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- PDB-2wws: Physalis Mottle Virus: Natural Empty Capsid -

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Basic information

Entry
Database: PDB / ID: 2wws
TitlePhysalis Mottle Virus: Natural Empty Capsid
ComponentsCOAT PROTEIN
KeywordsVIRUS / PLANT RNA VIRUS
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 / OTHER / Resolution: 3.9 Å
AuthorsSagurthi, S.R. / Rajaram, V. / Savithri, H.S. / Murthy, M.R.N.
CitationJournal: To be Published
Title: Crystal Structure of the Physalis Mottle Virus
Authors: Sagurthi, S.R. / Rajaram, V. / Savithri, H.S. / Murthy, M.R.N.
History
DepositionOct 27, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_struct_oper_list / struct_sheet
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 / _struct_sheet.number_strands
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 in distinct coordinate
  • icosahedral asymmetric unit, std point frame
TypeNameSymmetry operationNumber
transform to point frame1
6
A: COAT PROTEIN
B: COAT PROTEIN
C: COAT PROTEIN
x 60


  • crystal asymmetric unit, crystal frame
  • 3.6 MDa, 180 polymers
Theoretical massNumber of molelcules
Total (without water)3,598,186180
Polymers3,598,186180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)325.760, 325.760, 738.940
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.309017, -0.808973, -0.500072), (0.80897, 0.500056, -0.309049), (0.500076, -0.309041, 0.808961)0.0015, 0.00093, 0.00057
3generate(-0.809017, -0.499976, -0.309056), (0.499968, -0.308869, -0.809093), (0.309069, -0.809088, 0.499852)0.00093, 0.00243, 0.0015
4generate(-0.809017, 0.499968, 0.309069), (-0.499976, -0.308869, -0.809088), (-0.309056, -0.809093, 0.499852)-0.00093, 0.00243, 0.0015
5generate(0.309017, 0.80897, 0.500076), (-0.808973, 0.500056, -0.309041), (-0.500072, -0.309049, 0.808961)-0.0015, 0.00093, 0.00057
6generate(-0.809013, -0.500033, 0.308974), (-0.500033, 0.309163, -0.808941), (0.308974, -0.808941, -0.50015)0.00057, 0.0015, 0.00208
7generate(-0.5, 0.308939, 0.809047), (-0.308947, 0.809108, -0.499895), (-0.809044, -0.4999, -0.309108)-0.00093, 0.00057, 0.0015
8generate(0.499999, 0.308945, 0.809045), (0.309089, 0.809018, -0.499954), (-0.80899, 0.500043, 0.309017)-0.00093, 0.00057, -0.00036
9generate(0.809019, -0.500024, 0.308971), (0.499969, 0.309017, -0.809036), (0.30906, 0.809002, 0.499998)0.00057, 0.0015, -0.00093
10generate(5.0E-6, -1, -9.0E-5), (-9.5E-5, 9.0E-5, -1), (1, 5.0E-6, -9.5E-5)0.0015, 0.00208, 0.00057
11generate(-0.500006, -0.308941, -0.809043), (-0.308941, -0.809109, 0.499898), (-0.809043, 0.499898, 0.309115)0.00093, 0.00243, -0.00036
12generate(-0.809017, 0.500031, -0.308967), (-0.500026, -0.309165, 0.808945), (0.308975, 0.808942, 0.500148)-0.00057, 0.0015, -0.00093
13generate(3.0E-6, 1, 9.0E-5), (-8.7E-5, -9.0E-5, 1), (1, -3.0E-6, 8.7E-5)-0.0015, 0.00093, 0.00057
14generate(0.809016, 0.500027, -0.308978), (0.499977, -0.309016, 0.809032), (0.309059, -0.809001, -0.5)-0.00057, 0.0015, 0.00208
15generate(0.499994, -0.308943, -0.809049), (0.309095, -0.809017, 0.499952), (-0.808991, -0.500046, -0.309011)0.00093, 0.00243, 0.0015
16generate(0.309019, 0.808974, 0.500069), (0.808974, -0.500054, 0.309043), (0.500069, 0.309043, -0.808964)-0.0015, 0.00208, 0.00057
17generate(1, 3.0E-6, -8.0E-6), (3.0E-6, -1), (-8.0E-6, -1)0.00301, 0.00115
18generate(0.309015, -0.808969, -0.500079), (-0.808969, -0.500059, 0.309048), (-0.500079, 0.309048, -0.808957)0.0015, 0.00208, 0.00057
19generate(-0.809018, -0.49997, -0.309063), (-0.49997, 0.308868, 0.809092), (-0.309063, 0.809092, -0.49985)0.00093, 0.00057, -0.00036
20generate(-0.809016, 0.499973, 0.309063), (0.499973, 0.308871, 0.809089), (0.309063, 0.809089, -0.499855)-0.00093, 0.00057, -0.00036
21generate(-0.309013, -0.809061, 0.499931), (0.80897, -0.5, -0.309139), (0.500078, 0.308901, 0.809013)0.00093, 0.00243, -0.00036
22generate(-0.499993, -0.309092, 0.808993), (-0.309092, -0.808926, -0.5001), (0.808993, -0.5001, 0.308919)0.00301, 0.00115
23generate(5.0E-6, -9.5E-5, 1), (-1, 9.0E-5, 5.0E-6), (-9.0E-5, -1, -9.5E-5)-0.00057, 0.0015, 0.00208
24generate(0.500001, -0.309093, 0.808987), (-0.308942, 0.809016, 0.500048), (-0.809045, -0.499954, 0.309017)0.00115
25generate(0.309017, -0.809062, 0.499928), (0.809064, 0.499944, 0.308986), (-0.499925, 0.308991, 0.809073)0.00093, 0.00057, -0.00036
26generate(0.809018, -0.50003, 0.308965), (-0.499967, -0.309018, 0.809037), (-0.309067, -0.808998, -0.5)0.00057, 0.0015, 0.00208
27generate(-3.0E-6, -1, -9.3E-5), (9.5E-5, -9.3E-5, 1), (-1, 3.0E-6, 9.5E-5)0.0015, 0.00093, 0.00057
28generate(-0.809017, -0.500026, 0.308975), (0.500031, -0.309165, 0.808942), (-0.308967, 0.808945, 0.500148)0.00057, 0.0015, -0.00093
29generate(-0.499994, 0.308945, 0.809048), (0.308945, -0.809107, 0.499898), (0.809048, 0.499898, 0.309102)-0.00093, 0.00243, -0.00036
30generate(0.500006, 0.308943, 0.809041), (-0.309087, -0.809017, 0.499957), (0.808986, -0.500046, -0.309023)-0.00093, 0.00243, 0.0015
31generate(-5.0E-6, 1, 9.3E-5), (8.7E-5, 9.3E-5, -1), (-1, -5.0E-6, -8.7E-5)-0.0015, 0.00208, 0.00057
32generate(0.809015, 0.500032, -0.308971), (-0.499974, 0.309017, -0.809033), (-0.309065, 0.808997, 0.500002)-0.00057, 0.0015, -0.00093
33generate(0.500001, -0.308942, -0.809045), (-0.309093, 0.809016, -0.499954), (0.808987, 0.500048, 0.309017)0.00093, 0.00057, -0.00036
34generate(-0.5, -0.308947, -0.809044), (0.308939, 0.809108, -0.4999), (0.809047, -0.499895, -0.309108)0.00093, 0.00057, 0.0015
35generate(-0.809021, 0.500023, -0.308969), (0.500023, 0.309166, -0.808945), (-0.308969, -0.808945, -0.500145)-0.00057, 0.0015, 0.00208
36generate(-0.5, 0.309091, -0.808989), (-0.309091, 0.808926, 0.500102), (0.808989, 0.500102, -0.308926)
37generate(-0.309019, 0.80906, -0.499928), (0.808971, 0.500002, 0.309133), (0.500072, -0.3089, -0.809017)-0.00093, 0.00057, 0.0015
38generate(0.309011, 0.809063, -0.49993), (0.809063, -0.499941, -0.308993), (-0.49993, -0.308993, -0.80907)-0.00093, 0.00243, 0.0015
39generate(0.499994, 0.309095, -0.808991), (-0.308943, -0.809017, -0.500046), (-0.809049, 0.499952, -0.309011)0.00301
40generate(-3.0E-6, 9.5E-5, -1), (-1, -9.3E-5, 3.0E-6), (-9.3E-5, 1, 9.5E-5)0.00057, 0.0015, -0.00093
41generate(-0.309013, 0.80897, 0.500078), (-0.809061, -0.5, 0.308901), (0.499931, -0.309139, 0.809013)-0.0015, 0.00208, 0.00057
42generate(0.809019, 0.499969, 0.30906), (-0.500024, 0.309017, 0.809002), (0.308971, -0.809036, 0.499998)-0.00093, 0.00057, 0.0015
43generate(0.809015, -0.499974, -0.309065), (0.500032, 0.309017, 0.808997), (-0.308971, -0.809033, 0.500002)0.00093, 0.00057, 0.0015
44generate(-0.309021, -0.808972, -0.50007), (0.809064, -0.5, 0.308893), (-0.499921, -0.309134, 0.809021)0.0015, 0.00208, 0.00057
45generate(-1, 8.0E-6), (-1, -0.000183), (8.0E-6, -0.000183, 1)0.00301
46generate(-5.0E-6, 8.7E-5, -1), (1, 9.3E-5, -5.0E-6), (9.3E-5, -1, -8.7E-5)0.00057, 0.0015, 0.00208
47generate(-0.500007, 0.309089, -0.808985), (0.309089, -0.808925, -0.500105), (-0.808985, -0.500105, 0.308932)0.00301, 0.00115
48generate(-0.309021, 0.809064, -0.499921), (-0.808972, -0.5, -0.309134), (-0.50007, 0.308893, 0.809021)-0.00093, 0.00243, -0.00036
49generate(0.309017, 0.809064, -0.499925), (-0.809062, 0.499944, 0.308991), (0.499928, 0.308986, 0.809073)-0.00093, 0.00057, -0.00036
50generate(0.499999, 0.309089, -0.80899), (0.308945, 0.809018, 0.500043), (0.809045, -0.499954, 0.309017)0.00115
51generate(-0.5, -0.309091, 0.808989), (0.309091, 0.808926, 0.500102), (-0.808989, 0.500102, -0.308926)
52generate(3.0E-6, -8.7E-5, 1), (1, -9.0E-5, -3.0E-6), (9.0E-5, 1, 8.7E-5)-0.00057, 0.0015, -0.00093
53generate(0.500006, -0.309087, 0.808986), (0.308943, -0.809017, -0.500046), (0.809041, 0.499957, -0.309023)0.00301
54generate(0.309023, -0.809063, 0.499922), (-0.809063, -0.499946, -0.308985), (0.499922, -0.308985, -0.809077)0.00093, 0.00243, 0.0015
55generate(-0.309015, -0.809065, 0.499924), (-0.808971, 0.499998, 0.309141), (-0.500075, -0.308895, -0.809017)0.00093, 0.00057, 0.0015
56generate(0.809018, -0.499967, -0.309067), (-0.50003, -0.309018, -0.808998), (0.308965, 0.809037, -0.5)0.00093, 0.00243, -0.00036
57generate(-0.309015, -0.808971, -0.500075), (-0.809065, 0.499998, -0.308895), (0.499924, 0.309141, -0.809017)0.0015, 0.00093, 0.00057
58generate(-1, -3.0E-6), (-3.0E-6, 1, 0.000183), (0.000183, -1)0.00115
59generate(-0.309019, 0.808971, 0.500072), (0.80906, 0.500002, -0.3089), (-0.499928, 0.309133, -0.809017)-0.0015, 0.00093, 0.00057
60generate(0.809016, 0.499977, 0.309059), (0.500027, -0.309016, -0.809001), (-0.308978, 0.809032, -0.5)-0.00093, 0.00243, -0.00036

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Components

#1: Protein COAT PROTEIN / VIRION PROTEIN


Mass: 19989.924 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PHYSALIS MOTTLE VIRUS / Description: NATURAL PURIFICATION FROM INFECTED PLANTS / Production host: NICOTIANA GLUTINOSA (plant) / References: UniProt: P36351

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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

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 41.31 % / Description: NONE
Crystal growpH: 5.5
Details: 100MM SODIUM ACETATE, 2MM CALCL2, 10% GLYCEROL, 3% PEG8000 PH 5.5.

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 18, 2004 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.9→19 Å / Num. obs: 266460 / % possible obs: 87.9 % / Observed criterion σ(I): 2 / Redundancy: 2.5 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 8
Reflection shellResolution: 3.9→4.04 Å / % possible all: 89.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALAdata scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 3.9→20 Å / Data cutoff high absF: 10000 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2425 1036 0.4 %RANDOM
Rwork0.2299 ---
obs0.2299 210129 79.4 %-
Solvent computationBsol: 10 Å2 / ksol: 0.54758 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--5.897 Å2-6.708 Å2-0 Å2
2---5.897 Å2-0 Å2
3---11.794 Å2
Refinement stepCycle: LAST / Resolution: 3.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3976 0 0 0 3976
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.010626
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.53205
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellHighest resolution: 3.9 Å / Total num. of bins used: 10
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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