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- PDB-1c8e: FELINE PANLEUKOPENIA VIRUS EMPTY CAPSID STRUCTURE -

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Basic information

Entry
Database: PDB / ID: 1c8e
TitleFELINE PANLEUKOPENIA VIRUS EMPTY CAPSID STRUCTURE
ComponentsFELINE PANLEUKOPENIA VIRUS CAPSID
KeywordsVIRUS / Beta Barrel / Viral Capsid / Icosahedral Symmetry / Icosahedral virus
Function / homology
Function and homology information


permeabilization of host organelle membrane involved in viral entry into host cell / symbiont entry into host cell via permeabilization of inner membrane / microtubule-dependent intracellular transport of viral material towards nucleus / T=1 icosahedral viral capsid / viral penetration into host nucleus / clathrin-dependent endocytosis of virus by host cell / host cell nucleus / virion attachment to host cell / structural molecule activity / metal ion binding
Similarity search - Function
Empty Capsid Viral Protein 2 / Parvovirus coat protein VP1/VP2 / Phospholipase A2-like domain / Phospholipase A2-like domain / Parvovirus coat protein VP2 / Parvovirus coat protein VP1/VP2 / Parvovirus coat protein VP2 / Capsid/spike protein, ssDNA virus / Beta Complex / Mainly Beta
Similarity search - Domain/homology
Capsid protein VP1 / Capsid protein 2
Similarity search - Component
Biological speciesFeline parvovirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å
AuthorsRossmann, M.G. / Simpson, A.A.
Citation
Journal: J.Mol.Biol. / Year: 2000
Title: Host range and variability of calcium binding by surface loops in the capsids of canine and feline parvoviruses.
Authors: Simpson, A.A. / Chandrasekar, V. / Hebert, B. / Sullivan, G.M. / Rossmann, M.G. / Parrish, C.R.
#1: Journal: Protein Sci. / Year: 1993
Title: Structure Determination of Feline Panleukopenia Virus Empty Particles
Authors: Agbandje, M. / McKenna, R. / Rossmann, M.G. / Strassheim, M.L. / Parrish, C.R.
#2: Journal: Acta Crystallogr.,Sect.D / Year: 1996
Title: Structural Refinement of the DNA-Containing Capsid of Canine Parvovirus using RSRef, a Resolution-Dependent Stereochemically Restrained Real-Space Refinement Method
Authors: Chapman, M.S. / Rossmann, M.G.
#3: Journal: Virology / Year: 1996
Title: Structural Analysis of a Mutation in Canine Parvovirus which Controls Antigenicity and Host Range
Authors: Llamas-Saiz, A.L. / Agbandje-McKenna, M. / Parker, J.S. / Wahid, A.T. / Parrish, C.R. / Rossmann, M.G.
#4: Journal: Science / Year: 1991
Title: The 3-Dimensional Structure of Canine Parvovirus and its Functional Implications
Authors: Tsao, J. / Chapman, M.S. / Agbandje, M. / Keller, W. / Smith, K. / Wu, H. / Luo, M. / Smith, T.J. / Rossmann, M.G. / Compans, R.W. / Parrish, C.R.
History
DepositionMay 5, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 30, 2011Group: Advisory
Revision 1.4Oct 4, 2017Group: Refinement description / Category: software
Revision 1.5Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 2.0Apr 19, 2023Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / atom_sites ...atom_site / atom_sites / cell / database_2 / database_PDB_matrix / pdbx_database_remark / pdbx_struct_oper_list / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_ncs_oper / struct_ref_seq_dif
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_sites.fract_transf_matrix[1][3] / _cell.Z_PDB / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _database_PDB_matrix.origx[1][1] / _database_PDB_matrix.origx[1][2] / _database_PDB_matrix.origx[1][3] / _database_PDB_matrix.origx[2][1] / _database_PDB_matrix.origx[2][2] / _database_PDB_matrix.origx[2][3] / _database_PDB_matrix.origx[3][1] / _database_PDB_matrix.origx[3][2] / _database_PDB_matrix.origx[3][3] / _database_PDB_matrix.origx_vector[1] / _database_PDB_matrix.origx_vector[2] / _database_PDB_matrix.origx_vector[3] / _pdbx_validate_rmsd_angle.angle_deviation / _pdbx_validate_rmsd_angle.angle_value / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _struct_ref_seq_dif.details
Details: Coordinates and associated matrices have been transformed from the icosahedral point symmetry frame to the crystallographic frame
Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FELINE PANLEUKOPENIA VIRUS CAPSID


Theoretical massNumber of molelcules
Total (without water)61,6211
Polymers61,6211
Non-polymers00
Water0
1
A: FELINE PANLEUKOPENIA VIRUS CAPSID
x 60


Theoretical massNumber of molelcules
Total (without water)3,697,23060
Polymers3,697,23060
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: FELINE PANLEUKOPENIA VIRUS CAPSID
x 5


  • icosahedral pentamer
  • 308 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)308,1035
Polymers308,1035
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: FELINE PANLEUKOPENIA VIRUS CAPSID
x 6


  • icosahedral 23 hexamer
  • 370 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)369,7236
Polymers369,7236
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
Unit cell
Length a, b, c (Å)254.154, 253.962, 380.288
Angle α, β, γ (deg.)90, 92.825, 90
Int Tables number4
Space group name H-MP1211
SymmetryPoint symmetry: (Hermann–Mauguin notation: 532 / Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.63492653, -0.56607986, 0.52575836), (-0.07969405, 0.62890953, 0.77338466), (-0.76844966, -0.53294165, 0.35419791)-28.98472, -68.84279, 105.33478
3generate(0.04422608, -0.99563067, 0.08224296), (-0.6950274, 0.0284715, 0.71842041), (-0.71762007, -0.08893502, -0.69073156)46.96327, -28.36447, 201.60663
4generate(0.04422657, -0.69502781, -0.71762298), (-0.99563028, 0.02847086, -0.08893403), (0.082244, 0.7184178, -0.69073141)122.88643, 65.49531, 155.77112
5generate(0.63492734, -0.07969422, -0.76845193), (-0.56607972, 0.62890849, -0.53294227), (0.5257576, 0.77338266, 0.35419816)93.86153, 83.02551, 31.17137
6generate(0.11796375, -0.39932583, -0.90918942), (-0.39932083, -0.85736647, 0.32474959), (-0.90918946, 0.32475368, -0.26059729)136.84445, -7.94247, 171.75604
7generate(0.80538851, 0.16662818, -0.56884504), (-0.4347661, -0.48623104, -0.75799471), (-0.40289355, 0.85779767, -0.31915746)65.14675, 96.86265, 148.30173
8generate(0.93521204, -0.04795895, 0.35082369), (0.34518596, 0.34428394, -0.87310569), (-0.07891274, 0.93763936, 0.33853801)-29.58753, 63.09453, 67.30792
9generate(0.32802265, -0.7465351, 0.57886585), (0.86266812, 0.48643501, 0.13849611), (-0.38497749, 0.45394024, 0.80357632)-16.43883, -62.58046, 40.7053
10generate(-0.17706458, -0.96369176, -0.19986507), (0.40253762, -0.25622578, 0.8788114), (-0.89811671, 0.07515606, 0.43329035)86.4218, -106.48374, 105.25779
11generate(-0.98133648, -0.16655948, 0.09610298), (-0.16656327, 0.48646582, -0.85767434), (0.09610557, -0.85767789, -0.50512934)104.41662, 90.95511, 137.35947
12generate(-0.68365307, 0.39954668, -0.61072093), (0.51455568, 0.85732147, -0.01513329), (0.51753827, -0.32460077, -0.79170238)154.44979, -28.0497, 140.41113
13generate(0.00339732, 0.96375957, -0.26674912), (0.2700108, 0.2559632, 0.92821105), (0.96285096, -0.07518134, -0.25936052)82.42922, -103.57842, 64.36306
14generate(0.13033441, 0.74635614, 0.65266106), (-0.56224519, -0.4865523, 0.66868887), (0.81663664, -0.45410878, 0.3562179)-12.11511, -31.25292, 14.3111
15generate(-0.47826454, 0.04778055, 0.876916), (-0.8320628, -0.34409385, -0.435049), (0.28095852, -0.93771824, 0.20432441)1.47385, 88.97541, 59.42536
16generate(-0.13662727, 0.56588532, 0.81308643), (0.5658841, -0.62909936, 0.53292475), (0.81308389, 0.53292422, -0.23427338)-12.04467, -83.01264, 70.56405
17generate(-0.75666197, -9.501E-5, 0.65380761), (-9.553E-5, -1, -0.00025666), (0.65380494, -0.00025525, 0.75666193)38.60459, 0.02984, -14.36808
18generate(-0.98283543, 0.07983005, -0.16631753), (0.07983063, -0.62871865, -0.77352577), (-0.16631815, -0.773523, 0.61155408)129.41144, 68.84836, 46.40196
19generate(-0.50258363, 0.69520676, -0.51390394), (0.69520734, -0.02835356, -0.71825095), (-0.51390315, -0.71824927, -0.4690628)134.88391, 28.33807, 168.89204
20generate(0.02040178, 0.99560543, 0.091401), (0.9956049, -0.02858886, 0.08917987), (0.0914006, 0.08917951, -0.99181292)47.45922, -65.51719, 183.82503
21generate(-0.4824739, -0.51069313, 0.7116244), (0.21866307, 0.71648845, 0.66244297), (-0.84817888, 0.47521785, -0.23401456)17.40452, -75.4093, 165.73665
22generate(-0.81248381, -0.4273153, -0.39657104), (-0.42731896, -0.02621779, 0.90372104), (-0.39657491, 0.90372212, -0.16129841)141.50523, -61.29397, 132.95568
23generate(-0.17706816, 0.40253728, -0.89811389), (-0.96369087, -0.25622254, 0.07515316), (-0.19986751, 0.87881517, 0.4332907)152.6997, 48.08991, 65.24521
24generate(0.54565021, 0.83203654, -0.09988897), (-0.64920492, 0.34433295, -0.67820802), (-0.52989962, 0.43491755, 0.72805082)35.51756, 101.57753, 56.17881
25generate(0.35689908, 0.26762911, 0.89498401), (0.08153001, 0.9455014, -0.31524296), (-0.93057808, 0.18548069, 0.3156335)-48.09946, 25.25082, 118.28593
26generate(-0.49998543, 0.8616181, 0.08736539), (-0.86260062, -0.48648019, -0.13875766), (-0.07705518, -0.1447332, 0.98646562)77.6626, 62.60141, 5.70026
27generate(-0.45325576, 0.77835086, 0.43443534), (-0.40229017, 0.25629854, -0.87890348), (-0.79543918, -0.57313331, 0.19695723)42.04096, 106.4783, 121.80666
28generate(-0.68365574, 0.51456255, 0.51753771), (0.3995429, 0.85732122, -0.32459584), (-0.61072184, -0.01513361, -0.79169947)47.35575, 7.91516, 205.06478
29generate(-0.87278043, 0.43479964, 0.22182784), (0.43479256, 0.48599494, 0.75813094), (0.22182374, 0.75812928, -0.61321452)86.26212, -96.8771, 140.41473
30generate(-0.75926593, 0.64929176, -0.04403327), (-0.34525504, -0.34452001, 0.87298526), (0.55164788, 0.67803233, 0.48575195)104.99278, -63.07914, 17.20068
31generate(0.62692302, -0.77841867, 0.03217885), (-0.27025825, -0.25603596, -0.92811897), (0.73070494, 0.57315859, -0.37088706)18.32443, 103.58386, 88.25206
32generate(0.43535758, -0.86159286, -0.26100936), (0.56202312, 0.48659754, -0.66884262), (0.70327465, 0.14448871, 0.69607886)57.13131, 31.28024, -11.45236
33generate(0.54565646, -0.64920837, -0.52989879), (0.83203635, 0.34432996, 0.43491276), (-0.09988871, -0.67820871, 0.72804756)76.33368, -88.96097, 31.53773
34generate(0.80539037, -0.43477333, -0.40289339), (0.16663235, -0.48622975, 0.85779477), (-0.5688407, -0.75799379, -0.31916061)49.39453, -90.9705, 157.81148
35generate(0.85561586, -0.51462969, -0.05551031), (-0.51462318, -0.85727629, 0.01539483), (-0.0555056, 0.01539372, -0.99833956)13.54284, 28.02874, 192.86287
36generate(0.35553631, 0.4274937, -0.83116864), (0.9141958, 0.0260277, 0.40443365), (0.19452913, -0.90364324, -0.38156401)115.82485, -90.77596, 119.99059
37generate(0.83038199, 0.5105573, 0.22314506), (0.26758602, -0.71667829, 0.64402507), (0.48873944, -0.47507752, -0.73173768)-11.4611, -76.46456, 136.36958
38generate(0.31506744, -0.26789146, 0.91047497), (-0.26788838, -0.94542865, -0.18547008), (0.91047806, -0.18547285, -0.36963879)-47.17274, 32.9559, 77.83184
39generate(-0.47826015, -0.83206286, 0.28095452), (0.04778002, -0.34409814, -0.93771769), (0.87691658, -0.43505304, 0.20432431)58.04219, 86.27007, 25.27453
40generate(-0.45324901, -0.40229119, -0.79544043), (0.77834822, 0.2562949, -0.57313714), (0.43443579, -0.87890674, 0.19695412)158.78024, 9.79957, 51.33007
41generate(-0.48247345, 0.218667, -0.84817575), (-0.5106998, 0.71649071, 0.47521742), (0.71162297, 0.66243934, -0.23401725)165.46056, -15.84239, 76.35387
42generate(0.32801871, 0.86266844, -0.38497283), (-0.74653757, 0.48644155, 0.45393925), (0.57886631, 0.13849652, 0.80357373)75.04886, -0.3082, -14.52665
43generate(0.43535047, 0.56202368, 0.70327655), (-0.86159248, 0.48660448, 0.14449241), (-0.26100572, -0.66884068, 0.69607903)-34.3982, 35.65758, 43.80484
44generate(-0.308807, -0.26778645, 0.91264873), (-0.69686256, 0.71675433, -0.0254781), (-0.64731853, -0.64385969, -0.40794733)-11.62851, 42.35146, 170.73621
45generate(-0.87605338, -0.47999254, -0.04620152), (-0.47999895, 0.85883182, 0.1789212), (-0.04620094, 0.1789166, -0.98277845)111.89099, 10.52273, 190.85262
46generate(0.62691978, -0.27026183, 0.73070407), (-0.7784164, -0.25603087, 0.57316255), (0.03218591, -0.92812067, -0.37088891)-47.97932, -9.79808, 128.28024
47generate(-0.14192303, -0.91427953, 0.37940582), (-0.91427966, -0.02583661, -0.4042563), (0.37941084, -0.40426158, -0.83224036)29.42371, 90.76394, 152.17426
48generate(-0.30880233, -0.69686051, -0.64732224), (-0.26779078, 0.71675143, -0.64385854), (0.91265007, -0.02548525, -0.4079491)136.4435, 76.46049, 81.34378
49generate(0.3569034, 0.08152954, -0.93057682), (0.26762458, 0.9455018, 0.18547797), (0.89498513, -0.31524769, 0.31562879)125.18232, -32.94153, 13.67412
50generate(0.93521146, 0.34518202, -0.07890973), (-0.0479594, 0.34428927, 0.93763838), (0.35082834, -0.87310705, 0.33853325)11.20275, -86.25226, 42.68245
51generate(0.3555325, 0.91419613, 0.19452625), (0.42749835, 0.02602665, -0.90364173), (-0.83117, 0.40443797, -0.38155915)18.46622, 61.27617, 178.76689
52generate(0.00339739, 0.27001574, 0.96285024), (0.96375905, 0.25595851, -0.07517857), (-0.26675419, 0.92821225, -0.25935591)-34.28422, -48.0914, 134.82403
53generate(-0.75926349, -0.34525072, 0.55165179), (0.64928877, -0.34452405, 0.67803067), (-0.04404035, 0.87298728, 0.48575355)48.45028, -101.56551, 51.33591
54generate(-0.87847875, -0.0813259, -0.47080683), (-0.08132525, -0.94557454, 0.31507644), (-0.47081143, 0.31508207, 0.82405328)152.33347, -25.24675, 43.68027
55generate(-0.18949693, 0.69705505, -0.69152256), (-0.21839927, -0.71656161, -0.66245087), (-0.95728431, 0.02550268, 0.28802456)133.8023, 75.39494, 122.43695
56generate(-0.49997883, -0.8626013, -0.07705457), (0.86161786, -0.48648649, -0.14473824), (0.08736112, -0.13875663, 0.98646531)93.26895, -35.6357, -3.72144
57generate(-0.18949307, -0.21840465, -0.95728323), (0.69705817, -0.71656346, 0.02549562), (-0.69152296, -0.66244718, 0.28802255)159.02805, -42.36433, 107.20792
58generate(0.63271535, 0.48008755, -0.6076061), (0.48009448, -0.85883186, -0.17866454), (-0.607604, -0.17866134, -0.77388348)78.72082, -10.55256, 203.19503
59generate(0.83038235, 0.26758281, 0.48873492), (0.51056323, -0.71668159, -0.47507631), (0.22314484, 0.64402531, -0.73173474)-36.67088, 15.83683, 151.58896
60generate(0.13033885, -0.56224453, 0.8166338), (0.74635763, -0.48655949, -0.45410871), (0.65265691, 0.66868777, 0.35622064)-27.67964, 0.3346, 23.70755

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Components

#1: Protein FELINE PANLEUKOPENIA VIRUS CAPSID


Mass: 61620.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Feline parvovirus / Genus: ParvovirusParvoviridae / References: UniProt: P90438, UniProt: P24840*PLUS
Source detailsVIRUS GROWN IN A CELL CULTURE OF NORDEN LABORATORY FELINE KIDNEY CELL.

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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: 294 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: 0.75-1.5% PEG8000, 5 mM EDTA, 20 mM BIS-Tris pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Temperature: 19 ℃ / pH: 7.5 / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
10.75-1.50 %(w/v)PEG80001reservoir
28 mM1reservoiror 5mM EDTACaCl2
310 mg/mlvirus1drop
420 mMBis-Tris1drop
520 mMTris-HCl1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jan 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3→60 Å / Num. all: 908009 / Num. obs: 810220 / % possible obs: 89.2 % / Redundancy: 3 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 12.3
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.221 / Num. unique all: 44760 / % possible all: 47.3
Reflection shell
*PLUS
% possible obs: 47.3 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
GLRFphasing
TRANSFmodel building
ENVELOPEmodel building
CNS0.5refinement
TRANSFphasing
ENVELOPEphasing
RefinementResolution: 3→9 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: restrained least squares with strictly enforced icosahedral symmetry
RfactorNum. reflection% reflection
all0.283 908009 -
obs0.288 725465 79.9 %
Rfree-0 -
Refinement stepCycle: LAST / Resolution: 3→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4255 0 0 0 4255
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0098
X-RAY DIFFRACTIONc_angle_deg1.68
Software
*PLUS
Name: CNS / Version: 0.5 / Classification: refinement
LS refinement shell
*PLUS
Rfactor Rwork: 0.357

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