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- PDB-1vb4: T=1 capsid structure of Sesbania mosaic virus coat protein deleti... -

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Basic information

Entry
Database: PDB / ID: 1vb4
TitleT=1 capsid structure of Sesbania mosaic virus coat protein deletion mutant CP-N(delta)36
Componentscoat protein
KeywordsVIRUS / T=1 capsids / Deletion Mutant / Icosahedral virus
Function / homology
Function and homology information


T=3 icosahedral viral capsid / structural molecule activity / metal ion binding
Similarity search - Function
Plant viruses icosahedral capsid proteins 'S' region signature. / Icosahedral viral capsid protein, S domain / Viral coat protein (S domain) / Jelly Rolls - #20 / Viral coat protein subunit / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesSesbania mosaic virus
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsSangita, V. / Lokesh, G.L. / Satheshkumar, P.S. / Vijay, C.S. / Saravanan, V. / Savithri, H.S. / Murthy, M.R.
CitationJournal: J.Mol.Biol. / Year: 2004
Title: T=1 capsid structures of Sesbania mosaic virus coat protein mutants: determinants of T=3 and T=1 capsid assembly
Authors: Sangita, V. / Lokesh, G.L. / Satheshkumar, P.S. / Vijay, C.S. / Saravanan, V. / Savithri, H.S. / Murthy, M.R.
History
DepositionFeb 21, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 23, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_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_atom_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)24,5042
Polymers24,4641
Non-polymers401
Water1,60389
1
A: coat protein
hetero molecules
x 60


Theoretical massNumber of molelcules
Total (without water)1,470,224120
Polymers1,467,81960
Non-polymers2,40560
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
  • 123 kDa, 5 polymers
Theoretical massNumber of molelcules
Total (without water)122,51910
Polymers122,3185
Non-polymers2005
Water905
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation4
4
A: coat protein
hetero molecules
x 6


  • icosahedral 23 hexamer
  • 147 kDa, 6 polymers
Theoretical massNumber of molelcules
Total (without water)147,02212
Polymers146,7826
Non-polymers2406
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
6
A: coat protein
hetero molecules
x 60


  • crystal asymmetric unit, crystal frame
  • 1.47 MDa, 60 polymers
Theoretical massNumber of molelcules
Total (without water)1,470,224120
Polymers1,467,81960
Non-polymers2,40560
Water1,08160
TypeNameSymmetry operationNumber
identity operation1_555x,y,z2
point symmetry operation59
Unit cell
Length a, b, c (Å)187.302, 193.308, 268.368
Angle α, β, γ (deg.)90.00, 92.28, 90.00
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(0.46379824, -0.51524644, 0.72070264), (0.84952038, 0.48949601, -0.19674547), (-0.25140866, 0.70350178, 0.66473974)-26.47621, -22.50936, 33.49784
3generate(-0.40379444, 0.01583412, 0.91471271), (0.85930641, -0.3365168, 0.38516093), (0.31391488, 0.94154433, 0.12227725)-3.01598, -62.61023, 46.58616
4generate(-0.40379444, 0.85930641, 0.31391488), (0.01583412, -0.3365168, 0.94154433), (0.91471271, 0.38516093, 0.12227725)37.95945, -64.88457, 21.17735
5generate(0.46379824, 0.84952038, -0.25140866), (-0.51524644, 0.48949601, 0.70350178), (0.72070264, -0.19674547, 0.66473974)39.82343, -26.18932, -7.61448
6generate(-0.40015784, -0.01876851, 0.91625403), (-0.01876851, -0.99941275, -0.02866875), (0.91625403, -0.02866875, 0.39957059)-3.2719, 2.9618, 2.20267
7generate(-0.43189094, 0.84157914, 0.32436827), (-0.85051873, -0.49970666, 0.16404616), (0.30014681, -0.20503124, 0.9315976)38.43777, 24.99452, -8.02619
8generate(0.43307938, 0.86267356, -0.26122134), (-0.86022271, 0.3090291, -0.40560808), (-0.26918237, 0.40036902, 0.87592551)41.79483, 64.2563, 19.84868
9generate(0.99939353, 0.01536298, -0.03124987), (-0.03446988, 0.3091492, -0.95038866), (-0.00493993, 0.95088945, 0.30949126)2.15995, 66.4887, 47.30517
10generate(0.48442461, -0.52939818, 0.69646993), (0.48557742, -0.49951234, -0.71742734), (0.72770006, 0.68572953, 0.01508773)-25.69282, 28.60661, 36.39934
11generate(-0.99960068, 0.02825563, 0.00031736), (0.02825563, 0.99934845, 0.02245652), (0.00031736, 0.02245652, -0.99974777)84.73362, -2.73245, 136.66082
12generate(-0.43968909, 0.52909498, -0.72576305), (0.85642602, 0.49041667, -0.16132563), (0.27056972, -0.69249548, -0.66876157)110.57388, -25.223, 102.65755
13generate(0.42801306, -0.02503748, -0.90342567), (0.8543865, -0.31470633, 0.41350168), (-0.29466682, -0.94885882, -0.11330673)85.99409, -64.34095, 88.67945
14generate(0.40437089, -0.86834953, -0.28714679), (0.02495561, -0.30336792, 0.95254665), (-0.91425456, -0.39234806, -0.10100297)44.9627, -66.02661, 114.04379
15generate(-0.47794292, -0.83541257, 0.27139712), (-0.48562135, 0.50876259, 0.71086745), (-0.73194431, 0.20795783, -0.64885366)44.18369, -27.95047, 143.69791
16generate(0.39975852, -0.00948712, -0.91657139), (-0.00948712, -0.9999357, 0.00621223), (-0.91657139, 0.00621223, -0.39982282)88.0886, 0.18443, 134.52418
17generate(0.40778179, -0.85542767, -0.31930786), (-0.85542767, -0.48020602, 0.19402494), (-0.31930786, 0.19402494, -0.92757577)47.01489, 23.15162, 145.25848
18generate(-0.457298, -0.8534702, 0.2499343), (-0.8534702, 0.34219403, -0.39305453), (0.2499343, -0.39305453, -0.88489603)44.77738, 63.10865, 118.27338
19generate(-0.99996999, -0.00631986, 0.00448178), (-0.00631986, 0.33073553, -0.94370232), (0.00448178, -0.94370232, -0.33076554)84.46823, 64.83626, 90.86137
20generate(-0.47027992, 0.51529037, -0.71645839), (0.51529037, -0.49874626, -0.69694189), (-0.71645839, -0.69694189, -0.03097382)111.23603, 25.94695, 100.90492
21generate(0.47771722, 0.53314584, 0.69824191), (0.83310421, -0.02270473, -0.55264986), (-0.27878958, 0.84571863, -0.45501249)-25.63953, 2.56443, 111.17535
22generate(0.4989386, 0.50604509, 0.70354718), (0.50604509, -0.82915802, 0.23751914), (0.70354718, 0.23751914, -0.66978058)-26.89885, -37.49452, 84.27813
23generate(0.48442461, 0.48557742, 0.72770006), (-0.52939818, -0.49951234, 0.68572953), (0.69646993, -0.71742734, 0.01508773)-27.93229, -24.27248, 37.86826
24generate(0.45423309, 0.50002844, 0.73732208), (-0.8422782, 0.51067318, 0.17256979), (-0.29024081, -0.69941723, 0.65312771)-27.31168, 23.95814, 36.08261
25generate(0.4500877, 0.52942734, 0.71911595), (-0.00020541, 0.80535649, -0.59279076), (-0.89298433, 0.26666012, 0.3625898)-25.89467, 40.54426, 81.38889
26generate(0.43859832, -0.56181651, 0.70142264), (-0.83931471, 0.02289905, 0.54316338), (-0.32122007, -0.82694488, -0.46149738)-24.0855, -1.44595, 113.59013
27generate(-0.45019718, -0.00754109, 0.89289733), (-0.50637545, 0.82577932, -0.24833933), (-0.7354634, -0.56394295, -0.37558214)0.44435, 38.45528, 125.24965
28generate(-0.43968909, 0.85642602, 0.27056972), (0.52909498, 0.49041667, -0.69249548), (-0.72576305, -0.16132563, -0.66876157)42.44374, 24.95559, 144.83474
29generate(0.45560076, 0.83611164, -0.30552458), (0.83611164, -0.51972911, -0.17549638), (-0.30552458, -0.17549638, -0.93587165)43.87094, -23.28891, 145.27947
30generate(0.99841224, -0.04041045, -0.03924284), (-0.00961206, -0.80867089, 0.5881828), (-0.05550327, -0.5868717, -0.80777534)2.75361, -39.60596, 125.96923
31generate(-0.46224049, 0.56197675, -0.68594158), (-0.83358847, -0.01156065, 0.55226499), (0.30243016, 0.82707223, 0.47380114)108.8047, -2.30717, 23.05923
32generate(0.43547604, 0.03069202, -0.89967695), (-0.53528207, 0.81236401, -0.23138242), (0.72376358, 0.58234244, 0.37019394)85.41578, 38.523, 12.30648
33generate(0.45423309, -0.8422782, -0.29024081), (0.50002844, 0.51067318, -0.69941723), (0.73732208, 0.17256979, 0.65312771)43.05793, 26.65863, -7.5635
34generate(-0.43189094, -0.85051873, 0.30014681), (0.84157914, -0.49970666, -0.20503124), (0.32436827, 0.16404616, 0.9315976)40.26826, -21.50412, -9.09106
35generate(-0.99830276, 0.01735856, 0.05559028), (0.01735856, -0.82246492, 0.56855091), (0.05559028, 0.56855091, 0.82076768)80.902, -39.40597, 9.83483
36generate(-0.45407505, -0.53330608, -0.71372297), (0.83979896, 0.01136633, -0.54277851), (0.29757949, -0.84584599, 0.44270872)110.47066, 1.60246, 25.56296
37generate(-0.48421746, -0.52919602, -0.69676756), (0.53561243, -0.80898531, 0.24220261), (-0.69184737, -0.25591863, 0.67516877)110.58905, -39.06999, 51.55342
38generate(-0.49896861, -0.49972524, -0.70802896), (-0.49972524, -0.50157751, 0.70618318), (-0.70802896, 0.70618318, 0.00054612)111.98094, -26.92797, 98.24818
39generate(-0.47794292, -0.48562135, -0.73194431), (-0.83541257, 0.50876259, 0.20795783), (0.27139712, 0.71086745, -0.64885366)112.7228, 21.24866, 101.11667
40generate(-0.45019718, -0.50637545, -0.7354634), (-0.00754109, 0.82577932, -0.56394295), (0.89289733, -0.24833933, -0.37558214)111.78939, 38.88143, 56.19473
41generate(0.47771722, 0.83310421, -0.27878958), (0.53314584, -0.02270473, 0.84571863), (0.69824191, -0.55264986, -0.45501249)41.10653, -80.29523, 69.906
42generate(0.99939353, -0.03446988, -0.00493993), (0.01536298, 0.3091492, 0.95088945), (-0.03124987, -0.95038866, 0.30949126)0.3669, -65.5701, 48.61706
43generate(0.43547604, -0.53528207, 0.72376358), (0.03069202, 0.81236401, 0.58234244), (-0.89967695, -0.23138242, 0.37019394)-25.48284, -41.08286, 81.20437
44generate(-0.43472045, 0.02277305, 0.90027747), (0.55794875, 0.79151393, 0.24939704), (-0.70690263, 0.61072668, -0.35679349)-0.71922, -40.67405, 122.63337
45generate(-0.40861396, 0.86848229, 0.28066554), (0.86848229, 0.27541307, 0.41217248), (0.28066554, 0.41217248, -0.86679911)40.43528, -64.90863, 115.6506
46generate(-0.46224049, -0.83358847, 0.30243016), (0.56197675, -0.01156065, 0.82707223), (-0.68594158, 0.55226499, 0.47380114)41.3969, -80.24404, 64.98235
47generate(-0.99857028, 0.0428897, 0.03190416), (0.0428897, 0.28663138, 0.95708042), (0.03190416, 0.95708042, -0.2880611)82.52957, -67.1577, 86.58367
48generate(-0.43472045, 0.55794875, -0.70690263), (0.02277305, 0.79151393, 0.61072668), (0.90027747, 0.24939704, -0.35679349)109.07123, -42.68502, 54.54627
49generate(0.4500877, -0.00020541, -0.89298433), (0.52942734, 0.80535649, 0.26666012), (0.71911595, -0.59279076, 0.3625898)84.3422, -40.64641, 13.14476
50generate(0.43307938, -0.86022271, -0.26918237), (0.86267356, 0.3090291, 0.40036902), (-0.26122134, -0.40560808, 0.87592551)42.51716, -63.85916, 19.59461
51generate(-0.45407505, 0.83979896, 0.29757949), (-0.53330608, 0.01136633, -0.84584599), (-0.71372297, -0.54277851, 0.44270872)41.20921, 80.51879, 68.39828
52generate(0.42801306, 0.8543865, -0.29466682), (-0.02503748, -0.31470633, -0.94885882), (-0.90342567, 0.41350168, -0.11330673)44.29633, 66.04885, 114.34234
53generate(0.99841224, -0.00961206, -0.05550327), (-0.04041045, -0.80867089, -0.5868717), (-0.03924284, 0.5881828, -0.80777534)3.86177, 42.01087, 125.15844
54generate(0.4688502, -0.55818007, 0.68455423), (-0.55818007, -0.78788512, -0.26013853), (0.68455423, -0.26013853, -0.68096509)-24.21528, 41.62451, 85.8991
55generate(-0.42883631, -0.03321519, 0.90277138), (-0.86280632, -0.28107424, -0.42019344), (0.26770259, -0.95911106, 0.09187657)-1.13329, 65.42372, 50.81939
56generate(0.43859832, -0.83931471, -0.32122007), (-0.56181651, 0.02289905, -0.82694488), (0.70142264, 0.54316338, -0.46149738)45.83768, 80.43425, 70.10105
57generate(-0.42883631, -0.86280632, 0.26770259), (-0.03321519, -0.28107424, -0.95911106), (0.90277138, -0.42019344, 0.09187657)42.35752, 67.09272, 23.84461
58generate(-0.99916783, -0.01305462, 0.03864232), (-0.01305462, -0.79520705, -0.60619743), (0.03864232, -0.60619743, 0.79437488)82.10016, 42.17078, 12.4786
59generate(-0.48421746, 0.53561243, -0.69184737), (-0.52919602, -0.80898531, -0.25591863), (-0.69676756, 0.24220261, 0.67516877)110.14262, 40.10972, 51.71045
60generate(0.40437089, 0.02495561, -0.91425456), (-0.86834953, -0.30336792, -0.39234806), (-0.28714679, 0.95254665, -0.10100297)87.73118, 63.75784, 87.32309

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Components

#1: Protein coat protein


Mass: 24463.658 Da / Num. of mol.: 1 / Fragment: residues 37-268
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sesbania mosaic virus / Genus: Sobemovirus / Plasmid: pRSET C / Production host: Escherichia coli (E. coli) / References: UniProt: Q9EB06
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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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: 290 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350, magnesium chloride, isopropanol , pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 29, 2002 / Details: MIRRORS
RadiationMonochromator: OSMIC MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 3.3→15 Å / Num. all: 288416 / Num. obs: 205217 / % possible obs: 71.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.156 / Rsym value: 0.152
Reflection shellResolution: 3.3→3.5 Å / Rmerge(I) obs: 0.226 / % possible all: 73.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
GLRFphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→15 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 248421.5 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.259 19598 9.9 %RANDOM
Rwork0.255 ---
obs0.255 197581 69.7 %-
all-288416 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.248255 e/Å3
Displacement parametersBiso mean: 25.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.53 Å0.5 Å
Refinement stepCycle: LAST / Resolution: 3.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1454 0 1 89 1544
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_mcbond_it1.091.5
X-RAY DIFFRACTIONc_mcangle_it1.942
X-RAY DIFFRACTIONc_scbond_it1.442
X-RAY DIFFRACTIONc_scangle_it2.222.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.3→3.5 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.307 3393 10.1 %
Rwork0.299 30364 -
obs--71.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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