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- PDB-1ohf: The refined structure of Nudaurelia capensis omega virus -

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Basic information

Entry
Database: PDB / ID: 1ohf
TitleThe refined structure of Nudaurelia capensis omega virus
ComponentsNUDAURELIA CAPENSIS OMEGA VIRUS CAPSID PROTEIN
KeywordsVIRUS / VIRAL COAT / AUTO-CATALYTIC CLEAVAGE / QUASIEQUIVALENCE / NWV / ICOSAHEDRAL VIRUS
Function / homology
Function and homology information


V-type ATP synthase subunit C fold - #30 / Mutm (Fpg) Protein; Chain: A, domain 2 - #70 / V-type ATP synthase subunit C fold - #20 / V-type ATP synthase subunit C fold / Peptidase N2 / Peptidase family A21 / Mutm (Fpg) Protein; Chain: A, domain 2 / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls ...V-type ATP synthase subunit C fold - #30 / Mutm (Fpg) Protein; Chain: A, domain 2 - #70 / V-type ATP synthase subunit C fold - #20 / V-type ATP synthase subunit C fold / Peptidase N2 / Peptidase family A21 / Mutm (Fpg) Protein; Chain: A, domain 2 / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Up-down Bundle / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
p70 / Capsid protein
Similarity search - Component
Biological speciesNUDAURELIA CAPENSIS OMEGA VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.8 Å
AuthorsHelgstrand, C. / Munshi, S. / Johnson, J.E. / Liljas, L.
Citation
Journal: Virology / Year: 2004
Title: The Refined Structure of Nudaurelia Capensis Omega Virus Reveals Control Elements for a T = 4 Capsid Maturation
Authors: Helgstrand, C. / Munshi, S. / Johnson, J.E. / Liljas, L.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 1998
Title: The Structure Determination of Nudaurelia Capensis W Virus
Authors: Munshi, S. / Liljas, L. / Johnson, J.E.
#2: Journal: J.Mol.Biol. / Year: 1996
Title: The 2.8 A Resolution Structure of a T=4 Animal Virus and its Implication for Membrane Translocation of RNA
Authors: Munshi, S. / Liljas, L. / Cavarelli, J. / Bomu, W. / Mckinney, B. / Reddy, V. / Johnson, J.E.
History
DepositionMay 26, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 26, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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: NUDAURELIA CAPENSIS OMEGA VIRUS CAPSID PROTEIN
B: NUDAURELIA CAPENSIS OMEGA VIRUS CAPSID PROTEIN
C: NUDAURELIA CAPENSIS OMEGA VIRUS CAPSID PROTEIN
D: NUDAURELIA CAPENSIS OMEGA VIRUS CAPSID PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)279,6658
Polymers279,5684
Non-polymers974
Water9,296516
1
A: NUDAURELIA CAPENSIS OMEGA VIRUS CAPSID PROTEIN
B: NUDAURELIA CAPENSIS OMEGA VIRUS CAPSID PROTEIN
C: NUDAURELIA CAPENSIS OMEGA VIRUS CAPSID PROTEIN
D: NUDAURELIA CAPENSIS OMEGA VIRUS CAPSID PROTEIN
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)16,779,902480
Polymers16,774,069240
Non-polymers5,833240
Water4,324240
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: NUDAURELIA CAPENSIS OMEGA VIRUS CAPSID PROTEIN
B: NUDAURELIA CAPENSIS OMEGA VIRUS CAPSID PROTEIN
C: NUDAURELIA CAPENSIS OMEGA VIRUS CAPSID PROTEIN
D: NUDAURELIA CAPENSIS OMEGA VIRUS CAPSID PROTEIN
hetero molecules
x 5


  • icosahedral pentamer
  • 1.4 MDa, 20 polymers
Theoretical massNumber of molelcules
Total (without water)1,398,32540
Polymers1,397,83920
Non-polymers48620
Water36020
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: NUDAURELIA CAPENSIS OMEGA VIRUS CAPSID PROTEIN
B: NUDAURELIA CAPENSIS OMEGA VIRUS CAPSID PROTEIN
C: NUDAURELIA CAPENSIS OMEGA VIRUS CAPSID PROTEIN
D: NUDAURELIA CAPENSIS OMEGA VIRUS CAPSID PROTEIN
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 1.68 MDa, 24 polymers
Theoretical massNumber of molelcules
Total (without water)1,677,99048
Polymers1,677,40724
Non-polymers58324
Water43224
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
A: NUDAURELIA CAPENSIS OMEGA VIRUS CAPSID PROTEIN
B: NUDAURELIA CAPENSIS OMEGA VIRUS CAPSID PROTEIN
C: NUDAURELIA CAPENSIS OMEGA VIRUS CAPSID PROTEIN
D: NUDAURELIA CAPENSIS OMEGA VIRUS CAPSID PROTEIN
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 16.8 MDa, 240 polymers
Theoretical massNumber of molelcules
Total (without water)16,779,902480
Polymers16,774,069240
Non-polymers5,833240
Water4,324240
TypeNameSymmetry operationNumber
transform to crystal frame1
point symmetry operation60
Unit cell
Length a, b, c (Å)413.550, 410.220, 419.670
Angle α, β, γ (deg.)59.13, 58.90, 64.04
Int Tables number1
Space group name H-MP1
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrix
1given(1), (1), (1)
2generate(0.337966, -0.691844, 0.638068), (0.476235, 0.710472, 0.518102), (-0.811775, 0.128769, 0.569596)
3generate(-0.733227, -0.643192, 0.22064), (0.07872, 0.242005, 0.967076), (-0.675412, 0.726455, -0.126812)
4generate(-0.733227, 0.07872, -0.675412), (-0.643192, 0.242005, 0.726455), (0.22064, 0.967076, -0.126812)
5generate(0.337966, 0.476235, -0.811775), (-0.691844, 0.710472, 0.128769), (0.638068, 0.518102, 0.569596)
6generate(-0.416678, -0.385496, -0.823269), (-0.385496, -0.745239, 0.544069), (-0.823269, 0.544069, 0.161917)
7generate(0.343899, -0.09162, -0.934526), (-0.926855, -0.192709, -0.322184), (-0.150573, 0.976969, -0.151191)
8generate(0.831219, -0.423356, -0.36034), (-0.14348, 0.462838, -0.874754), (0.537111, 0.778814, 0.323977)
9generate(0.371822, -0.922257, 0.105784), (0.882032, 0.315458, -0.350009), (0.289428, 0.223446, 0.930754)
10generate(-0.399421, -0.898859, -0.180322), (0.732457, -0.431175, 0.526872), (-0.551334, 0.078366, 0.830596)
11generate(-0.530526, 0.845311, -0.063175), (0.845311, 0.522025, -0.11375), (-0.063175, -0.11375, -0.991499)
12generate(0.274551, 0.959476, 0.063462), (0.626633, -0.228587, 0.745037), (0.729351, -0.164783, -0.663998)
13generate(0.498209, 0.499906, 0.708436), (-0.501883, -0.499999, 0.705773), (0.707038, -0.707174, 0.00179)
14generate(-0.16864, 0.101711, 0.980416), (-0.980665, 0.082871, -0.177281), (-0.09928, -0.991356, 0.085769)
15generate(-0.804434, 0.315183, 0.503534), (-0.148054, 0.714517, -0.683773), (-0.575297, -0.6246, -0.528117)
16generate(-0.052796, -0.459815, 0.886444), (-0.459815, -0.776786, -0.430319), (0.886444, -0.430319, -0.170419)
17generate(-0.956416, -0.176012, 0.232997), (-0.176012, -0.289176, -0.940955), (0.232997, -0.940955, 0.245592)
18generate(-0.596201, 0.566642, -0.568737), (0.566642, -0.204844, -0.798095), (-0.568737, -0.798095, -0.198955)
19generate(0.530045, 0.741825, -0.410788), (0.741825, -0.640334, -0.199166), (-0.410788, -0.199166, -0.889711)
20generate(0.865888, 0.10744, 0.488563), (0.10744, -0.993813, 0.028132), (0.488563, 0.028132, -0.872075)
21generate(-0.299891, -0.387366, 0.871787), (0.953686, -0.09932, 0.283933), (-0.0234, 0.916561, 0.399211)
22generate(-0.993526, 0.044525, 0.104521), (0.044525, -0.693804, 0.718786), (0.104521, 0.718786, 0.68733)
23generate(-0.399421, 0.732457, -0.551334), (-0.898859, -0.431175, 0.078366), (-0.180322, 0.526872, 0.830596)
24generate(0.66139, 0.725733, -0.189407), (-0.57274, 0.325624, -0.752289), (-0.484285, 0.606037, 0.63102)
25generate(0.722903, 0.033644, 0.69013), (0.572196, 0.530722, -0.625241), (-0.387302, 0.846878, 0.364409)
26generate(-0.443429, 0.878599, 0.177295), (-0.592846, -0.139147, -0.793203), (-0.672238, -0.456838, 0.582576)
27generate(0.124632, 0.953834, 0.273253), (0.377274, 0.209157, -0.902174), (-0.917677, 0.215531, -0.333789)
28generate(0.274551, 0.626633, 0.729351), (0.959476, -0.228587, -0.164783), (0.063462, 0.745037, -0.663998)
29generate(-0.200856, 0.349176, 0.915277), (0.349176, -0.847432, 0.399919), (0.915277, 0.399919, 0.048287)
30generate(-0.644592, 0.5049, 0.574088), (-0.610212, -0.792155, 0.011534), (0.46059, -0.34288, 0.818712)
31generate(-0.22342, -0.554882, -0.801368), (-0.607849, 0.722017, -0.330471), (0.761973, 0.413277, -0.498597)
32generate(0.310768, -0.342848, -0.886498), (0.406685, 0.890955, -0.202005), (0.859087, -0.297749, 0.416311)
33generate(0.66139, -0.57274, -0.484285), (0.725733, 0.325624, 0.606037), (-0.189407, -0.752289, 0.63102)
34generate(0.343899, -0.926855, -0.150573), (-0.09162, -0.192709, 0.976969), (-0.934526, -0.322184, -0.151191)
35generate(-0.202943, -0.915818, -0.346541), (-0.915818, 0.052276, 0.398176), (-0.346541, 0.398176, -0.849333)
36generate(0.96674, 0.063648, -0.247715), (0.247009, -0.483551, 0.839741), (-0.066335, -0.872999, -0.483189)
37generate(0.558126, -0.655511, 0.508725), (-0.828484, -0.406308, 0.385393), (-0.045931, -0.636568, -0.769852)
38generate(-0.53652, -0.78635, 0.306267), (-0.78635, 0.334139, -0.51962), (0.306267, -0.51962, -0.797619)
39generate(-0.804434, -0.148054, -0.575297), (0.315183, 0.714517, -0.6246), (0.503534, -0.683773, -0.528117)
40generate(0.124632, 0.377274, -0.917677), (0.953834, 0.209157, 0.215531), (0.273253, -0.902174, -0.333789)
41generate(-0.299891, 0.953686, -0.0234), (-0.387366, -0.09932, 0.916561), (0.871787, 0.283933, 0.399211)
42generate(0.371822, 0.882032, 0.289428), (-0.922257, 0.315458, 0.223446), (0.105784, -0.350009, 0.930754)
43generate(0.310768, 0.406685, 0.859087), (-0.342848, 0.890955, -0.297749), (-0.886498, -0.202005, 0.416311)
44generate(-0.398679, 0.18456, 0.898328), (0.550139, 0.831855, 0.073249), (-0.733759, 0.523408, -0.433176)
45generate(-0.776087, 0.522625, 0.352921), (0.522625, 0.219831, 0.823734), (0.352921, 0.823734, -0.443745)
46generate(-0.22342, -0.607849, 0.761973), (-0.554882, 0.722017, 0.413277), (-0.801368, -0.330471, -0.498597)
47generate(-0.983538, -0.179169, -0.023468), (-0.179169, 0.950082, 0.255427), (-0.023468, 0.255427, -0.966543)
48generate(-0.398679, 0.550139, -0.733759), (0.18456, 0.831855, 0.523408), (0.898328, 0.073249, -0.433176)
49generate(0.722903, 0.572196, -0.387302), (0.033644, 0.530722, 0.846878), (0.69013, -0.625241, 0.364409)
50generate(0.831219, -0.14348, 0.537111), (-0.423356, 0.462838, 0.778814), (-0.36034, -0.874754, 0.323977)
51generate(0.96674, 0.247009, -0.066335), (0.063648, -0.483551, -0.872999), (-0.247715, 0.839741, -0.483189)
52generate(0.498209, -0.501883, 0.707037), (0.499906, -0.499999, -0.707174), (0.708436, 0.705773, 0.00179)
53generate(-0.644592, -0.610212, 0.46059), (0.5049, -0.792155, -0.34288), (0.574088, 0.011534, 0.818712)
54generate(-0.88235, 0.071729, -0.465095), (0.071729, -0.956268, -0.28356), (-0.465095, -0.28356, 0.838618)
55generate(0.113508, 0.60152, -0.790752), (-0.20098, -0.765541, -0.611191), (-0.972997, 0.2283, 0.033999)
56generate(-0.443429, -0.592846, -0.672238), (0.878599, -0.139147, -0.456838), (0.177295, -0.793203, 0.582576)
57generate(0.113508, -0.20098, -0.972997), (0.60152, -0.765541, 0.2283), (-0.790752, -0.611191, 0.033999)
58generate(0.732503, -0.346612, -0.585918), (-0.346612, -0.930655, 0.117221), (-0.585918, 0.117221, -0.801848)
59generate(0.558126, -0.828484, -0.045931), (-0.655511, -0.406308, -0.636568), (0.508725, 0.385393, -0.769852)
60generate(-0.16864, -0.980665, -0.09928), (0.101711, 0.082871, -0.991356), (0.980416, -0.177281, 0.085769)

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Components

#1: Protein
NUDAURELIA CAPENSIS OMEGA VIRUS CAPSID PROTEIN


Mass: 69891.953 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) NUDAURELIA CAPENSIS OMEGA VIRUS / References: UniProt: Q90063, UniProt: Q4TVT6*PLUS
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 516 / Source method: isolated from a natural source / Formula: H2O
Compound detailsALL CHAINS ARE AUTOCATALYTICALLY CLEAVED BETWEEN RESIDUES 570 AND 571
Sequence detailsTHE SWISSPROT ENTRY HAS TWO SEQUENCE ERRORS THAT WERE DISCOVERED AFTER ITS SUBMISSION

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 200

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Sample preparation

Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
pH: 5 / Method: vapor diffusion, sitting drop / Details: Cavarelli, J., (1998) Acta Crystallogr., B47, 23.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.075 MMOPS1reservoirpH7.0
22 %PEG80001reservoir
30.25 M1reservoirCaCl2
40.001 M1reservoirNaN3
58-10 mg/mlvirus1drop
60.07 Msodium acetate1droppH5.0

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Data collection

DiffractionMean temperature: 287 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: A1 / Wavelength: 1.565
DetectorDetector: FILM
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.565 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. obs: 2465275 / % possible obs: 50.9 % / Observed criterion σ(I): 2 / Biso Wilson estimate: 19.4 Å2 / Rmerge(I) obs: 0.121
Reflection
*PLUS
% possible obs: 51 % / Rmerge(I) obs: 0.121

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Processing

Software
NameVersionClassification
CNS1.1refinement
PURDUEDATA PROCESSING PACKAGEdata reduction
PURDUEDATA PROCESSING PACKAGEdata scaling
PURDUEDATA PROCESSING PACKAGEphasing
RefinementMethod to determine structure: OTHER / Resolution: 2.8→20 Å / Rfactor Rfree error: 0.001 / Data cutoff high absF: 1436942.95 / Data cutoff low absF: 0 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.221 24978 1 %RANDOM
Rwork0.219 ---
obs0.219 2465275 50.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 45.2338 Å2 / ksol: 0.307644 e/Å3
Displacement parametersBiso mean: 39.3 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.38 Å
Luzzati d res low-5 Å
Luzzati sigma a0.67 Å0.64 Å
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17331 0 4 516 17851
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
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_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d25.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
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 shellResolution: 2.8→2.85 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.358 451 1 %
Rwork0.34 45950 -
obs--19.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION3ION.PARAMWATER.TOP
Refinement
*PLUS
Rfactor Rfree: 0.222 / Rfactor Rwork: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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