUPIED WATER MAY BE PRESENT ...Details: FLEXIBILITY OF THE TYR 155 CARBONYL IS OBSERVED. DENSITY FOR THIS CARBONYL GROUP IS AMBIGUOUS AND DOES NOT CLEARLY INDICATE ITS EXACT ORIENTATION. A PARTIALLY OCCUPIED WATER MAY BE PRESENT THIS IS NOT MODELLED IN THE COORDINATES. A POLYETHYLENE GLYCOL MOLECULE FROM THE RESERVOIR SOLUTION IS MODELLED (THIS IS PARTIALLY DEFINED IN THE DENSITY). HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT.
RfactorNum. reflection% reflectionSelection details
Rfree0.24923 533 4.8 %RANDOM
Rwork0.18295 ---
obs0.18605 10639 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.505 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2→38.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1280 0 45 216 1541
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.021380
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2511.9631892
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3065160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.33625.55663
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.2615207
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.434153
X-RAY DIFFRACTIONr_chiral_restr0.0760.2218
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211035
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3271.5804
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.64721326
X-RAY DIFFRACTIONr_scbond_it1.0263530
X-RAY DIFFRACTIONr_scangle_it1.7464.5509
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 30 -
Rwork0.188 641 -
obs--96.83 %

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