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- PDB-2p3k: Crystal structure of Rhesus rotavirus VP8* at 100K -

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Basic information

Entry
Database: PDB / ID: 2p3k
TitleCrystal structure of Rhesus rotavirus VP8* at 100K
ComponentsVP4
KeywordsVIRAL PROTEIN / Beta-sandwich
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
2-O-methyl-5-N-acetyl-alpha-D-neuraminic acid / Outer capsid protein VP4 / Outer capsid protein VP4
Similarity search - Component
Biological speciesRhesus rotavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.56 Å
AuthorsBlanchard, H.
CitationJournal: Glycobiology / Year: 2009
Title: Effects on sialic acid recognition of amino acid mutations in the carbohydrate-binding cleft of the rotavirus spike protein
Authors: Kraschnefski, M.J. / Bugarcic, A. / Fleming, F.E. / Yu, X. / von Itzstein, M. / Coulson, B.S. / Blanchard, H.
History
DepositionMar 9, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 11, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Mar 13, 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: VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6684
Polymers18,1561
Non-polymers5113
Water4,234235
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.887, 47.887, 129.932
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-4019-

HOH

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Components

#1: Protein VP4 / rotavirus spike protein


Mass: 18156.062 Da / Num. of mol.: 1 / Fragment: VP8* domain (fragment 64-224)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhesus rotavirus / Species: Rotavirus A / Strain: Rhesus / Plasmid: pGEX-VP8*(64-224) / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21 DE3 / References: UniProt: Q91HI9, UniProt: P12473*PLUS
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Sugar ChemComp-MNA / 2-O-methyl-5-N-acetyl-alpha-D-neuraminic acid / 2-O-METHYL-5-N-ACETYL-ALPHA-D- NEURAMINIC ACID


Type: D-saccharide / Mass: 323.296 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H21NO9
IdentifierTypeProgram
2-O-methyl-5-N-acetyl-a-D-neuraminic acidIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 235 / 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: 2.05 Å3/Da / Density % sol: 40.01 %
Crystal growTemperature: 303 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.7M (NH4)2SO4, 2.4% v/v PEG 400, 0.1M PIPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 303K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.9794 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 16, 2004 / Details: mirrors
RadiationMonochromator: silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.55→55 Å / Num. obs: 21759 / % possible obs: 96.1 % / Redundancy: 11.8 % / Rmerge(I) obs: 0.087 / Net I/σ(I): 6.2
Reflection shellResolution: 1.55→1.64 Å / Rmerge(I) obs: 0.115 / Mean I/σ(I) obs: 5.3 / Num. unique all: 2991 / % possible all: 93.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
Xnemodata collection
FIPBM30Adata collection
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.56→20 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.93 / SU B: 1.25 / SU ML: 0.047 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20009 1118 5.2 %RANDOM
Rwork0.17193 ---
obs0.17336 20572 96.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.573 Å2
Baniso -1Baniso -2Baniso -3
1--0.4 Å20 Å20 Å2
2---0.4 Å20 Å2
3---0.81 Å2
Refinement stepCycle: LAST / Resolution: 1.56→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1280 0 33 235 1548
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221384
X-RAY DIFFRACTIONr_angle_refined_deg1.1711.9651906
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4365166
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.16225.55663
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.415215
X-RAY DIFFRACTIONr_dihedral_angle_4_deg5.08153
X-RAY DIFFRACTIONr_chiral_restr0.0790.2223
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021046
X-RAY DIFFRACTIONr_nbd_refined0.2050.2639
X-RAY DIFFRACTIONr_nbtor_refined0.3080.2972
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.2216
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.247
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2570.234
X-RAY DIFFRACTIONr_mcbond_it0.5341.5840
X-RAY DIFFRACTIONr_mcangle_it0.89721366
X-RAY DIFFRACTIONr_scbond_it1.483629
X-RAY DIFFRACTIONr_scangle_it2.1084.5537
LS refinement shellResolution: 1.555→1.595 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.24 76 -
Rwork0.198 1381 -
obs--89.99 %

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