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- PDB-1pgl: BEAN POD MOTTLE VIRUS (BPMV), MIDDLE COMPONENT -

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Basic information

Entry
Database: PDB / ID: 1pgl
TitleBEAN POD MOTTLE VIRUS (BPMV), MIDDLE COMPONENT
Components
  • 5'-R(*AP*GP*UP*CP*UP*C)-3'
  • BEAN POD MOTTLE VIRUS LARGE (L) SUBUNIT
  • BEAN POD MOTTLE VIRUS SMALL (S) SUBUNIT
KeywordsVirus/RNA / COMOVIRUS / VIRUS / VIRAL COAT PROTEIN / BEAN POD MOTTLE VIRUS (BPMV) / Icosahedral virus / Virus-RNA COMPLEX
Function / homology
Function and homology information


transport of virus in host, cell to cell / host cell plasmodesma / T=3 icosahedral viral capsid / symbiont-mediated suppression of host innate immune response / 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
RNA / RNA2 polyprotein
Similarity search - Component
Biological speciesBean-pod mottle virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsLin, T. / Cavarelli, J. / Johnson, J.E.
Citation
Journal: Virology / Year: 2003
Title: Evidence for assembly-dependent folding of protein and RNA in an icosahedral virus.
Authors: Lin, T. / Cavarelli, J. / Johnson, J.E.
#1: Journal: Science / Year: 1989
Title: Protein-/RNA Interactions in an Icosahedral Virus at 3.0 Angstroms Resolution
Authors: Chen, Z. / Stauffacher, C. / Li, Y. / Schmidt, T. / Bomu, W. / Kamer, G. / Shanks, M. / Lomonossoff, G. / Johnson, J.E.
History
DepositionMay 28, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 18, 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
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
Revision 1.5Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
3: 5'-R(*AP*GP*UP*CP*UP*C)-3'
1: BEAN POD MOTTLE VIRUS SMALL (S) SUBUNIT
2: BEAN POD MOTTLE VIRUS LARGE (L) SUBUNIT


Theoretical massNumber of molelcules
Total (without water)63,2753
Polymers63,2753
Non-polymers00
Water3,441191
1
3: 5'-R(*AP*GP*UP*CP*UP*C)-3'
1: BEAN POD MOTTLE VIRUS SMALL (S) SUBUNIT
2: BEAN POD MOTTLE VIRUS LARGE (L) SUBUNIT
x 60


Theoretical massNumber of molelcules
Total (without water)3,796,473180
Polymers3,796,473180
Non-polymers00
Water3,243180
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
3: 5'-R(*AP*GP*UP*CP*UP*C)-3'
1: BEAN POD MOTTLE VIRUS SMALL (S) SUBUNIT
2: BEAN POD MOTTLE VIRUS LARGE (L) SUBUNIT
x 5


  • icosahedral pentamer
  • 316 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)316,37315
Polymers316,37315
Non-polymers00
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
3: 5'-R(*AP*GP*UP*CP*UP*C)-3'
1: BEAN POD MOTTLE VIRUS SMALL (S) SUBUNIT
2: BEAN POD MOTTLE VIRUS LARGE (L) SUBUNIT
x 6


  • icosahedral 23 hexamer
  • 380 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)379,64718
Polymers379,64718
Non-polymers00
Water32418
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
3: 5'-R(*AP*GP*UP*CP*UP*C)-3'
1: BEAN POD MOTTLE VIRUS SMALL (S) SUBUNIT
2: BEAN POD MOTTLE VIRUS LARGE (L) SUBUNIT
x 30


  • crystal asymmetric unit, crystal frame
  • 1.9 MDa, 90 polymers
Theoretical massNumber of molelcules
Total (without water)1,898,23690
Polymers1,898,23690
Non-polymers00
Water1,62190
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)311.200, 284.200, 350.500
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))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.30901699, -0.87337965, 0.37645249), (0.87337965, 0.41727875, 0.25117011), (-0.37645249, 0.25117011, 0.89173825)53.65068, -67.81269, 29.22928
3generate(-0.80901699, -0.53977831, 0.23266043), (0.53977831, -0.52558404, 0.65757189), (-0.23266043, 0.65757189, 0.71656705)140.45932, -41.91055, 18.06469
4generate(-0.80901699, 0.53977831, -0.23266043), (-0.53977831, -0.52558404, 0.65757189), (0.23266043, 0.65757189, 0.71656705)140.45932, 41.91055, -18.06469
5generate(0.30901699, 0.87337965, -0.37645249), (-0.87337965, 0.41727875, 0.25117011), (0.37645249, 0.25117011, 0.89173825)53.65068, 67.81269, -29.22928
6generate(-0.5, -0.18751829, -0.84548027), (-0.18751829, -0.92967378, 0.31708602), (-0.84548027, 0.31708602, 0.42967378)116.466, 14.55967, 65.64647
7generate(0.14608306, -0.98927233), (-0.98927233, -0.14451593, -0.02134026), (-0.14608306, 0.97865974, 0.14451593)77.644, 76.81106, 11.34247
8generate(0.5, -0.18751829, -0.84548027), (-0.42388564, 0.79834686, -0.42774204), (0.75519598, 0.57225796, 0.31968712)38.822, 32.91218, -58.63644
9generate(0.30901699, -0.7272966, -0.61281984), (0.7272966, 0.59591026, -0.34048587), (0.61281984, -0.34048587, 0.71310674)53.65068, -56.47022, -47.58178
10generate(-0.30901699, -0.7272966, -0.61281984), (0.87337965, -0.47206524, 0.11984319), (-0.37645249, -0.4981908, 0.78108223)101.63732, -67.81269, 29.22928
11generate(0.30901699, 0.7272966, 0.61281984), (0.7272966, -0.59591026, 0.34048587), (0.61281984, 0.34048587, -0.71310674)53.65068, -56.47022, -47.58178
12generate(0.5, 0.18751829, 0.84548027), (-0.42388564, -0.79834686, 0.42774204), (0.75519598, -0.57225796, -0.31968712)38.822, 32.91218, -58.63644
13generate(-0.14608306, 0.98927233), (-0.98927233, 0.14451593, 0.02134026), (-0.14608306, -0.97865974, -0.14451593)77.644, 76.81106, 11.34247
14generate(-0.5, 0.18751829, 0.84548027), (-0.18751829, 0.92967378, -0.31708602), (-0.84548027, -0.31708602, -0.42967378)116.466, 14.55967, 65.64647
15generate(-0.30901699, 0.7272966, 0.61281984), (0.87337965, 0.47206524, -0.11984319), (-0.37645249, 0.4981908, -0.78108223)101.63732, -67.81269, 29.22928
16generate(-0.30901699, -0.87337965, 0.37645249), (0.7272966, -0.47206524, -0.4981908), (0.61281984, 0.11984319, 0.78108223)101.63732, -56.47022, -47.58178
17generate(-1), (-0.95731948, -0.28903185), (-0.28903185, 0.95731948)155.288
18generate(-0.30901699, 0.87337965, -0.37645249), (-0.7272966, -0.47206524, -0.4981908), (-0.61281984, 0.11984319, 0.78108223)101.63732, 56.47022, 47.58178
19generate(0.80901699, 0.53977831, -0.23266043), (-0.44949402, 0.31309262, -0.83661708), (-0.37874349, 0.78141691, 0.49592437)14.82868, 34.90051, 29.40716
20generate(0.80901699, -0.53977831, 0.23266043), (0.44949402, 0.31309262, -0.83661708), (0.37874349, 0.78141691, 0.49592437)14.82868, -34.90051, -29.40716
21generate(0.98927233, 0.14608306), (0.14608306, 0.14451593, -0.97865974), (-0.98927233, 0.02134026, -0.14451593)77.644, -11.34247, 76.81106
22generate(0.80901699, 0.44949402, 0.37874349), (0.53977831, -0.31309262, -0.78141691), (-0.23266043, 0.83661708, -0.49592437)14.82868, -41.91055, 18.06469
23generate(0.5, -0.42388564, 0.75519598), (0.18751829, -0.79834686, -0.57225796), (0.84548027, 0.42774204, -0.31968712)38.822, -14.55967, -65.64647
24generate(-0.5, -0.42388564, 0.75519598), (-0.42388564, -0.64064193, -0.64023346), (0.75519598, -0.64023346, 0.14064193)116.466, 32.91218, -58.63644
25generate(-0.80901699, 0.44949402, 0.37874349), (-0.44949402, -0.05792068, -0.89140357), (-0.37874349, -0.89140357, 0.24890369)140.45932, 34.90051, 29.40716
26generate(-0.5, 0.42388564, -0.75519598), (-0.42388564, 0.64064193, 0.64023346), (0.75519598, 0.64023346, -0.14064193)116.466, 32.91218, -58.63644
27generate(0.5, 0.42388564, -0.75519598), (0.18751829, 0.79834686, 0.57225796), (0.84548027, -0.42774204, 0.31968712)38.822, -14.55967, -65.64647
28generate(0.80901699, -0.44949402, -0.37874349), (0.53977831, 0.31309262, 0.78141691), (-0.23266043, -0.83661708, 0.49592437)14.82868, -41.91055, 18.06469
29generate(-0.98927233, -0.14608306), (0.14608306, -0.14451593, 0.97865974), (-0.98927233, -0.02134026, 0.14451593)77.644, -11.34247, 76.81106
30generate(-0.80901699, -0.44949402, -0.37874349), (-0.44949402, 0.05792068, 0.89140357), (-0.37874349, 0.89140357, -0.24890369)140.45932, 34.90051, 29.40716

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Components

#1: RNA chain 5'-R(*AP*GP*UP*CP*UP*C)-3'


Mass: 1852.150 Da / Num. of mol.: 1 / Source method: obtained synthetically
#2: Protein BEAN POD MOTTLE VIRUS SMALL (S) SUBUNIT / BPMV / GENOME POLYPROTEIN M [CONTAINS: COAT PROTEIN VP37 / COAT PROTEIN VP23]


Mass: 20638.260 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bean-pod mottle virus (strain Kentucky G7)
Genus: Comovirus / Species: Bean pod mottle virus / Strain: Kentucky G7 / References: UniProt: P23009
#3: Protein BEAN POD MOTTLE VIRUS LARGE (L) SUBUNIT / BPMV / GENOME POLYPROTEIN M [CONTAINS: COAT PROTEIN VP37 / COAT PROTEIN VP23]


Mass: 40784.133 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Source: (natural) Bean-pod mottle virus (strain Kentucky G7)
Genus: Comovirus / Species: Bean pod mottle virus / Strain: Kentucky G7 / References: UniProt: P23009
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

Crystal growpH: 7
Details: PEG 8000, POTASIUM PHOSPHATE, PH 7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K, pH 7.00
Components of the solutions
IDNameCrystal-IDSol-ID
1PEG 800011
2POTASIUM PHOSPHATE11
Crystal grow
*PLUS
Method: other / Details: Chen, Z., (1989) Science, 245, 154.
Components of the solutions
*PLUS
IDCrystal-ID
11
21

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 1.566
DetectorType: KODAK / Detector: FILM / Details: MIRROR
RadiationMonochromator: SILICON / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.566 Å / Relative weight: 1
ReflectionResolution: 2.8→30 Å / Num. obs: 577990 / % possible obs: 76.7 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 22 Å2
Reflection shellResolution: 2.8→2.92 Å / % possible all: 37.3
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å / Num. obs: 577995 / Rmerge(I) obs: 0.096

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Processing

Software
NameVersionClassification
MGROSCdata collection
MGROSCdata reduction
X-PLOR3.851refinement
MGROSCdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: COWPEA MOSAIC VIRUS

Resolution: 2.8→10 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflection
Rwork0.196 --
obs0.196 562649 76.4 %
Displacement parametersBiso mean: 17.8 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyzeLuzzati coordinate error obs: 0.34 Å / Luzzati d res low obs: 10 Å / Luzzati sigma a obs: 0.38 Å
Refinement stepCycle: LAST / Resolution: 2.8→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4303 122 0 191 4616
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.017
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_deg1.7
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d27.3
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.42
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: 2.8→2.92 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rwork0.305 34388 -
obs--40.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 10 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.019
X-RAY DIFFRACTIONx_angle_deg1.81
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.04
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.44

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