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- PDB-4bcu: Satellite Tobacco Necrosis Virus (STNV) virus like particle in co... -

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Basic information

Entry
Database: PDB / ID: 4bcu
TitleSatellite Tobacco Necrosis Virus (STNV) virus like particle in complex with the B3 aptamer
ComponentsCOAT PROTEIN
KeywordsVIRUS / VLP / RNA APTAMER / METAL BINDING
Function / homology
Function and homology information


viral capsid / structural molecule activity / RNA binding / metal ion binding
Similarity search - Function
Satellite tobacco necrosis virus coat protein-like / Satellite tobacco necrosis virus coat protein / Satellite virus coat / Satellite virus coat domain superfamily / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesTOBACCO NECROSIS SATELLITE VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.29 Å
AuthorsFord, R.J. / Barker, A.M. / Bakker, S.E. / Coutts, R.H. / Ranson, N.A. / Phillips, S.E.V. / Pearson, A.R. / Stockley, P.G.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Sequence-Specific, RNA-Protein Interactions Overcome Electrostatic Barriers Preventing Assembly of Satellite Tobacco Necrosis Virus Coat Protein.
Authors: Ford, R.J. / Barker, A.M. / Bakker, S.E. / Coutts, R.H. / Ranson, N.A. / Phillips, S.E.V. / Pearson, A.R. / Stockley, P.G.
History
DepositionOct 3, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2013Provider: repository / Type: Initial release
Revision 1.1Jan 30, 2013Group: Database references
Revision 1.2Mar 20, 2013Group: Database references
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_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
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_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.type / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: COAT PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,8203
Polymers21,7401
Non-polymers802
Water3,963220
1
A: COAT PROTEIN
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)1,309,188180
Polymers1,304,37960
Non-polymers4,809120
Water1,08160
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
hetero molecules
x 5


  • icosahedral pentamer
  • 109 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)109,09915
Polymers108,6985
Non-polymers40110
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: COAT PROTEIN
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 131 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)130,91918
Polymers130,4386
Non-polymers48112
Water1086
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)315.020, 300.550, 183.510
Angle α, β, γ (deg.)90.00, 94.37, 90.00
Int Tables number5
Space group name H-MC121
SymmetryPoint symmetry: (Schoenflies symbol: I (icosahedral))
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.496631, -0.568684, 0.65571), (0.860349, 0.422373, -0.285308), (-0.114704, 0.705832, 0.699031)6.90682, -50.28831, 22.32082
3generate(-0.317838, -0.059801, 0.946257), (0.82339, -0.512248, 0.244195), (0.470115, 0.856753, 0.212052)53.57112, -71.95474, 1.63639
4generate(-0.317838, 0.82339, 0.470115), (-0.059801, -0.512248, 0.856753), (0.946257, 0.244195, 0.212052)75.50443, -35.05702, -33.4681
5generate(0.496631, 0.860349, -0.114704), (-0.568684, 0.422373, 0.705832), (0.65571, -0.285308, 0.69903)42.39565, 9.41345, -34.47945
6generate(0.535107, 0.5977, 0.597005), (0.5977, -0.767283, 0.232446), (0.597005, 0.232447, -0.767824)6.82778, -54.80155, 37.3088
7generate(0.711503, 0.369531, 0.597671), (-0.389957, -0.499914, 0.773317), (0.584549, -0.783283, -0.211589)-6.20804, -6.89959, 12.6044
8generate(0.602725, 0.173315, 0.7789), (-0.712468, 0.556445, 0.427503), (-0.359322, -0.812608, 0.458864)-6.5364, 32.80794, 51.30894
9generate(0.3591, 0.280216, 0.890239), (0.075867, 0.941942, -0.327093), (-0.93021, 0.184999, 0.316992)6.29648, 9.44659, 99.93405
10generate(0.31731, 0.542501, 0.777822), (0.885596, 0.123833, -0.447644), (-0.339168, 0.830878, -0.441143)14.55599, -44.69905, 91.28148
11generate(-0.63633, -0.18633, -0.748576), (-0.18633, -0.904533, 0.383539), (-0.748576, 0.383539, 0.540862)154.94677, -3.99924, 76.27113
12generate(-0.390465, -0.245199, -0.887364), (-0.914744, -0.005373, 0.403997), (-0.103827, 0.969458, -0.222196)143.21312, 48.76212, 63.88581
13generate(-0.303089, -0.507844, -0.806369), (-0.505253, 0.803086, -0.315868), (0.807995, 0.311684, -0.499997)133.0402, 51.7319, 9.45669
14generate(-0.494953, -0.611299, -0.617523), (0.476242, 0.403581, -0.781227), (0.726784, -0.680761, 0.091372)138.48664, 0.80595, -11.79704
15generate(-0.700907, -0.412592, -0.581805), (0.673347, -0.651785, -0.34897), (-0.23523, -0.636353, 0.734658)152.02564, -33.63779, 29.49656
16generate(-0.898777, -0.411371, 0.151571), (-0.411371, 0.671815, -0.615986), (0.151571, -0.615986, -0.773038)132.88473, 58.6077, 70.3204
17generate(-0.817669, 0.444352, -0.366017), (0.444352, 0.082914, -0.892007), (-0.366017, -0.892007, -0.265245)150.74737, 8.23268, 85.0893
18generate(0.018202, 0.394331, -0.918788), (0.394331, -0.847283, -0.35583), (-0.918788, -0.35583, -0.170919)114.58435, -12.77819, 121.4983
19generate(0.453691, -0.492307, -0.742831), (-0.492307, -0.833275, 0.251567), (-0.742831, 0.251567, -0.620416)74.37173, 24.6114, 129.23141
20generate(-0.113034, -0.990258, -0.081313), (-0.990258, 0.105579, 0.090782), (-0.081313, 0.090782, -0.992546)85.68199, 68.7303, 97.60173
21generate(-0.474753, -0.275198, 0.835988), (0.606392, 0.586152, 0.537321), (-0.637886, 0.762031, -0.1114)70.18949, -69.39312, 98.12324
22generate(-0.568434, 0.743816, 0.351597), (0.743816, 0.281988, 0.605987), (0.351597, 0.605987, -0.713554)99.40962, -82.68804, 52.90969
23generate(0.31731, 0.885596, -0.339168), (0.542501, 0.123833, 0.830878), (0.777822, -0.447644, -0.441143)65.92624, -78.2052, 8.93692
24generate(0.958411, -0.045793, -0.281692), (0.280657, 0.330253, 0.901202), (0.051761, -0.942781, 0.32937)16.01224, -62.13972, 26.97381
25generate(0.46889, -0.763203, 0.444594), (0.320144, 0.615982, 0.719774), (-0.823195, -0.19516, 0.533163)18.64707, -56.69355, 82.09399
26generate(0.08056, 0.121717, -0.98929), (0.995611, 0.037594, 0.0857), (0.047623, -0.991853, -0.118154)113.21895, -77.32806, 47.85122
27generate(0.258203, -0.692676, -0.673447), (0.516966, -0.48982, 0.702014), (-0.816136, -0.529411, 0.231617)85.57265, -70.42922, 95.42143
28generate(-0.390465, -0.914744, -0.103827), (-0.245199, -0.005373, 0.969458), (-0.887364, 0.403997, -0.222196)107.15765, -26.5569, 121.57759
29generate(-0.969007, -0.237597, -0.067627), (-0.237597, 0.821446, 0.518434), (-0.067627, 0.518434, -0.852439)148.14421, -6.34116, 90.17277
30generate(-0.677898, 0.402972, -0.614873), (0.529266, 0.848002, -0.027758), (0.510227, -0.344249, -0.788138)151.8903, -37.71946, 44.60737
31generate(-0.272424, 0.65802, 0.701994), (-0.897308, -0.437099, 0.061499), (0.347308, -0.613151, 0.709523)61.49042, 63.20328, -12.25928
32generate(0.350311, 0.928343, 0.124346), (-0.828743, 0.369074, -0.420677), (-0.436425, 0.044317, 0.898648)42.18721, 80.35941, 36.81098
33generate(0.958411, 0.280657, 0.051761), (-0.045793, 0.330253, -0.942781), (-0.281692, 0.901202, 0.32937)0.69746, 46.68545, 51.62659
34generate(0.711503, -0.389957, 0.584549), (0.369531, -0.499914, -0.783283), (0.597671, 0.773317, -0.211589)-5.6414, 8.71768, 11.71289
35generate(-0.049195, -0.156734, 0.986415), (-0.156734, -0.974163, -0.162604), (0.986415, -0.162604, 0.023359)31.93072, 18.92626, -27.77075
36generate(0.666617, -0.504539, -0.548692), (-0.704695, -0.186648, -0.68452), (0.242955, 0.842973, -0.479969)49.76041, 83.32481, 50.18514
37generate(-0.04008, -0.979482, 0.197504), (-0.432038, -0.161242, -0.887324), (0.900964, -0.120894, -0.416711)67.48978, 72.56477, -1.24177
38generate(-0.885257, -0.251509, 0.391234), (-0.251509, -0.448713, -0.857555), (0.391234, -0.857555, 0.333969)120.87792, 57.88356, 1.75922
39generate(-0.700907, 0.673347, -0.23523), (-0.412592, -0.651785, -0.636353), (-0.581805, -0.34897, 0.734658)136.14422, 59.57011, 55.04085
40generate(0.258203, 0.516966, -0.816136), (-0.692676, -0.48982, -0.529411), (-0.673447, 0.702014, 0.231617)92.19118, 75.29367, 84.96972
41generate(-0.474753, 0.606392, -0.637886), (-0.275198, 0.586152, 0.762031), (0.835988, 0.537321, -0.1114)137.99353, -14.78203, -10.46028
42generate(0.3591, 0.075867, -0.93021), (0.280216, 0.941942, 0.184999), (0.890239, -0.327093, 0.316992)89.98193, -29.15022, -34.19377
43generate(0.350311, -0.828743, -0.436425), (0.928343, 0.369074, 0.044317), (0.124346, -0.420677, 0.898648)67.88388, -70.45414, -4.52056
44generate(-0.488973, -0.857298, 0.161075), (0.773493, -0.340767, 0.534403), (-0.403254, 0.385899, 0.82974)102.23813, -81.61317, 37.55198
45generate(-0.998891, 0.029664, 0.036565), (0.029664, -0.206605, 0.977975), (0.036565, 0.977975, 0.205496)145.56827, -47.20591, 33.88103
46generate(-0.272424, -0.897308, 0.347308), (0.65802, -0.437099, -0.613151), (0.701994, 0.061499, 0.709523)77.72204, -20.35261, -38.35456
47generate(-0.94713, 0.021066, 0.320157), (0.021066, -0.991606, 0.127567), (0.320157, 0.127567, 0.938737)128.71678, -7.51285, -20.76155
48generate(-0.488973, 0.773493, -0.403254), (-0.857298, -0.340767, 0.385899), (0.161075, 0.534403, 0.82974)128.26191, 45.34624, -4.01203
49generate(0.46889, 0.320144, -0.823195), (-0.763203, 0.615982, -0.19516), (0.444594, 0.719774, 0.533163)76.98605, 65.17519, -11.25327
50generate(0.602725, -0.712468, -0.359322), (0.173315, 0.556445, -0.812607), (0.7789, 0.427503, 0.458864)45.7507, 24.57107, -32.47812
51generate(0.666617, -0.704695, 0.242955), (-0.504539, -0.186648, 0.842973), (-0.548692, -0.68452, -0.479969)13.35473, -1.64623, 108.42791
52generate(-0.303089, -0.505253, 0.807995), (-0.507844, 0.803086, 0.311684), (-0.806369, -0.315868, -0.499997)58.8198, 23.07105, 128.34824
53generate(-0.677898, 0.529266, 0.510227), (0.402972, 0.848001, -0.344249), (-0.614873, -0.027758, -0.788138)100.16984, -13.86533, 127.50292
54generate(0.060164, 0.969192, -0.238844), (0.969192, -0.113973, -0.218349), (-0.238844, -0.218349, -0.946191)80.2605, -61.41054, 107.06014
55generate(0.89112, 0.206562, -0.404027), (0.40832, -0.753421, 0.515394), (-0.197942, -0.62425, -0.755732)26.60581, -53.85872, 95.27113
56generate(0.08056, 0.995611, 0.047623), (0.121717, 0.037594, -0.991853), (-0.98929, 0.0857, -0.118154)65.58897, 36.58777, 124.28725
57generate(0.89112, 0.40832, -0.197942), (0.206562, -0.753421, -0.62425), (-0.404027, 0.515394, -0.755732)17.14076, 13.39893, 110.50739
58generate(0.81656, -0.474016, 0.329452), (-0.474016, -0.876309, -0.085968), (0.329452, -0.085968, -0.94025)-1.65637, 38.78014, 64.93
59generate(-0.04008, -0.432038, 0.900964), (-0.979482, -0.161242, -0.120894), (0.197504, -0.887324, -0.416711)35.17458, 77.65543, 50.54148
60generate(-0.494953, 0.476242, 0.726784), (-0.611299, 0.403581, -0.680761), (-0.617523, -0.781227, 0.091372)76.73449, 76.30047, 87.22628

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Components

#1: Protein COAT PROTEIN


Mass: 21739.645 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) TOBACCO NECROSIS SATELLITE VIRUS / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P03606
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsFOR CONSISTENCY WITH PREVIOUS STRUCTURES, THE FIRST MET IS NUMBERED 0

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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

CrystalDescription: NONE
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.29→217 Å / Num. obs: 756410 / % possible obs: 99.6 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.3
Reflection shellResolution: 2.29→2.35 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 3.3 / % possible all: 99.2

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
xia2data reduction
xia2data scaling
RefinementMethod to determine structure: OTHER
Starting model: NONE

Resolution: 2.29→217.15 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.92 / SU B: 4.767 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.174 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. RESIDUES 0-7 ARE DISORDERED, 60-FOLD NCS APPLIED
RfactorNum. reflection% reflectionSelection details
Rfree0.19821 37936 5 %RANDOM
Rwork0.15512 ---
obs0.15729 718474 99.58 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.402 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å2-0.07 Å2
2---0.04 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 2.29→217.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1457 0 2 220 1679
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.02289580
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.7561.932121560
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.294511460
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.01724.2254260
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.7961515540
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr
X-RAY DIFFRACTIONr_gen_planes_refined
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.961.556100
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.714290900
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.327333480
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.0824.530540
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.29→2.35 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 2722 -
Rwork0.209 52951 -
obs--99.14 %

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