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- PDB-1ny7: COWPEA MOSAIC VIRUS (CPMV) -

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Basic information

Entry
Database: PDB / ID: 1ny7
TitleCOWPEA MOSAIC VIRUS (CPMV)
Components
  • COWPEA MOSAIC VIRUS, LARGE (L) SUBUNIT
  • COWPEA MOSAIC VIRUS, SMALL (S) SUBUNIT
KeywordsVIRUS / COMOVIRUS / VIRAL COAT PROTEIN / COWPEA MOSAIC VIRUS (CPMV) / Icosahedral virus
Function / homology
Function and homology information


transport of virus in host, cell to cell / host cell plasmodesma / T=3 icosahedral viral capsid / host cell nucleus / GTP binding / structural molecule activity / DNA binding / RNA binding
Similarity search - Function
Large coat protein / RNA2 polyprotein / Large coat protein / Small coat protein / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesCowpea mosaic virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIR, molecular replacement / Resolution: 3 Å
AuthorsLin, T. / Chen, Z. / Usha, R. / Stauffacher, C.V. / Dai, J.-B. / Schmidt, T. / Johnson, J.E.
Citation
Journal: Virology / Year: 1999
Title: The Refined Crystal Structure of Cowpea Mosaic Virus at 2.8A Resolution
Authors: Lin, T. / Chen, Z. / Usha, R. / Stauffacher, C.V. / Dai, J.-B. / Schmidt, T. / Johnson, J.E.
#1: Journal: Crystallography in Molecular Biology / Year: 1987
Title: The structure of cowpea mosaic virus at 3.5 A resolution
Authors: Stauffacher, C.V. / Usha, R. / Harrington, M. / Schmidt, T. / Hosur, M. / Johnson, J.E.
History
DepositionFeb 11, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 18, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 9, 2014Group: Database references
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
1: COWPEA MOSAIC VIRUS, SMALL (S) SUBUNIT
2: COWPEA MOSAIC VIRUS, LARGE (L) SUBUNIT


Theoretical massNumber of molelcules
Total (without water)61,8202
Polymers61,8202
Non-polymers00
Water1,15364
1
1: COWPEA MOSAIC VIRUS, SMALL (S) SUBUNIT
2: COWPEA MOSAIC VIRUS, LARGE (L) SUBUNIT
x 60


Theoretical massNumber of molelcules
Total (without water)3,709,200120
Polymers3,709,200120
Non-polymers00
Water2,162120
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
1: COWPEA MOSAIC VIRUS, SMALL (S) SUBUNIT
2: COWPEA MOSAIC VIRUS, LARGE (L) SUBUNIT
x 5


  • icosahedral pentamer
  • 309 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)309,10010
Polymers309,10010
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
point symmetry operation5
4
1: COWPEA MOSAIC VIRUS, SMALL (S) SUBUNIT
2: COWPEA MOSAIC VIRUS, LARGE (L) SUBUNIT
x 6


  • icosahedral 23 hexamer
  • 371 kDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)370,92012
Polymers370,92012
Non-polymers00
Water21612
TypeNameSymmetry operationNumber
point symmetry operation6
5


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
1: COWPEA MOSAIC VIRUS, SMALL (S) SUBUNIT
2: COWPEA MOSAIC VIRUS, LARGE (L) SUBUNIT
x 5


  • crystal asymmetric unit, crystal frame
  • 309 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)309,10010
Polymers309,10010
Non-polymers00
Water18010
TypeNameSymmetry operationNumber
transform to crystal frame1
point symmetry operation5
Unit cell
Length a, b, c (Å)317.000, 317.000, 317.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.30901699, -0.80901699, 0.5), (0.80901699, 0.5, 0.30901699), (-0.5, 0.30901699, 0.80901699)
3generate(-0.80901699, -0.5, 0.30901699), (0.5, -0.30901699, 0.80901699), (-0.30901699, 0.80901699, 0.5)
4generate(-0.80901699, 0.5, -0.30901699), (-0.5, -0.30901699, 0.80901699), (0.30901699, 0.80901699, 0.5)
5generate(0.30901699, 0.80901699, -0.5), (-0.80901699, 0.5, 0.30901699), (0.5, 0.30901699, 0.80901699)

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Components

#1: Protein COWPEA MOSAIC VIRUS, SMALL (S) SUBUNIT / / CPMV / Genome polyprotein M [Contains: Coat protein VP37 / Coat protein VP23]


Mass: 20961.564 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cowpea mosaic virus / Genus: Comovirus / References: UniProt: P03599
#2: Protein COWPEA MOSAIC VIRUS, LARGE (L) SUBUNIT / / CPMV / Genome polyprotein M [Contains: Coat protein VP37 / Coat protein VP23]


Mass: 40858.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Cowpea mosaic virus / Genus: Comovirus / References: UniProt: P03599
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 64 / 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: 10

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Sample preparation

Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 8000, potasium phosphate, ammonium sulfate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
pH: 7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
10.4 Mammonium sulfate1reservoir
22 %(w/v)PEG80001reservoir
30.05 Mpotassium phosphate1reservoirpH7.0
435 mg/mlprotein1drop
50.05 Mpotassium phosphate1droppH7.0

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 1.5 Å
DetectorType: KODAK / Detector: FILM / Details: mirror
RadiationMonochromator: silicon / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 3→30 Å / Num. all: 105051 / Num. obs: 89846 / % possible obs: 85.53 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Biso Wilson estimate: 14.8 Å2
Reflection shellResolution: 3→3.18 Å / % possible all: 71.5
Reflection
*PLUS
Highest resolution: 2.8 Å / Num. obs: 102333 / Num. measured all: 285379 / Rmerge(I) obs: 0.109

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
MGROSCdata reduction
MGROSCdata scaling
RefinementMethod to determine structure: SIR, molecular replacement / Resolution: 3→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflection
Rwork0.202 --
obs0.202 88089 86.2 %
all-88089 -
Displacement parametersBiso mean: 14.1 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.29 Å / Luzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.22 Å
Refinement stepCycle: LAST / Resolution: 3→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4343 0 0 64 4407
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.016
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg2
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.75
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3→3.18 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rwork0.258 12129 -
obs--71.5 %
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.75

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