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- PDB-2dwr: Crystal structure of the human Wa rotavirus VP8* carbohydrate-rec... -

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Basic information

Entry
Database: PDB / ID: 2dwr
TitleCrystal structure of the human Wa rotavirus VP8* carbohydrate-recognising domain
ComponentsOuter capsid protein
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 / receptor-mediated virion attachment to host cell / virion attachment to host cell / host cell plasma membrane / membrane
Similarity search - Function
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
ISOPROPYL ALCOHOL / Outer capsid protein VP4 / Outer capsid protein VP4
Similarity search - Component
Biological speciesHuman rotavirus A
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBlanchard, H.
Citation
Journal: J.Mol.Biol. / Year: 2007
Title: Insight into Host Cell Carbohydrate-recognition by Human and Porcine Rotavirus from Crystal Structures of the Virion Spike Associated Carbohydrate-binding Domain (VP8*)
Authors: Blanchard, H. / Yu, X. / Coulson, B.S. / von Itzstein, M.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2005
Title: Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of the VP8* carbohydrate-binding protein of the human rotavirus strain Wa
Authors: Kraschnefski, M.J. / Scott, S.A. / Holloway, G. / Coulson, B.S. / von Itzstein, M. / Blanchard, H.
History
DepositionAug 16, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Outer capsid protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,7015
Polymers18,3961
Non-polymers3044
Water1,67593
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.762, 74.762, 70.090
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-5069-

HOH

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Components

#1: Protein Outer capsid protein / spike protein


Mass: 18396.184 Da / Num. of mol.: 1 / Fragment: VP8* domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human rotavirus A / Species: Rotavirus A / Strain: strain Wa / Plasmid: pGEX-VP8(64-223) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21 DE3 / References: UniProt: Q86202, UniProt: P11193*PLUS
#2: 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
#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL / Isopropyl alcohol


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 93 / 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: 3.07 Å3/Da / Density % sol: 59.97 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 25% PEG 4000, 20% 2-propanol, 0.1M sodium citrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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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: 2.5→64.6 Å / Num. obs: 8135

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XNEMOdata collection
FIPBM30Adata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Homology model based on the structure of porcine CRW-8 VP8* that we have solved.

Resolution: 2.5→64.55 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.91 / SU B: 7.301 / SU ML: 0.163 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.402 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23508 355 4.5 %RANDOM
Rwork0.17718 ---
obs0.17973 7491 96.54 %-
all-8114 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.888 Å2
Baniso -1Baniso -2Baniso -3
1-1.36 Å20.68 Å20 Å2
2--1.36 Å20 Å2
3----2.04 Å2
Refinement stepCycle: LAST / Resolution: 2.5→64.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1300 0 20 93 1413
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0221356
X-RAY DIFFRACTIONr_angle_refined_deg1.1061.9251846
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6535161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.67824.36671
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.86515209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.765158
X-RAY DIFFRACTIONr_chiral_restr0.0820.2200
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021057
X-RAY DIFFRACTIONr_nbd_refined0.1970.2583
X-RAY DIFFRACTIONr_nbtor_refined0.3070.2909
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1150.2102
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2060.240
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1690.210
X-RAY DIFFRACTIONr_mcbond_it0.5281.5829
X-RAY DIFFRACTIONr_mcangle_it0.94921322
X-RAY DIFFRACTIONr_scbond_it1.1933608
X-RAY DIFFRACTIONr_scangle_it1.9734.5523
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.237 23 -
Rwork0.271 533 -
obs--97.2 %

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