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- PDB-2i2s: Crystal Structure of the porcine CRW-8 rotavirus VP8* carbohydrat... -

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Basic information

Entry
Database: PDB / ID: 2i2s
TitleCrystal Structure of the porcine CRW-8 rotavirus VP8* carbohydrate-recognising domain
ComponentsOuter capsid protein VP4
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 speciesPorcine rotavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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: Crystallization and preliminary X-ray diffraction analysis of the sialic acid-binding domain (VP8*) of porcine rotavirus strain CRW-8
Authors: Scott, S.A. / Holloway, G. / Coulson, B.S. / Szyczew, A.J. / Kiefel, M.J. / von Itzstein, M. / Blanchard, H.
History
DepositionAug 16, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 3, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_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 / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Mar 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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,52713
Polymers36,8992
Non-polymers1,62911
Water6,539363
1
A: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,3336
Polymers18,4491
Non-polymers8845
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,1947
Polymers18,4491
Non-polymers7456
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.929, 64.663, 109.886
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a monomer of VP8* which forms part of the rotavirus spike protein (VP4). The spike protein is considered to be formed of a dimer (though some evidence suggests a trimer) of VP4. The crystallographic asymmetric unit contains two molecules of VP8*.

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Components

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Protein / Sugars , 2 types, 5 molecules AB

#1: Protein Outer capsid protein VP4 / spike protein


Mass: 18449.479 Da / Num. of mol.: 2 / Fragment: VP8* domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine rotavirus / Species: Rotavirus C / Strain: strain CRW-8 / Plasmid: pGex-VP8*(64-224) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21 DE3 / References: UniProt: P11114, UniProt: P0C6Y8*PLUS
#4: 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.: 3 / Source method: obtained synthetically / Formula: C12H21NO9
IdentifierTypeProgram
2-O-methyl-5-N-acetyl-a-D-neuraminic acidIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 371 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: 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
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.59 Å3/Da / Density % sol: 52.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 70% MPD, 0.1M HEPES pH 7.5, methyl-alpha-D-N-acetylneuraminide , 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: 2.3→55.9 Å / Num. obs: 17704

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XNEWMOdata 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 Rhesus rotavirus VP8*

Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.913 / SU B: 5.307 / SU ML: 0.133 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.32 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21952 901 5.1 %RANDOM
Rwork0.16256 ---
all0.183 17658 --
obs0.1654 16756 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.243 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å20 Å2
2--1.74 Å20 Å2
3----0.74 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2606 0 106 363 3075
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222796
X-RAY DIFFRACTIONr_angle_refined_deg1.061.9743842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1085324
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.63724.88125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.93415413
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.175158
X-RAY DIFFRACTIONr_chiral_restr0.0630.2447
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022098
X-RAY DIFFRACTIONr_nbd_refined0.1870.21241
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21926
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2353
X-RAY DIFFRACTIONr_metal_ion_refined0.080.26
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1380.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.236
X-RAY DIFFRACTIONr_mcbond_it0.3061.51633
X-RAY DIFFRACTIONr_mcangle_it0.59322704
X-RAY DIFFRACTIONr_scbond_it0.89231217
X-RAY DIFFRACTIONr_scangle_it1.434.51138
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.223 72 -
Rwork0.178 1212 -
obs--99.92 %

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