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- PDB-1oop: The Crystal Structure of Swine Vesicular Disease Virus -

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Basic information

Entry
Database: PDB / ID: 1oop
TitleThe Crystal Structure of Swine Vesicular Disease Virus
Components(Coat protein ...) x 4
KeywordsVIRUS / PICORNAVIRUS STRUCTURE / VIRUS/VIRAL PROTEIN / VIRUS-RECEPTOR INTERACTIONS / HOST ADAPTATION / CAR / DAF / COXSACKIEVIRUS / Icosahedral virus
Function / homology
Function and homology information


: / positive stranded viral RNA replication / RNA-protein covalent cross-linking / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid ...: / positive stranded viral RNA replication / RNA-protein covalent cross-linking / : / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of RIG-I activity / picornain 2A / symbiont-mediated suppression of host mRNA export from nucleus / symbiont genome entry into host cell via pore formation in plasma membrane / picornain 3C / T=pseudo3 icosahedral viral capsid / host cell cytoplasmic vesicle membrane / endocytosis involved in viral entry into host cell / : / nucleoside-triphosphate phosphatase / protein complex oligomerization / monoatomic ion channel activity / RNA helicase activity / DNA replication / induction by virus of host autophagy / RNA-directed RNA polymerase / symbiont-mediated suppression of host gene expression / viral RNA genome replication / cysteine-type endopeptidase activity / RNA-dependent RNA polymerase activity / DNA-templated transcription / host cell nucleus / virion attachment to host cell / structural molecule activity / RNA binding / ATP binding / membrane / metal ion binding
Similarity search - Function
Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A ...Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / Picornavirus coat protein VP4 superfamily / Poliovirus 3A protein-like / Poliovirus 3A protein like / Picornavirus 2B protein / Poliovirus core protein 3a, soluble domain / Picornavirus 2B protein / Peptidase C3, picornavirus core protein 2A / Picornavirus core protein 2A / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirales 3C/3C-like protease domain / Picornavirales 3C/3C-like protease domain profile. / Peptidase C3A/C3B, picornaviral / 3C cysteine protease (picornain 3C) / Picornavirus capsid / picornavirus capsid protein / Helicase, superfamily 3, single-stranded RNA virus / Superfamily 3 helicase of positive ssRNA viruses domain profile. / Helicase, superfamily 3, single-stranded DNA/RNA virus / RNA helicase / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Few Secondary Structures / Irregular / RNA-directed RNA polymerase, C-terminal domain / Viral RNA-dependent RNA polymerase / Reverse transcriptase/Diguanylate cyclase domain / Jelly Rolls / RNA-directed RNA polymerase, catalytic domain / RdRp of positive ssRNA viruses catalytic domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / DNA/RNA polymerase superfamily / Sandwich / P-loop containing nucleoside triphosphate hydrolase / Mainly Beta
Similarity search - Domain/homology
MYRISTIC ACID / SPHINGOSINE / Genome polyprotein
Similarity search - Component
Biological speciesSwine vesicular disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsFry, E.E. / Knowles, N.J. / Newman, J.W.I. / Wilsden, G. / Rao, Z. / King, A.M.Q. / Stuart, D.I.
CitationJournal: J.Virol. / Year: 2003
Title: Crystal Structure of Swine Vesicular Disease Virus and Implications for Host Adaptation
Authors: Fry, E.E. / Knowles, N.J. / Newman, J.W.I. / Wilsden, G. / Rao, Z. / King, A.M.Q. / Stuart, D.I.
History
DepositionMar 4, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 22, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / 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 / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Apr 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: Coat protein VP1
B: Coat protein VP2
C: Coat protein VP3
D: Coat protein VP4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2606
Polymers93,7334
Non-polymers5282
Water0
1
A: Coat protein VP1
B: Coat protein VP2
C: Coat protein VP3
D: Coat protein VP4
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,655,623360
Polymers5,623,951240
Non-polymers31,672120
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation59
2


  • Idetical with deposited unit
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Coat protein VP1
B: Coat protein VP2
C: Coat protein VP3
D: Coat protein VP4
hetero molecules
x 5


  • icosahedral pentamer
  • 471 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)471,30230
Polymers468,66320
Non-polymers2,63910
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Coat protein VP1
B: Coat protein VP2
C: Coat protein VP3
D: Coat protein VP4
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 566 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)565,56236
Polymers562,39524
Non-polymers3,16712
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
Unit cell
Length a, b, c (Å)354.1, 371.7, 318.6
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP22121
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))

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Components

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Coat protein ... , 4 types, 4 molecules ABCD

#1: Protein Coat protein VP1


Mass: 31538.373 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Swine vesicular disease virus (STRAIN UKG/27/72)
Genus: Enterovirus / Species: Human enterovirus B / Strain: UKG-27-72 / References: UniProt: P13900
#2: Protein Coat protein VP2


Mass: 28652.350 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Swine vesicular disease virus (STRAIN UKG/27/72)
Genus: Enterovirus / Species: Human enterovirus B / Strain: UKG-27-72 / References: UniProt: P13900
#3: Protein Coat protein VP3


Mass: 26084.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Swine vesicular disease virus (STRAIN UKG/27/72)
Genus: Enterovirus / Species: Human enterovirus B / Strain: UKG-27-72 / References: UniProt: P13900
#4: Protein Coat protein VP4


Mass: 7457.220 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Swine vesicular disease virus (STRAIN UKG/27/72)
Genus: Enterovirus / Species: Human enterovirus B / Strain: UKG-27-72 / References: UniProt: P13900

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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-SPH / SPHINGOSINE / Sphingosine


Mass: 299.492 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H37NO2
#6: Chemical ChemComp-MYR / MYRISTIC ACID / Myristic acid


Mass: 228.371 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H28O2

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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

Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.6
Details: 15-25% saturated ammonium sulfate, 100mM phosphate buffer, pH 7.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
215-25 %satammonium sulfate1reservoir
3100 mMphosphate buffer1reservoirpH7.6

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 29, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3→20 Å / Num. obs: 406689 / % possible obs: 49.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.207 / Net I/σ(I): 5.1
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.482 / % possible all: 45.9
Reflection shell
*PLUS
% possible obs: 46 %

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Processing

Software
NameVersionClassification
Adxvdata processing
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.1refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Coxsackievirus A9

Resolution: 3→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: A free R value is absent because the high non-crystallographic symmetry of viruses makes this less relevant.
RfactorNum. reflection
all0.245 253299
obs0.245 253299
Displacement parametersBiso mean: 14 Å2
Refinement stepCycle: LAST / Resolution: 3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6363 0 36 0 6399
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.018
X-RAY DIFFRACTIONx_angle_deg2.2
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 15 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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