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Database: PDB / ID: 3jbm
TitleElectron cryo-microscopy of a virus-like particle of orange-spotted grouper nervous necrosis virus
Componentsvirus-like particle of orange-spotted grouper nervous necrosis virus
KeywordsVIRUS / virus-like particle / orange-spotted grouper nervous necrosis virus / betanodavirus
Function / homologyNodavirus capsid / Viral coat protein subunit / nodavirus capsid protein / Virus-like particle of orange-spotted grouper nervous necrosis virus
Function and homology information
Biological speciesOrange-spotted grouper nervous necrosis virus
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.9 Å
AuthorsXie, J. / Li, K. / Gao, Y. / Huang, R. / Lai, Y. / Shi, Y. / Yang, S. / Zhu, G. / Zhang, Q. / He, J.
CitationJournal: Vet. Res. / Year: 2016
Title: Structural analysis and insertion study reveal the ideal sites for surface displaying foreign peptides on a betanodavirus-like particle.
Authors: Junfeng Xie / Kunpeng Li / Yuanzhu Gao / Runqing Huang / Yuxiong Lai / Yan Shi / Shaowei Yang / Guohua Zhu / Qinfen Zhang / Jianguo He /
Abstract: Betanodavirus infection causes fatal disease of viral nervous necrosis in many cultured marine and freshwater fish worldwide and the virus-like particles (VLP) are effective vaccines against ...Betanodavirus infection causes fatal disease of viral nervous necrosis in many cultured marine and freshwater fish worldwide and the virus-like particles (VLP) are effective vaccines against betanodavirus. But vaccine and viral vector designs of betanodavirus VLP based on their structures remain lacking. Here, the three-dimensional structure of orange-spotted grouper nervous necrosis virus (OGNNV) VLP (RBS) at 3.9 Å reveals the organization of capsid proteins (CP). Based on the structural results, seven putative important sites were selected to genetically insert a 6× histidine (His)-tag for VLP formation screen, resulting in four His-tagged VLP (HV) at positions N-terminus, Ala220, Pro292 and C-terminus. The His-tags of N-terminal HV (NHV) were concealed inside virions while those of 220HV and C-terminal HV (CHV) were displayed at the outer surface. NHV, 220HV and CHV maintained the same cell entry ability as RBS in the Asian sea bass (SB) cell line, indicating that their similar surface structures can be recognized by the cellular entry receptor(s). For application of vaccine design, chromatography-purified CHV could provoke NNV-specific antibody responses as strong as those of RBS in a sea bass immunization assay. Furthermore, in carrying capacity assays, N-terminus and Ala220 can only carry short peptides and C-terminus can even accommodate large protein such as GFP to generate fluorescent VLP (CGV). For application of a viral vector, CGV could be real-time visualized to enter SB cells in invasion study. All the results confirmed that the C-terminus of CP is a suitable site to accommodate foreign peptides for vaccine design and viral vector development.
Validation Report
SummaryFull reportAbout validation report
History
DepositionSep 6, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 19, 2016Provider: repository / Type: Initial release
Revision 1.1Oct 26, 2016Group: Other
Revision 1.2Feb 22, 2017Group: Database references
Revision 1.3Nov 6, 2019Group: Author supporting evidence / Data collection ...Author supporting evidence / Data collection / Database references / Source and taxonomy
Category: database_2 / em_image_scans ...database_2 / em_image_scans / em_software / em_virus_natural_host / entity_src_gen
Item: _em_software.name / _em_virus_natural_host.ncbi_tax_id ..._em_software.name / _em_virus_natural_host.ncbi_tax_id / _em_virus_natural_host.organism / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.4Dec 18, 2019Group: Data collection / Category: em_software / Item: _em_software.image_processing_id

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Structure visualization

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  • Biological unit as complete icosahedral assembly
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  • Biological unit as icosahedral pentamer
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  • Biological unit as icosahedral 23 hexamer
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  • Deposited structure unit
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  • Simplified surface model + fitted atomic model
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Structure viewerMolecule:
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Assembly

Deposited unit
A: virus-like particle of orange-spotted grouper nervous necrosis virus
B: virus-like particle of orange-spotted grouper nervous necrosis virus
C: virus-like particle of orange-spotted grouper nervous necrosis virus


Theoretical massNumber of molelcules
Total (without water)111,3083
Polymers111,3083
Non-polymers00
Water0
1
A: virus-like particle of orange-spotted grouper nervous necrosis virus
B: virus-like particle of orange-spotted grouper nervous necrosis virus
C: virus-like particle of orange-spotted grouper nervous necrosis virus
x 60


Theoretical massNumber of molelcules
Total (without water)6,678,489180
Polymers6,678,489180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation60
2


  • Idetical with deposited unit in distinct coordinate
  • icosahedral asymmetric unit
TypeNameSymmetry operationNumber
point symmetry operation1
3
A: virus-like particle of orange-spotted grouper nervous necrosis virus
B: virus-like particle of orange-spotted grouper nervous necrosis virus
C: virus-like particle of orange-spotted grouper nervous necrosis virus
x 5


  • icosahedral pentamer
  • 557 kDa, 15 polymers
Theoretical massNumber of molelcules
Total (without water)556,54115
Polymers556,54115
Non-polymers00
Water0
TypeNameSymmetry operationNumber
point symmetry operation5
4
A: virus-like particle of orange-spotted grouper nervous necrosis virus
B: virus-like particle of orange-spotted grouper nervous necrosis virus
C: virus-like particle of orange-spotted grouper nervous necrosis virus
x 6


  • icosahedral 23 hexamer
  • 668 kDa, 18 polymers
Theoretical massNumber of molelcules
Total (without water)667,84918
Polymers667,84918
Non-polymers00
Water0
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: virus-like particle of orange-spotted grouper nervous necrosis virus
B: virus-like particle of orange-spotted grouper nervous necrosis virus
C: virus-like particle of orange-spotted grouper nervous necrosis virus
x 60


  • crystal asymmetric unit, crystal frame
  • 6.68 MDa, 180 polymers
Theoretical massNumber of molelcules
Total (without water)6,678,489180
Polymers6,678,489180
Non-polymers00
Water0
TypeNameSymmetry operationNumber
transform to crystal frame1
point symmetry operation60
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.30901984, -0.95105556, 0.00025907), (0.95105219, 0.30901799, -0.00275785), (0.00254282, 0.00109861, 0.99999616)367.4404, -57.82835, -0.8144
3generate(-0.80900956, -0.58778802, 0.002962), (0.58777922, -0.80901439, -0.00336368), (0.00437342, -0.00098026, 0.99998996)535.98454, 273.7589, -0.758
4generate(-0.80900956, 0.58777922, 0.00437343), (-0.58778802, -0.80901438, -0.00098025), (0.00296198, -0.00336369, 0.99998996)272.71014, 536.51944, 0.09126
5generate(0.30901983, 0.95105219, 0.00254281), (-0.95105556, 0.30901799, 0.00109862), (0.00025906, -0.00275785, 0.99999616)-58.54652, 367.32713, 0.55973
6generate(-0.94812927, -0.16169839, 0.27368692), (-0.16169839, -0.49593214, -0.85317345), (0.27368691, -0.85317345, 0.44406141)410.91234, 562.82463, 254.64686
7generate(-0.44607843, 0.85205657, 0.27388617), (-0.52379483, -0.00040511, -0.85184436), (-0.72570863, -0.52344955, 0.44648354)71.6592, 532.78387, 404.18646
8generate(0.67319963, 0.68784707, 0.27141971), (-0.16441435, 0.49709695, -0.85197568), (-0.72095088, 0.52892442, 0.44773741)-141.74412, 341.03766, 167.43839
9generate(0.86290068, -0.42739495, 0.2696961), (0.41979143, 0.30904309, -0.85338592), (0.28138512, 0.84960339, 0.44609022)65.61852, 252.57274, -128.41956
10generate(-0.13913569, -0.95244292, 0.27109731), (0.42146999, -0.30468264, -0.85412619), (0.89610508, -0.00458007, 0.44381833)407.17899, 389.64462, -74.52176
11generate(-0.86819052, -0.41589409, -0.27069785), (-0.4158941, 0.31225684, 0.85412398), (-0.27069786, 0.85412398, -0.44406633)572.37149, 54.78282, 194.53475
12generate(-0.66451341, 0.69688127, -0.26977476), (0.17062491, 0.49296973, 0.8531518), (0.72753629, 0.52090052, -0.4464903)277.63414, -116.78638, 46.03849
13generate(0.45673665, 0.84704165, -0.27186778), (0.52373583, -0.00899998, 0.85183319), (0.71909139, -0.53145032, -0.44773667)-6.61472, -83.29433, 283.60552
14generate(0.94603019, -0.1729295, -0.27408443), (0.15545137, -0.49994719, 0.85199043), (-0.284362, -0.84861546, -0.446083)112.44716, 108.97409, 578.92629
15generate(0.12718017, -0.95346671, -0.27336137), (-0.42527186, -0.30139956, 0.85340621), (-0.8960854, 0.00771655, -0.4438146)470.28032, 194.31046, 523.87752
16generate(0.81631978, 0.57759248, -0.00298906), (0.57759249, -0.8163247, -0.00095053), (-0.00298905, -0.00095052, -0.99999508)-87.3865, 277.13263, 450.94357
17generate(0.801572, -0.59788228, -0.00437048), (-0.59788228, -0.80158261, 0.00145042), (-0.00437047, 0.00145042, -0.9999894)179.16358, 536.57094, 450.71464
18generate(-0.32092672, -0.94710069, -0.00251393), (-0.94710069, 0.32091741, 0.00350616), (-0.00251393, 0.00350617, -0.99999069)508.27163, 363.23785, 449.83927
19generate(-0.99992131, 0.01254523, 1.49E-5), (0.01254522, 0.99991848, 0.00237574), (1.49E-5, 0.00237576, -0.99999718)445.12151, -3.32619, 449.52719
20generate(-0.29706431, 0.95485743, -0.00027875), (0.95485743, 0.2970642, -0.00037864), (-0.00027873, -0.00037863, -0.99999989)76.98454, -56.54214, 450.20969
21generate(-0.13251865, -0.42577056, 0.89507444), (0.94961067, -0.31331811, -0.00844679), (0.28403942, 0.84885286, 0.44583676)147.47385, 82.98196, -128.78914
22generate(-0.44360491, -0.00455483, 0.89621088), (-0.00455482, -0.99996271, -0.00733665), (0.89621087, -0.00733667, 0.44356762)122.6738, 450.03284, -73.87243
23generate(-0.1391357, 0.42146998, 0.89610508), (-0.95244292, -0.30468264, -0.00458006), (0.2710973, -0.85412619, 0.44381834)-40.79105, 506.19139, 255.49468
24generate(0.36012289, 0.26355205, 0.89490325), (-0.58410449, 0.81166868, -0.00398652), (-0.72741559, -0.52128136, 0.44624242)-117.01783, 173.8484, 404.13804
25generate(0.36421245, -0.2600714, 0.89426627), (0.59142927, 0.80633167, -0.00637629), (-0.71941692, 0.53121757, 0.44748987)-0.66373, -87.70941, 166.63758
26generate(0.43946138, -0.53107239, 0.72445554), (-0.8520024, 0.00904058, 0.52345981), (-0.28454455, -0.84727822, -0.44850195)81.31404, 294.69461, 579.21239
27generate(-0.36743312, -0.58126721, 0.72603123), (-0.25335652, 0.8136704, 0.52321214), (-0.89487618, 0.00830073, -0.44623728)272.91094, -19.31461, 524.02119
28generate(-0.66451342, 0.17062491, 0.7275363), (0.69688126, 0.49296973, 0.52090052), (-0.26977476, 0.8531518, -0.4464903)170.92361, -159.88736, 195.09093
29generate(-0.04122464, 0.68551462, 0.72689079), (0.68551463, -0.50986402, 0.51971952), (0.72689079, 0.51971952, -0.44891134)-83.70494, 67.24313, 46.99204
30generate(0.64106931, 0.25184184, 0.72498678), (-0.27174812, -0.80894868, 0.52130125), (0.71776257, -0.53120403, -0.45015461)-139.0867, 348.19023, 284.39216
31generate(0.04983216, 0.68666849, -0.72526075), (-0.69184929, -0.49998779, -0.52091914), (-0.72032028, 0.52772966, 0.45015563)222.42212, 607.70439, 167.02023
32generate(0.66661249, 0.16400298, -0.72713879), (-0.69063424, 0.50290961, -0.51971749), (0.28044986, 0.84863711, 0.44851189)201.61422, 382.82872, -128.5389
33generate(0.3601229, -0.58410449, -0.72741559), (0.26355206, 0.81166868, -0.52128137), (0.89490324, -0.00398652, 0.44624241)437.66274, 100.40262, -74.93084
34generate(-0.44607842, -0.52379482, -0.72570863), (0.85205657, -0.00040511, -0.52344955), (0.27388618, -0.85184436, 0.44648353)604.35666, 150.72937, 253.75988
35generate(-0.63784864, 0.26158607, -0.72437687), (0.26158606, -0.8110534, -0.52322569), (-0.72437686, -0.52322569, 0.44890204)471.33064, 464.25911, 403.29386
36generate(-0.35677489, 0.27017446, -0.89426922), (0.59424103, 0.80426532, 0.00590612), (0.72082541, -0.5293043, -0.44749043)444.68733, -90.64089, 282.6817
37generate(0.14442554, 0.42181906, -0.89510332), (0.94854558, -0.3166173, 0.003842), (-0.28178455, -0.84960118, -0.44584223)298.69837, 81.19313, 578.51531
38generate(0.44352621, -0.0079904, -0.89622579), (-0.0079904, -0.99995577, 0.00496091), (-0.89622578, 0.00496091, -0.44357044)328.10203, 448.03343, 524.47041
39generate(0.12718017, -0.42527185, -0.89608541), (-0.95346671, -0.30139955, 0.00771655), (-0.27336138, 0.85340621, -0.44381461)492.26344, 502.91919, 195.23522
40generate(-0.36743311, -0.25335651, -0.89487618), (-0.58126721, 0.81367041, 0.00830072), (0.72603122, 0.52321215, -0.44623729)564.31712, 170.00015, 45.80157
41generate(-0.13251865, 0.94961066, 0.28403942), (-0.42577056, -0.31331811, 0.84885288), (0.89507442, -0.00844679, 0.44583676)-22.67633, 198.1128, -73.8802
42generate(0.86290067, 0.41979142, 0.28138512), (-0.42739495, 0.30904308, 0.8496034), (0.26969609, -0.85338592, 0.44609023)-126.51478, 59.09486, 255.13168
43generate(0.66661249, -0.69063425, 0.28044987), (0.16400297, 0.5029096, 0.84863712), (-0.72713878, -0.51971749, 0.4485119)166.04478, -116.51069, 403.21552
44generate(-0.4501196, -0.84709581, 0.28252616), (0.53113137, 0.0003645, 0.8472894), (-0.71783828, 0.53144007, 0.4497551)450.69499, -86.02294, 165.72449
45generate(-0.94400981, 0.16663129, 0.28474463), (0.16663129, -0.50409197, 0.84742275), (0.28474461, 0.84742273, 0.44810178)334.05892, 108.42507, -129.13688
46generate(0.04983217, -0.69184929, -0.72032028), (0.68666848, -0.4999878, 0.52772967), (-0.72526074, -0.52091915, 0.45015564)529.66414, 62.973, 402.69379
47generate(-0.6444173, -0.26197839, -0.71839659), (-0.26197839, -0.80698533, 0.52928443), (-0.71839659, 0.52928442, 0.45140263)588.56962, 343.76643, 165.96098
48generate(-0.4501196, 0.53113139, -0.71783829), (-0.84709582, 0.0003645, 0.53144007), (0.28252614, 0.84728939, 0.4497551)367.51951, 293.74056, -128.98223
49generate(0.36421245, 0.59142928, -0.71941693), (-0.2600714, 0.80633167, 0.53121757), (0.89426626, -0.00637629, 0.44748987)171.99754, -17.97056, -74.53434
50generate(0.67319964, -0.16441435, -0.72095088), (0.68784707, 0.49709694, 0.52892441), (0.27141972, -0.85197567, 0.44773741)272.20843, -160.59275, 254.05951
51generate(-0.3567749, 0.59424103, 0.72082541), (0.27017446, 0.80426533, -0.52930431), (-0.89426921, 0.00590613, -0.44749043)8.75166, 102.38081, 524.70288
52generate(0.45673664, 0.52373583, 0.71909138), (0.84704165, -0.00899997, -0.53145033), (-0.27186777, 0.85183319, -0.44773668)-157.29288, 155.57555, 196.13514
53generate(0.64106931, -0.27174813, 0.71776256), (0.25184185, -0.80894867, -0.53120403), (0.72498678, 0.52130124, -0.45015462)-20.34179, 467.76614, 47.34446
54generate(-0.05851838, -0.69287905, 0.71867533), (-0.69287904, -0.49007887, -0.52890579), (0.71867533, -0.52890579, -0.45140274)230.34317, 607.5158, 283.95451
55generate(-0.67522002, -0.15766831, 0.72056827), (-0.68154886, 0.50694221, -0.5277317), (-0.28207991, -0.84743748, -0.44975618)248.32391, 381.69524, 578.97824
56generate(0.43946138, -0.8520024, -0.28454455), (-0.53107238, 0.00904059, -0.84727823), (0.72445553, 0.52345981, -0.44850197)380.15787, 531.27347, 46.60871
57generate(-0.67522001, -0.68154886, -0.28207991), (-0.1576683, 0.50694221, -0.8474375), (0.72056827, -0.52773169, -0.44975619)591.13536, 336.30325, 282.89739
58generate(-0.8575622, 0.43125099, -0.28037415), (0.43125099, 0.30567457, -0.84887316), (-0.28037414, -0.84887315, -0.44811238)382.67482, 249.74407, 578.54742
59generate(0.14442553, 0.94854559, -0.28178457), (0.42181906, -0.31661729, -0.84960119), (-0.89510331, 0.00384201, -0.44584223)42.86163, 391.21778, 524.98051
60generate(0.94603019, 0.15545137, -0.28436202), (-0.17292949, -0.49994718, -0.84861546), (-0.27408442, 0.85199042, -0.44608301)41.30606, 565.21252, 196.22431

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Components

#1: Protein/peptide virus-like particle of orange-spotted grouper nervous necrosis virus / Coordinate model: Cα atoms only


Mass: 37102.719 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Orange-spotted grouper nervous necrosis virus
Production host: Escherichia coli (E. coli) / References: UniProt: A0A1L1QJU5*PLUS
Sequence detailsTHE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT ...THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION.

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Orange-spotted grouper nervous necrosis virus / Type: VIRUS / Source: NATURAL
Molecular weightValue: 6.8 MDa / Experimental value: NO
Details of virusEmpty: NO / Enveloped: NO / Host category: VERTEBRATES / Isolate: SPECIES / Type: VIRUS-LIKE PARTICLE
Natural hostOrganism: Orange-spotted grouper nervous necrosis virus
Buffer solutionName: PBS buffer / pH: 8 / Details: PBS buffer
SpecimenConc.: 1.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportDetails: 300 mesh Quantifoil copper grid with thin carbon support, glow discharged in air atmosphere
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Temp: 100 K / Humidity: 100 % / Method: blot for 5 min before plunging

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS / Date: Feb 26, 2011 / Details: Weak beam illumination
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 96000 X / Nominal defocus max: 2910 nm / Nominal defocus min: 1000 nm / Cs: 2.7 mm
Astigmatism: Objective lens astigmatism was corrected at 200000 times magnification
Camera length: 0 mm
Specimen holderModel: FEI TITAN KRIOS AUTOGRID HOLDER / Temperature: 100 K / Temperature (max): 105 K / Temperature (min): 95 K / Tilt angle max: 0 ° / Tilt angle min: 0 °
Image recordingElectron dose: 20 e/Å2 / Film or detector model: GATAN ULTRASCAN 4000 (4k x 4k)

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Processing

EM software
IDNameCategory
1EMAN3D reconstruction
2jspr3D reconstruction
CTF correctionDetails: Each particle
SymmetryPoint symmetry: I (icosahedral)
3D reconstructionMethod: Cross-common lines / Resolution: 3.9 Å / Resolution method: FSC 0.143 / Num. of particles: 32000 / Actual pixel size: 0.933 Å
Details: (Single particle details: The particles were selected manually.) (Single particle--Applied symmetry: I)
Symmetry type: POINT
Atomic model buildingMethod: Local refinement / Space: REAL
Atomic model buildingPDB-ID: 4NWW
Refinement stepCycle: LAST
ProteinNucleic acidLigandSolventTotal
Num. atoms526 0 0 0 526

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Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary. This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated. See below links for details.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software). Now, EM Navigator and Yorodumi are based on the updated data.

External links: wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Jun 16, 2017. Omokage search with filter

Omokage search with filter

  • Result of Omokage search can be filtered by keywords and the database types

Related info.: Omokage search

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Sep 15, 2016. EM Navigator & Yorodumi renewed

EM Navigator & Yorodumi renewed

  • New versions of EM Navigator and Yorodumi started

Related info.: Changes in new EM Navigator and Yorodumi

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Aug 31, 2016. New EM Navigator & Yorodumi

New EM Navigator & Yorodumi

  • In 15th Sep 2016, the development versions of EM Navigator and Yorodumi will replace the official versions.
  • Current version will continue as 'legacy version' for some time.

Related info.: Changes in new EM Navigator and Yorodumi / EM Navigator / Yorodumi

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.

Related info.: EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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