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- PDB-3nap: Structure of Triatoma Virus (TrV) -

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Basic information

Entry
Database: PDB / ID: 3nap
TitleStructure of Triatoma Virus (TrV)
Components(Capsid proteinCapsid) x 3
KeywordsVIRUS / INSECT CRIPAVIRUS / ICOSAHEDRAL VIRUS
Function / homology
Function and homology information


viral capsid / structural molecule activity
Similarity search - Function
Dicistrovirus, capsid-polyprotein, C-terminal / CRPV capsid protein like / Jelly Rolls - #20 / Picornavirus capsid / picornavirus capsid protein / Picornavirus/Calicivirus coat protein / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesTriatoma virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / ML / Resolution: 2.5 Å
AuthorsSquires, G. / Pous, J.
CitationJournal: To be Published
Title: The crystallographic structure of Triatoma Virus (TrV) highlights the Dicistroviridae and Picornaviridae family differences
Authors: Squires, G. / Pous, J. / Rozas-Dennis, G.S. / Costabel, M.D. / Agirre, J. / Marti, G. / Navaza, J. / Guerin, D.M.A. / Rey, F.A.
History
DepositionJun 2, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 28, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jul 27, 2011Group: Other
Revision 1.3Mar 20, 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 / struct_ref_seq_dif
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 / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Capsid protein
B: Capsid protein
C: Capsid protein


Theoretical massNumber of molelcules
Total (without water)90,1943
Polymers90,1943
Non-polymers00
Water9,962553
1
A: Capsid protein
B: Capsid protein
C: Capsid protein
x 60


Theoretical massNumber of molelcules
Total (without water)5,411,634180
Polymers5,411,634180
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
A: Capsid protein
B: Capsid protein
C: Capsid protein
x 5


  • icosahedral pentamer
  • 451 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)450,96915
Polymers450,96915
Non-polymers00
Water27015
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: Capsid protein
B: Capsid protein
C: Capsid protein
x 6


  • icosahedral 23 hexamer
  • 541 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)541,16318
Polymers541,16318
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
A: Capsid protein
B: Capsid protein
C: Capsid protein
x 30


  • crystal asymmetric unit, crystal frame
  • 2.71 MDa, 90 polymers
Theoretical massNumber of molelcules
Total (without water)2,705,81790
Polymers2,705,81790
Non-polymers00
Water1,62190
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation29
Unit cell
Length a, b, c (Å)343.660, 360.460, 341.250
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.4318, -0.25647, -0.86474), (-0.26331, 0.88112, -0.39281), (0.86268, 0.39731, 0.31293)217.98869, 99.98325, -161.05547
3generate(0.31335, -0.7871, 0.53131), (0.83017, 0.49872, 0.24921), (-0.46113, 0.36299, 0.80969)214.47926, -74.31926, 30.71524
4generate(0.3149, -0.78551, -0.53274), (0.83193, 0.49862, -0.24344), (0.45686, -0.36655, 0.81051)305.02591, -31.91634, 3.63115
5generate(-0.12218, 0.01449, -0.9924), (-0.98471, 0.12329, 0.12303), (0.12414, 0.99227, -0.00079)275.86023, 316.44031, -113.75219
6generate(-0.80053, 0.5624, -0.20701), (-0.43895, -0.31508, 0.84146), (0.40801, 0.76448, 0.4991)225.6808, 239.67703, -164.47813
7generate(0.31066, 0.83493, -0.45429), (-0.78749, 0.49373, 0.3689), (0.5323, 0.24314, 0.81089)6.43835, 194.95976, -118.96017
8generate(-0.80156, -0.44023, 0.40461), (0.55979, -0.31473, 0.76654), (-0.21011, 0.84092, 0.49871)354.26199, 74.3605, -71.96158
9generate(-0.91248, -0.3501, -0.21167), (-0.35211, 0.40863, 0.84204), (-0.2083, 0.84289, -0.49614)410.62982, 94.90196, 12.29699
10generate(-0.12291, 0.01525, 0.9923), (-0.98475, 0.12222, -0.12385), (-0.12317, -0.99239, -1.0E-5)104.6859, 338.11612, 286.24969
11generate(0.3129, 0.83215, 0.45785), (-0.78526, 0.49783, -0.36815), (-0.53429, -0.24433, 0.80922)-71.24949, 257.08975, 152.16428
12generate(0.57785, 0.33576, 0.74388), (0.33733, 0.7317, -0.5923), (-0.74317, 0.59319, 0.30955)-52.17252, 40.83694, 80.50539
13generate(-0.10068, 0.88357, 0.45734), (0.88351, 0.29076, -0.36725), (-0.45747, 0.36709, -0.80992)-9.35629, 7.54935, 168.6925
14generate(0.12226, 0.98494, 0.12225), (-0.01563, -0.12124, 0.9925), (0.99237, -0.12326, 0.00057)-37.13394, 119.13033, -62.14228
15generate(-0.10065, 0.88463, -0.45529), (0.88146, 0.29151, 0.37155), (0.46141, -0.36393, -0.80911)68.50831, -56.25101, 141.93349
16generate(0.58037, 0.33674, -0.74147), (0.33799, 0.72877, 0.59553), (0.7409, -0.59624, 0.30914)75.46823, -60.36144, 39.76745
17generate(-0.47768, -0.14715, -0.86612), (0.4674, 0.7922, -0.39237), (0.74388, -0.59225, -0.30964)355.08484, -9.72004, 91.62596
18generate(0.80264, -0.55908, -0.20785), (0.43707, 0.31415, 0.84278), (-0.40588, -0.7673, 0.4965)152.52991, -24.04647, 252.04797
19generate(0.80008, 0.43867, 0.40919), (-0.56276, 0.31259, 0.76524), (0.20778, -0.84253, 0.49696)-80.26312, 154.98305, 160.01701
20generate(0.91414, 0.34953, -0.20539), (0.34723, -0.41355, 0.84167), (0.20925, -0.84072, -0.49941)-30.78969, 122.41209, 244.72223
21generate(-0.96935, 0.24568, 8.0E-5), (0.24568, 0.96935, -0.00063), (-0.00023, -0.0006, -1)293.92581, -36.49608, 172.67908
22generate(-0.12369, -0.98471, 0.12266), (0.01563, 0.12166, 0.99245), (-0.9922, 0.12468, 0.00034)360.05066, 70.11252, 233.98299
23generate(-0.49576, -0.68478, -0.53413), (-0.68495, 0.68642, -0.24428), (0.53392, 0.24474, -0.80934)426.34814, 195.10117, 20.28155
24generate(0.6692, -0.62236, 0.406), (-0.62156, -0.16939, 0.76484), (-0.40723, -0.76418, -0.50019)134.13402, 251.56085, 336.96387
25generate(-0.47944, -0.14819, 0.86497), (0.47096, 0.78824, 0.39609), (-0.7405, 0.59726, -0.30812)206.15646, -76.67967, 132.10077
26generate(-0.49409, -0.68854, 0.53085), (-0.68812, 0.68288, 0.24527), (-0.53138, -0.2441, -0.8112)335.66562, 154.50351, 291.58133
27generate(-0.67342, 0.6171, 0.40706), (0.61862, 0.16892, 0.76732), (0.40475, 0.76854, -0.4955)141.52892, -22.77399, -79.94066
28generate(0.42768, -0.26037, 0.86562), (-0.2649, 0.87947, 0.39542), (-0.86424, -0.39842, 0.30716)70.39125, 33.42769, 280.36407
29generate(-0.48309, 0.46557, 0.74153), (-0.14971, 0.79052, -0.59385), (-0.86268, -0.3979, -0.31219)107.34631, 114.39393, 333.49023
30generate(-0.47923, 0.46789, -0.74258), (-0.15183, 0.78911, 0.59519), (0.86446, 0.39798, -0.30712)234.11108, 13.01343, -107.86377
31generate(-1), (-1), (1)343.6601, 360.45895
32generate(-0.4318, 0.25647, 0.86474), (0.26331, -0.88112, 0.39281), (0.86268, 0.39731, 0.31293)125.6714, 260.47571, -161.05547
33generate(-0.31335, 0.7871, -0.53131), (-0.83017, -0.49872, -0.24921), (-0.46113, 0.36299, 0.80969)129.18085, 434.7782, 30.71524
34generate(-0.3149, 0.78551, 0.53274), (-0.83193, -0.49862, 0.24344), (0.45686, -0.36655, 0.81051)38.6342, 392.37531, 3.63115
35generate(0.12218, -0.01449, 0.9924), (0.98471, -0.12329, -0.12303), (0.12414, 0.99227, -0.00079)67.79988, 44.01864, -113.75219
36generate(0.80053, -0.5624, 0.20701), (0.43895, 0.31508, -0.84146), (0.40801, 0.76448, 0.4991)117.9793, 120.78192, -164.47813
37generate(-0.31066, -0.83493, 0.45429), (0.78749, -0.49373, -0.3689), (0.5323, 0.24314, 0.81089)337.22174, 165.49919, -118.96017
38generate(0.80156, 0.44023, -0.40461), (-0.55979, 0.31473, -0.76654), (-0.21011, 0.84092, 0.49871)-10.60188, 286.09845, -71.96158
39generate(0.91248, 0.3501, 0.21167), (0.35211, -0.40863, -0.84204), (-0.2083, 0.84289, -0.49614)-66.96972, 265.55698, 12.29699
40generate(0.12291, -0.01525, -0.9923), (0.98475, -0.12222, 0.12385), (-0.12317, -0.99239, -1.0E-5)238.9742, 22.34284, 286.24969
41generate(-0.3129, -0.83215, -0.45785), (0.78526, -0.49783, 0.36815), (-0.53429, -0.24433, 0.80922)414.90958, 103.36919, 152.16428
42generate(-0.57785, -0.33576, -0.74388), (-0.33733, -0.7317, 0.5923), (-0.74317, 0.59319, 0.30955)395.83261, 319.62201, 80.50539
43generate(0.10068, -0.88357, -0.45734), (-0.88351, -0.29076, 0.36725), (-0.45747, 0.36709, -0.80992)353.01639, 352.90961, 168.6925
44generate(-0.12226, -0.98494, -0.12225), (0.01563, 0.12124, -0.9925), (0.99237, -0.12326, 0.00057)380.79404, 241.32861, -62.14228
45generate(0.10065, -0.88463, 0.45529), (-0.88146, -0.29151, -0.37155), (0.46141, -0.36393, -0.80911)275.15179, 416.70996, 141.93349
46generate(-0.58037, -0.33674, 0.74147), (-0.33799, -0.72877, -0.59553), (0.7409, -0.59624, 0.30914)268.19186, 420.8204, 39.76745
47generate(0.47768, 0.14715, 0.86612), (-0.4674, -0.7922, 0.39237), (0.74388, -0.59225, -0.30964)-11.42473, 370.17899, 91.62596
48generate(-0.80264, 0.55908, 0.20785), (-0.43707, -0.31415, -0.84278), (-0.40588, -0.7673, 0.4965)191.1302, 384.50543, 252.04797
49generate(-0.80008, -0.43867, -0.40919), (0.56276, -0.31259, -0.76524), (0.20778, -0.84253, 0.49696)423.92322, 205.47591, 160.01701
50generate(-0.91414, -0.34953, 0.20539), (-0.34723, 0.41355, -0.84167), (0.20925, -0.84072, -0.49941)374.4498, 238.04686, 244.72223
51generate(0.96935, -0.24568, -8.0E-5), (-0.24568, -0.96935, 0.00063), (-0.00023, -0.0006, -1)49.7343, 396.95502, 172.67908
52generate(0.12369, 0.98471, -0.12266), (-0.01563, -0.12166, -0.99245), (-0.9922, 0.12468, 0.00034)-16.39056, 290.34644, 233.98299
53generate(0.49576, 0.68478, 0.53413), (0.68495, -0.68642, 0.24428), (0.53392, 0.24474, -0.80934)-82.68804, 165.35777, 20.28155
54generate(-0.6692, 0.62236, -0.406), (0.62156, 0.16939, -0.76484), (-0.40723, -0.76418, -0.50019)209.52608, 108.8981, 336.96387
55generate(0.47944, 0.14819, -0.86497), (-0.47096, -0.78824, -0.39609), (-0.7405, 0.59726, -0.30812)137.50365, 437.13861, 132.10077
56generate(0.49409, 0.68854, -0.53085), (0.68812, -0.68288, -0.24527), (-0.53138, -0.2441, -0.8112)7.99449, 205.95544, 291.58133
57generate(0.67342, -0.6171, -0.40706), (-0.61862, -0.16892, -0.76732), (0.40475, 0.76854, -0.4955)202.1312, 383.23294, -79.94066
58generate(-0.42768, 0.26037, -0.86562), (0.2649, -0.87947, -0.39542), (-0.86424, -0.39842, 0.30716)273.26886, 327.03125, 280.36407
59generate(0.48309, -0.46557, -0.74153), (0.14971, -0.79052, 0.59385), (-0.86268, -0.3979, -0.31219)236.3138, 246.06502, 333.49023
60generate(0.47923, -0.46789, 0.74258), (0.15183, -0.78911, -0.59519), (0.86446, 0.39798, -0.30712)109.54901, 347.44553, -107.86377

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Components

#1: Protein Capsid protein / Capsid


Mass: 29741.439 Da / Num. of mol.: 1 / Fragment: VP1 (UNP RESIDUES 598-868) / Source method: isolated from a natural source / Source: (natural) Triatoma virus / References: UniProt: Q9QEY5
#2: Protein Capsid protein / Capsid


Mass: 28519.396 Da / Num. of mol.: 1 / Fragment: VP2 (UNP RESIDUES 1-255) / Source method: isolated from a natural source / Source: (natural) Triatoma virus / References: UniProt: Q9QEY5
#3: Protein Capsid protein / Capsid


Mass: 31933.062 Da / Num. of mol.: 1 / Fragment: VP3 (UNP RESIDUES 313-597) / Source method: isolated from a natural source / Source: (natural) Triatoma virus / References: UniProt: Q9QEY5
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 553 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE AUTHORS STATE THAT VP4 (UNP RESIDUES 256-312) OF CAPSID PROTEIN IS NOT PRESENT IN THE ELECTRON ...THE AUTHORS STATE THAT VP4 (UNP RESIDUES 256-312) OF CAPSID PROTEIN IS NOT PRESENT IN THE ELECTRON DENSITY. ITS EXISTENCE WAS CONFIRMED BY MASS SPECTROMETRY.

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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

Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 6% PEG 8000, 100mM sodium citrate pH 5.6, 5% 2-propanol, 500mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 18, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.5→30 Å / Num. obs: 1328043 / Redundancy: 4.2 %

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Phasing

PhasingMethod: ML

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Processing

Software
NameVersionClassificationNB
AMoREphasing
CNSrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→30 Å / WRfactor Rwork: 0.171 / Occupancy max: 1 / Occupancy min: 1
RfactorNum. reflection% reflection
Rfree0.1732 --
Rwork0.171 --
obs-1328043 92.2 %
Displacement parametersBiso max: 112.31 Å2 / Biso mean: 22.868 Å2 / Biso min: 1 Å2
Refinement stepCycle: LAST / Resolution: 2.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6196 0 0 553 6749

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