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- PDB-1qjz: Three Dimensional Structure of Physalis Mottle Virus : Implicatio... -

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Basic information

Entry
Database: PDB / ID: 1qjz
TitleThree Dimensional Structure of Physalis Mottle Virus : Implications for the Viral Assembly
ComponentsCOAT PROTEIN
KeywordsVIRUS / COAT PROTEIN (VIRAL) / ICOSAHEDRAL VIRUS / CAPSID PROTEIN / VIRION
Function / homology
Function and homology information


T=3 icosahedral viral capsid / structural molecule activity
Similarity search - Function
Tymovirus coat protein / Tymovirus coat protein / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesPHYSALIS MOTTLE VIRUS
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsKrishna, S.S. / Hiremath, C.N. / Munshi, S.K. / Prahadeeswaran, D. / Sastri, M. / Savithri, H.S. / Murthy, M.R.N.
Citation
Journal: J.Mol.Biol. / Year: 1999
Title: Three Dimensional Structure of Physalis Movirus: Implications for the Viral Assembly
Authors: Krishna, S.S. / Hiremath, C.N. / Munshi, S.K. / Prahadeeswaran, D. / Sastri, M. / Savithri, H.S. / Murthy, M.R.N.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: Identification of a Discrete Intermediate in the Assembly/Disassembly of Physalis Mottle Tymovirus Through Mutational Analysis
Authors: Sastri, M. / Reddy, S. / Krishna, S.S. / Murthy, M.R.N. / Savithri, H.S.
#2: Journal: J.Mol.Biol. / Year: 1997
Title: Assembly of Physalis Mottle Virus Capsid Protein in Escherichia Coli and the Role of Amino and Carboxy Termini in the Formation of the Icosahedral Particles
Authors: Sastri, M. / Kekuda, R. / Gopinath, K. / Kumar, C.T.R. / Jagath, J.R. / Savithri, H.S.
#3: Journal: Virology / Year: 1993
Title: Architecture of Physalis Mottle Tymovirus as Probed by Monoclonal Antibodies and Cross-Linking Studies
Authors: Kekuda, R. / Karande, A.A. / Jacob, A.N.K. / Savithri, H.S.
#4: Journal: Acta Crystallogr.,Sect.B / Year: 1990
Title: Structure of Belladonna Mottle Virus: Cross Rotation Function Studies with Southern Bean Mosaic Virus
Authors: Hiremath, C.N. / Munshi, S.K. / Murthy, M.R.N.
#5: Journal: J.Biol.Chem. / Year: 1989
Title: Primary Structure of Belladonna Mottle Virus Coat Protein
Authors: Suryanarayana, S. / Rao, N.A. / Murthy, M.R.N. / Savithri, H.S.
#6: Journal: J.Gen.Virol. / Year: 1987
Title: Stability of Belladonna Mottle Virus Particles: The Role of Polyamines and Calcium
Authors: Savithri, H.S. / Munshi, S.K. / Suryanarayana, S. / Divakar, S. / Murthy, M.R.N.
#7: Journal: Acta Crystallogr.,Sect.B / Year: 1987
Title: Symmetry of Belladonna Mottle Virus: Rotation Function Studies
Authors: Munshi, S.K. / Hiremath, C.N. / Murthy, M.R.N. / Savithri, H.S.
History
DepositionJul 7, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 1999Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 30, 2018Group: Data collection / Structure summary / Category: diffrn_detector / struct / Item: _diffrn_detector.detector / _struct.title
Revision 1.4Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN


Theoretical massNumber of molelcules
Total (without water)59,9703
Polymers59,9703
Non-polymers00
Water00
1
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
x 60


Theoretical massNumber of molelcules
Total (without water)3,598,186180
Polymers3,598,186180
Non-polymers00
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
B: COAT PROTEIN
C: COAT PROTEIN
x 5


  • icosahedral pentamer
  • 300 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)299,84915
Polymers299,84915
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
x 6


  • icosahedral 23 hexamer
  • 360 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)359,81918
Polymers359,81918
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation5
5


  • Idetical with deposited unit
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)294.650, 294.650, 294.650
Angle α, β, γ (deg.)59.91, 59.91, 59.91
Int Tables number146
Space group name H-MR3
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))

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Components

#1: Protein COAT PROTEIN / VIRION PROTEIN


Mass: 19989.924 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) PHYSALIS MOTTLE VIRUS / Strain: IOWA / References: UniProt: P36351

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 48

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Sample preparation

Crystal growpH: 5.6 / Details: pH 5.60
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
130-40 mg/mlvirus1drop
22 mMdithiothreitol1drop
30.1 Msodium citrate1drop
42.5 %PEG60001reservoirinner well
510 %PEG60001reservoirouter well

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS / Wavelength: 1.5418
DetectorDetector: OSCILLATION CAMERA / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.8→60 Å / Num. obs: 137259 / % possible obs: 40 % / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
X-PLOR3.1refinement
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AUY

1auy


Resolution: 3.8→10 Å / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.326 --
obs0.326 85644 40 %
Refinement stepCycle: LAST / Resolution: 3.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4038 0 0 0 4038
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.01
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_deg1.6
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.35
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: STRICT
Xplor fileSerial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO
Software
*PLUS
Version: 3.1 / Classification: refinement
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
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.35
LS refinement shell
*PLUS
Highest resolution: 3.8 Å / Lowest resolution: 3.96 Å / Rfactor Rwork: 0.42 / Num. reflection obs: 5434

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