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- PDB-1mqt: Swine Vesicular Disease Virus coat protein -

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Basic information

Entry
Database: PDB / ID: 1mqt
TitleSwine Vesicular Disease Virus coat protein
Components
  • (Polyprotein Capsid ...) x 3
  • Polyprotein
KeywordsVIRUS / swine vesicular disease virus / SVDV coat protein / enterovirus / Icosahedral virus
Function / homology
Function and homology information


symbiont genome entry into host cell via pore formation in plasma membrane / symbiont-mediated suppression of host gene expression / viral capsid / host cell cytoplasm / virion attachment to host cell / structural molecule activity / cytoplasm
Similarity search - Function
Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / Picornavirus coat protein VP4 superfamily / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit ...Picornavirus coat protein VP4 / Rhinovirus 14, subunit 4 / Jelly Rolls - #20 / Picornavirus coat protein VP4 superfamily / Picornavirus coat protein VP4 / Picornavirus coat protein (VP4) / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Few Secondary Structures / Irregular / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-SPL / Genome polyprotein
Similarity search - Component
Biological speciesSwine vesicular disease virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsVerdaguer, N. / Jimenez-Clavero, M.A. / Fita, I. / Ley, V.
CitationJournal: J.Virol. / Year: 2003
Title: STRUCTURE OF SWINE VESICULAR DISEASE VIRUS: MAPPING OF CHANGES OCCURRING DURING ADAPTATION OF HUMAN COXSACKIE B5 VIRUS TO INFECT SWINE
Authors: Verdaguer, N. / Jimenez-Clavero, M.A. / Fita, I. / Ley, V.
History
DepositionSep 17, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN The first residue of chain D is a myristic acid covalently attached to GLY D2 (not ...HETEROGEN The first residue of chain D is a myristic acid covalently attached to GLY D2 (not visible in the electron density)

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Polyprotein
B: Polyprotein Capsid Protein
C: Polyprotein Capsid Protein
D: Polyprotein Capsid Protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,7265
Polymers93,3004
Non-polymers4261
Water54030
1
A: Polyprotein
B: Polyprotein Capsid Protein
C: Polyprotein Capsid Protein
D: Polyprotein Capsid Protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)5,623,540300
Polymers5,597,999240
Non-polymers25,54160
Water4,324240
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: Polyprotein
B: Polyprotein Capsid Protein
C: Polyprotein Capsid Protein
D: Polyprotein Capsid Protein
hetero molecules
x 5


  • icosahedral pentamer
  • 469 kDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)468,62825
Polymers466,50020
Non-polymers2,1285
Water36020
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Polyprotein
B: Polyprotein Capsid Protein
C: Polyprotein Capsid Protein
D: Polyprotein Capsid Protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 562 kDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)562,35430
Polymers559,80024
Non-polymers2,5546
Water43224
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
6
A: Polyprotein
B: Polyprotein Capsid Protein
C: Polyprotein Capsid Protein
D: Polyprotein Capsid Protein
hetero molecules
x 15


  • crystal asymmetric unit, crystal frame
  • 1.41 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,405,88575
Polymers1,399,50060
Non-polymers6,38515
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation14
Unit cell
Length a, b, c (Å)318.350, 349.960, 371.720
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.5, -0.80901699, 0.30901699), (0.80901699, 0.30901699, -0.5), (0.30901699, 0.5, 0.80901699)
3generate(-0.30901699, -0.5, 0.80901699), (0.5, -0.80901699, -0.30901699), (0.80901699, 0.30901699, 0.5)
4generate(-0.30901699, 0.5, 0.80901699), (-0.5, -0.80901699, 0.30901699), (0.80901699, -0.30901699, 0.5)
5generate(0.5, 0.80901699, 0.30901699), (-0.80901699, 0.30901699, 0.5), (0.30901699, -0.5, 0.80901699)
6generate(-0.80901699, 0.30901699, 0.5), (0.30901699, -0.5, 0.80901699), (0.5, 0.80901699, 0.30901699)
7generate(1), (1), (1)
8generate(0.80901699, 0.30901699, -0.5), (0.30901699, 0.5, 0.80901699), (0.5, -0.80901699, 0.30901699)
9generate(0.5, -0.80901699, -0.30901699), (0.80901699, 0.30901699, 0.5), (-0.30901699, -0.5, 0.80901699)
10generate(-0.5, -0.80901699, 0.30901699), (0.80901699, -0.30901699, 0.5), (-0.30901699, 0.5, 0.80901699)
11generate(-1), (-1), (1)
12generate(-0.30901699, -0.5, -0.80901699), (-0.5, 0.80901699, -0.30901699), (0.80901699, 0.30901699, -0.5)
13generate(-0.80901699, -0.30901699, -0.5), (0.30901699, 0.5, -0.80901699), (0.5, -0.80901699, -0.30901699)
14generate(-0.80901699, 0.30901699, -0.5), (0.30901699, -0.5, -0.80901699), (-0.5, -0.80901699, 0.30901699)
15generate(-0.30901699, 0.5, -0.80901699), (-0.5, -0.80901699, -0.30901699), (-0.80901699, 0.30901699, 0.5)

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Polyprotein


Mass: 31370.240 Da / Num. of mol.: 1 / Fragment: SVDV COAT PROTEIN VP1 / Source method: isolated from a natural source / Source: (natural) Swine vesicular disease virus / Genus: Enterovirus / Species: Human enterovirus B / Strain: ISOLATE (SPA-2-'93) / References: UniProt: Q8B8X4

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Polyprotein Capsid ... , 3 types, 3 molecules BCD

#2: Protein Polyprotein Capsid Protein


Mass: 28505.158 Da / Num. of mol.: 1 / Fragment: SVDV COAT PROTEIN VP2 / Source method: isolated from a natural source / Source: (natural) Swine vesicular disease virus / Genus: Enterovirus / Species: Human enterovirus B / Strain: ISOLATE (SPA-2-'93) / References: UniProt: Q8B8X4
#3: Protein Polyprotein Capsid Protein


Mass: 26071.531 Da / Num. of mol.: 1 / Fragment: SVDV COAT PROTEIN VP3 / Source method: isolated from a natural source / Source: (natural) Swine vesicular disease virus / Genus: Enterovirus / Species: Human enterovirus B / Strain: ISOLATE (SPA-2-'93) / References: UniProt: Q8B8X4
#4: Protein Polyprotein Capsid Protein


Mass: 7353.049 Da / Num. of mol.: 1 / Fragment: SVDV COAT PROTEIN VP4 / Source method: isolated from a natural source / Source: (natural) Swine vesicular disease virus / Genus: Enterovirus / Species: Human enterovirus B / Strain: ISOLATE (SPA-2-'93) / References: UniProt: Q8B8X4

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Non-polymers , 2 types, 31 molecules

#5: Chemical ChemComp-SPL / OCTANOIC ACID (2-HYDROXY-1-HYDROXYMETHYL-HEPTADEC-3-ENYL)-AMIDE / CERAMIDE


Mass: 425.688 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H51NO3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2

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Sample preparation

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: ammonium sulfate, Potassium phosphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
pH: 6.2 / Method: vapor diffusion, hanging drop
Details: Jimenez-Clavero, M.A., (2003) Acta Cryst., D59, 541.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
15-10 mg/mlvirus solution1drop
21.2 Mammonium sulfate1reservoir
30.1 Msodium potassium phosphate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 19, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 3.3→30 Å / Num. all: 214790 / Num. obs: 214790 / % possible obs: 60 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.1 % / Biso Wilson estimate: 16.6 Å2 / Rmerge(I) obs: 0.196 / Net I/σ(I): 4.6
Reflection shellResolution: 3.3→3.5 Å / Rmerge(I) obs: 0.27 / % possible all: 44.1
Reflection
*PLUS
Highest resolution: 3 Å / Num. obs: 288614 / % possible obs: 70 % / Num. measured all: 459326 / Rmerge(I) obs: 0.1
Reflection shell
*PLUS
Highest resolution: 3 Å / Lowest resolution: 3.1 Å / % possible obs: 51 % / Rmerge(I) obs: 0.191

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
DMmodel building
CNSrefinement
DMphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1COV

1cov


Resolution: 3.3→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.279 9509 -RANDOM
Rwork0.257 ---
all-214655 --
obs-192613 62.6 %-
Displacement parametersBiso mean: 11.97 Å2
Refinement stepCycle: LAST / Resolution: 3.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6333 0 30 30 6393
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_d1.5
Refinement
*PLUS
Highest resolution: 3 Å / Lowest resolution: 30 Å / Num. reflection obs: 266789 / Rfactor Rwork: 0.235
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.9

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