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- PDB-2p3j: Crystal structure of the Arg101Ala mutant protein of Rhesus rotav... -

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Basic information

Entry
Database: PDB / ID: 2p3j
TitleCrystal structure of the Arg101Ala mutant protein of Rhesus rotavirus VP8*
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 / FOURIER SYNTHESIS / Resolution: 1.9 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: Version format compliance
Revision 1.2Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 23, 2019Group: Data collection / Database references / Category: reflns_shell / struct_ref_seq_dif
Item: _reflns_shell.Rmerge_I_obs / _struct_ref_seq_dif.details
Revision 1.4Jul 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 1.5Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4893
Polymers18,0701
Non-polymers4192
Water2,414134
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)48.531, 48.531, 131.403
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-3079-

HOH

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Components

#1: Protein VP4 / rotavirus spike protein


Mass: 18069.947 Da / Num. of mol.: 1 / Fragment: VP8* domain (fragment 64-224) / Mutation: R101A
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


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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / 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: 2.14 Å3/Da / Density % sol: 42.52 %
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: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Dec 21, 2004 / Details: mirrors
RadiationMonochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→65 Å / Num. obs: 12064 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.7 % / Rmerge(I) obs: 0.048 / Net I/σ(I): 11.8
Reflection shellResolution: 1.9→2.04 Å / Rmerge(I) obs: 0.107 / Mean I/σ(I) obs: 4.7 / Num. unique all: 1521 / % possible all: 63

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
PROTEUM PLUSPLUSdata collection
SAINTdata reduction
LSCALEdata scaling
AMoREphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: RRV VP8* PDB code 1KQR

1kqr


Resolution: 1.9→45.64 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.943 / SU B: 2.871 / SU ML: 0.086 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20586 587 4.9 %RANDOM
Rwork0.16075 ---
obs0.1629 11421 91.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.025 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å20 Å20 Å2
2---0.03 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.9→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1274 0 27 134 1435
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221357
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.9581870
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1425160
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.62725.87363
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.07315203
X-RAY DIFFRACTIONr_dihedral_angle_4_deg2.857152
X-RAY DIFFRACTIONr_chiral_restr0.0850.2220
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021033
X-RAY DIFFRACTIONr_nbd_refined0.20.2543
X-RAY DIFFRACTIONr_nbtor_refined0.3080.2959
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.2113
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1460.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1210.214
X-RAY DIFFRACTIONr_mcbond_it0.6931.5832
X-RAY DIFFRACTIONr_mcangle_it1.11521348
X-RAY DIFFRACTIONr_scbond_it1.7863611
X-RAY DIFFRACTIONr_scangle_it2.6484.5522
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.241 22 -
Rwork0.174 451 -
obs--50.48 %

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