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- PDB-3tay: Crystal structure of porcine rotavirus CRW-8 VP8* in complex with... -

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Basic information

Entry
Database: PDB / ID: 3tay
TitleCrystal structure of porcine rotavirus CRW-8 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
BENZAMIDINE / Chem-MN0 / Outer capsid protein VP4
Similarity search - Component
Biological speciesPorcine rotavirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 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 / Database references / Derived calculations
Category: chem_comp / pdbx_chem_comp_identifier ...chem_comp / pdbx_chem_comp_identifier / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._chem_comp.mon_nstd_flag / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_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_alt_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.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_ref_seq_dif.details
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

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)38,64714
Polymers36,8992
Non-polymers1,74812
Water6,539363
1
A: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,5999
Polymers18,4491
Non-polymers1,1498
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Outer capsid protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0485
Polymers18,4491
Non-polymers5994
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.982, 59.646, 111.964
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Sugars , 2 types, 4 molecules AB

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


Mass: 18449.479 Da / Num. of mol.: 2 / Mutation: R70Q, V82I, S151N, P157S, L201S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porcine rotavirus / Strain: serotype 3 / strain CRW-8 / Plasmid: P-GEX / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P0C6Y8
#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.: 2
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

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Non-polymers , 6 types, 373 molecules

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


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#6: Chemical ChemComp-BEN / BENZAMIDINE / Benzamidine


Mass: 120.152 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H8N2
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: 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

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Sample preparation

CrystalDensity Matthews: 2.44 Å3/Da / Density % sol: 49.64 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.85→59.65 Å / Num. obs: 29988

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Processing

SoftwareName: REFMAC / Version: 5.2.0019 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→40.03 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.911 / SU B: 2.945 / SU ML: 0.091 / Cross valid method: THROUGHOUT / ESU R Free: 0.136 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22503 1593 5 %RANDOM
Rwork0.18677 ---
obs0.18866 29988 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 14.626 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.85→40.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2606 0 114 363 3083
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222811
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.0451.9773869
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7225334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.29624.88125
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.66215411
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.26158
X-RAY DIFFRACTIONr_chiral_restr0.0570.2442
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022123
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1820.21241
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21935
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1010.2324
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1060.27
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.150.288
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0870.254
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3541.51646
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.68122719
X-RAY DIFFRACTIONr_scbond_it0.94431219
X-RAY DIFFRACTIONr_scangle_it1.4644.51145
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.898 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.254 127 -
Rwork0.236 2152 -
obs--99.04 %

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