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- PDB-2bfu: X-ray structure of CPMV top component -

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Basic information

Entry
Database: PDB / ID: 2bfu
TitleX-ray structure of CPMV top component
Components
  • COWPEA MOSAIC VIRUS, LARGE (L) SUBUNIT
  • COWPEA MOSAIC VIRUS, SMALL (S) SUBUNIT
KeywordsVIRUS / COMOVIRUS / VIRAL COAT PROTEIN / COWPEA MOSAIC VIRUS CPMV / TOP COMPONENT / NANOTECHNOLOGY / EMPTY PARTICLES / 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 / OTHER / Resolution: 4 Å
AuthorsOchoa, W.F. / Chatterji, A. / Lin, T. / Johnson, J.E.
CitationJournal: Chem.Biol. / Year: 2006
Title: Generation and Structural Analysis of Reactive Empty Particles Derived from an Icosahedral Virus.
Authors: Ochoa, W.F. / Chatterji, A. / Lin, T. / Johnson, J.E.
History
DepositionDec 13, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 12, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 4, 2018Group: Data collection / Category: diffrn_detector / diffrn_source / Item: _diffrn_source.pdbx_synchrotron_beamline
Revision 1.4May 22, 2019Group: Data collection / Refinement description / Category: refine / Item: _refine.pdbx_ls_cross_valid_method
Revision 1.5Oct 23, 2019Group: Data collection / Other / Category: diffrn_detector / pdbx_database_status
Item: _diffrn_detector.detector / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)61,8202
Polymers61,8202
Non-polymers00
Water0
1
L: COWPEA MOSAIC VIRUS, LARGE (L) SUBUNIT
S: COWPEA MOSAIC VIRUS, SMALL (S) SUBUNIT
x 60


Theoretical massNumber of molelcules
Total (without water)3,709,200120
Polymers3,709,200120
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


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


  • icosahedral pentamer
  • 309 kDa, 10 polymers
Theoretical massNumber of molelcules
Total (without water)309,10010
Polymers309,10010
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
L: COWPEA MOSAIC VIRUS, LARGE (L) SUBUNIT
S: COWPEA MOSAIC VIRUS, SMALL (S) SUBUNIT
x 6


  • icosahedral 23 hexamer
  • 371 kDa, 12 polymers
Theoretical massNumber of molelcules
Total (without water)370,92012
Polymers370,92012
Non-polymers00
Water0
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
L: COWPEA MOSAIC VIRUS, LARGE (L) SUBUNIT
S: COWPEA MOSAIC VIRUS, SMALL (S) 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
Water0
TypeNameSymmetry operationNumber
transform to crystal frame1
point symmetry operation5
Unit cell
Length a, b, c (Å)311.407, 311.407, 311.407
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number197
Space group name H-MI23
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.309017, -0.809017, 0.5), (0.809017, 0.5, 0.309017), (-0.5, 0.309017, 0.809017)
3generate(-0.809017, -0.5, 0.309017), (0.5, -0.309017, 0.809017), (-0.309017, 0.809017, 0.5)
4generate(-0.809017, 0.5, -0.309017), (-0.5, -0.309017, 0.809017), (0.309017, 0.809017, 0.5)
5generate(0.309017, 0.809017, -0.5), (-0.809017, 0.5, 0.309017), (0.5, 0.309017, 0.809017)

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Components

#1: Protein COWPEA MOSAIC VIRUS, LARGE (L) SUBUNIT / / CPMV


Mass: 40858.434 Da / Num. of mol.: 1 / Fragment: RESIDUES 460-828 / Source method: isolated from a natural source
Details: GENOME POLYPROTEIN M (CONTAINS\: COAT PROTEIN VP37, COAT PROTEIN VP23)
Source: (natural) COWPEA MOSAIC VIRUS / References: UniProt: P03599
#2: Protein COWPEA MOSAIC VIRUS, SMALL (S) SUBUNIT / / CPMV


Mass: 20961.564 Da / Num. of mol.: 1 / Fragment: RESIDUES 834-1022 / Source method: isolated from a natural source
Details: GENOME POLYPROTEIN M (CONTAINS\: COAT PROTEIN VP37, COAT PROTEIN VP23)
Source: (natural) COWPEA MOSAIC VIRUS / References: UniProt: P03599

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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

CrystalDescription: NONE
Crystal growpH: 7.5 / Details: pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Type: APS / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 4→50 Å / Num. obs: 39473 / % possible obs: 94 % / Observed criterion σ(I): 2 / Redundancy: 2.1 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 6

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Processing

SoftwareName: X-PLOR / Version: 3.8 / Classification: refinement
RefinementMethod to determine structure: OTHER / Resolution: 4→30 Å / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.23 --
obs0.23 39473 94 %
Refinement stepCycle: LAST / Resolution: 4→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4343 0 0 0 4343
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
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_deg1.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
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

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