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- PDB-5sb3: Tubulin-todalam-4-complex -

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Basic information

Entry
Database: PDB / ID: 5sb3
TitleTubulin-todalam-4-complex
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
  • Tubulin-Tyrosine Ligase
KeywordsCELL CYCLE / TUBULIN FOLD / CYTOSKELETON / MICROTUBULE
Function / homology
Function and homology information


tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / microtubule-based process / regulation of microtubule polymerization or depolymerization / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization ...tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / microtubule-based process / regulation of microtubule polymerization or depolymerization / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / neuron projection development / mitotic cell cycle / nervous system development / growth cone / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / neuron projection / protein heterodimerization activity / GTPase activity / nucleotide binding / GTP binding / Golgi apparatus / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. ...Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / Alpha tubulin / Tubulin-beta mRNA autoregulation signal. / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin / Tubulin, C-terminal / Tubulin C-terminal domain / Tubulin, conserved site / Tubulin subunits alpha, beta, and gamma signature. / Tubulin/FtsZ family, C-terminal domain / Tubulin/FtsZ-like, C-terminal domain / Tubulin/FtsZ, C-terminal / Tubulin/FtsZ, 2-layer sandwich domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ family, GTPase domain / Tubulin/FtsZ, GTPase domain / Tubulin/FtsZ, GTPase domain superfamily
Similarity search - Domain/homology
N-[4-(2-anilino-1,3-thiazol-4-yl)phenyl]acetamide / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin tyrosine ligase / Stathmin-4 / Tubulin alpha-1B chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Gallus gallus (chicken)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å
AuthorsMuehlethaler, T. / Milanos, L. / Ortega, J.A. / Blum, T.B. / Gioia, D. / Prota, A.E. / Cavalli, A. / Steinmetz, M.O.
Funding support Italy, Switzerland, 3items
OrganizationGrant numberCountry
NEON/Regione LombardiaID239047 Italy
Swiss National Science Foundation31003A_166608 Switzerland
Swiss National Science Foundation310030_192566 Switzerland
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Rational Design of a Novel Tubulin Inhibitor with a Unique Mechanism of Action.
Authors: Muhlethaler, T. / Milanos, L. / Ortega, J.A. / Blum, T.B. / Gioia, D. / Roy, B. / Prota, A.E. / Cavalli, A. / Steinmetz, M.O.
History
DepositionJul 8, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1May 11, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 22, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin alpha-1B chain
B: Tubulin beta-2B chain
C: Tubulin alpha-1B chain
D: Tubulin beta-2B chain
E: Stathmin-4
F: Tubulin-Tyrosine Ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,85622
Polymers261,6316
Non-polymers3,22416
Water12,196677
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.650, 157.714, 180.188
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 4 types, 6 molecules ACBDEF

#1: Protein Tubulin alpha-1B chain / Alpha-tubulin ubiquitous / Tubulin K-alpha-1 / Tubulin alpha-ubiquitous chain


Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Brain / References: UniProt: P81947
#2: Protein Tubulin beta-2B chain


Mass: 49999.887 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (cattle) / Organ: Brain / References: UniProt: Q6B856
#3: Protein Stathmin-4 / Stathmin-like protein B3 / RB3


Mass: 16844.162 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Stmn4 / Production host: Escherichia coli (E. coli) / References: UniProt: P63043
#4: Protein Tubulin-Tyrosine Ligase


Mass: 44378.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Gene: TTL / Production host: Escherichia coli (E. coli) / References: UniProt: E1BQ43

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Non-polymers , 8 types, 693 molecules

#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O14P3 / Comment: GTP, energy-carrying molecule*YM
#6: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM
#9: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#10: Chemical ChemComp-47F / N-[4-(2-anilino-1,3-thiazol-4-yl)phenyl]acetamide


Mass: 309.386 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H15N3OS / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-ACP / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE


Mass: 505.208 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H18N5O12P3 / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 677 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2% PEG 4K, 4% glycerol, 30 mM MgCl2, 30 mM CaCl2, 0.1 M MES/Imidazole, 5 mM L-tyrosine

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Jun 23, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 2.2→49.46 Å / Num. obs: 150862 / % possible obs: 99.9 % / Redundancy: 13.66 % / Biso Wilson estimate: 45.24 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.172 / Rrim(I) all: 0.179 / Χ2: 0.765 / Net I/σ(I): 13.04 / Num. measured all: 2060719 / Scaling rejects: 263
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.2-2.2613.8032.8790.9315144511084109720.3362.98899
2.26-2.3214.1592.3291.1915261910782107790.4642.415100
2.32-2.3914.0581.8561.5114726910478104760.5791.924100
2.39-2.4613.91.4681.9114168410194101930.681.523100
2.46-2.5413.7541.1932.37136056989498920.781.238100
2.54-2.6313.2490.9163126916958095790.8430.952100
2.63-2.7312.7040.7653.56117014921292110.870.797100
2.73-2.8414.0450.5814.94125279892189200.9380.602100
2.84-2.9713.7160.4576.28117480856685650.9590.475100
2.97-3.1112.8660.328.53105296818481840.9770.333100
3.11-3.2813.9680.23811.72108937779977990.9890.247100
3.28-3.4814.2720.16916.36105368738373830.9940.175100
3.48-3.7214.120.11922.4698094694769470.9970.123100
3.72-4.0213.8810.08129.8190434651665150.9990.084100
4.02-4.413.5780.06236.5580982596459640.9990.064100
4.4-4.9212.450.04741.6667778544454440.9990.049100
4.92-5.6913.7150.05440.7666271483248320.9990.056100
5.69-6.9612.7780.05839.1252567411441140.9990.06100
6.96-9.8514.2140.04354.8345995323632360.9990.045100
9.85-49.4612.5120.03760.9423235187818570.9990.03998.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.19.1_4122refinement
XSCALEdata scaling
PDB_EXTRACT3.28data extraction
XDSdata reduction
PHENIX1.19.1_4122phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5LXT
Resolution: 2.2→49.46 Å / SU ML: 0.34 / Cross valid method: THROUGHOUT / σ(F): 1.31 / Phase error: 25.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2249 14556 4.99 %
Rwork0.1952 276888 -
obs0.1967 291444 99.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 166.78 Å2 / Biso mean: 60.6471 Å2 / Biso min: 26.31 Å2
Refinement stepCycle: final / Resolution: 2.2→49.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17297 0 194 677 18168
Biso mean--54.17 53.15 -
Num. residues----2185
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2-2.230.37774820.37879105958798
2.23-2.250.34154810.343392169697100
2.25-2.280.34744820.341292159697100
2.28-2.310.37474800.334192479727100
2.31-2.340.34524780.318192559733100
2.34-2.370.33254880.310192309718100
2.37-2.410.32074880.299191949682100
2.41-2.440.32684880.282792529740100
2.44-2.480.28444840.272691989682100
2.48-2.520.29664860.266692399725100
2.52-2.560.28454900.263792619751100
2.56-2.610.27314870.24992409727100
2.61-2.660.30154860.256692229708100
2.66-2.720.31614800.258391969676100
2.72-2.770.28974890.249792479736100
2.77-2.840.26574900.234592399729100
2.84-2.910.27144840.225393179801100
2.91-2.990.24244850.211391759660100
2.99-3.080.23414850.200292729757100
3.08-3.180.22254810.194692069687100
3.18-3.290.224820.201992729754100
3.29-3.420.23944840.197992169700100
3.42-3.580.21954890.18392729761100
3.58-3.760.21114750.164992039678100
3.76-40.19164980.156892429740100
4-4.310.16214810.150192259706100
4.31-4.740.16234940.132292899783100
4.74-5.430.19324840.151292059689100
5.43-6.840.20614850.176792149699100
6.84-49.460.16954900.156192249714100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.9196-0.3525-0.31333.55011.01912.4043-0.00290.09580.1621-0.55920.3157-0.3865-0.77690.4051-0.29080.6066-0.15570.12730.4997-0.15350.475432.13989.51450.931
20.8609-0.3049-1.03592.3160.35371.55210.0224-0.1039-0.07490.48940.1401-0.24670.18550.3238-0.10530.47020.0188-0.00370.4496-0.13890.469430.0974.12959.133
31.2395-0.0350.24692.81930.90583.40440.1168-0.08040.03040.3712-0.1320.2981-0.0518-0.2018-0.00190.364-0.00470.08030.3094-0.10040.391917.08384.43166.959
40.90250.01560.08752.85121.37342.416-0.0245-0.11690.07380.5907-0.02120.30220.0286-0.0170.0380.5181-0.01550.10350.4532-0.09010.421718.9883.1573.359
50.76250.1981-0.2752.09280.37771.5494-0.0163-0.089-0.16290.56650.2363-0.25850.2520.5139-0.2120.45470.1117-0.05010.4259-0.13940.42531.62864.22759.745
62.3939-0.8701-0.75682.5632-0.09411.96670.13220.11690.4168-0.3128-0.1260.2982-0.7343-0.2743-0.00420.56760.07160.00530.3964-0.03260.514216.26370.01719.465
71.50290.0324-0.13922.10511.42243.10120.01720.03540.1143-0.0844-0.06970.0942-0.2267-0.0574-0.00880.25650.01720.02130.3264-0.07670.343520.39255.91825.466
82.0523-0.5980.77371.95660.14312.722-0.1879-0.11870.03280.2039-0.11610.3836-0.029-0.86850.27290.3860.02060.06320.5901-0.19740.47986.34660.01142.842
90.7957-0.45070.02172.85281.44922.59170.0016-0.1235-0.05760.5529-0.00130.00580.45390.1782-0.03570.3293-0.02460.00990.3684-0.04310.35621.02541.1731.314
101.0455-0.26710.09952.96130.48421.7441-0.05390.13620.0887-0.27370.1326-0.0313-0.16230.1535-0.07010.2813-0.07850.04030.3808-0.04140.342220.27133.083-12.007
110.771-0.12890.07041.53281.05421.6607-0.0044-0.01790.05510.0797-0.07680.10890.0853-0.18820.07290.239-0.05290.04420.3139-0.02630.33977.8825.943.101
122.9005-0.71190.74322.83510.09441.4981-0.13630.48710.0818-0.72410.22390.0110.07510.055-0.07320.6618-0.12260.05720.758-0.0670.385217.3949.936-43.999
131.53180.1458-0.5441.39230.22062.0687-0.10970.3812-0.1634-0.40410.2178-0.2220.25190.2069-0.09730.5563-0.03460.07030.5781-0.19190.446222.9-2.184-34.256
141.4774-1.2329-0.21862.15960.17891.423-0.04340.1242-0.3462-0.3121-0.09020.60780.613-0.53850.14460.6047-0.1231-0.02770.6827-0.19980.59872.249-6.17-24.895
151.7999-0.11640.01531.23340.0872.3441-0.18270.2432-0.1936-0.03920.11160.10490.2535-0.25890.05450.4819-0.09970.03020.4598-0.11260.40328.749-1.627-20.957
162.07890.02830.0531.74870.02921.806-0.21370.2983-0.89130.03880.0397-0.12130.73240.34610.00430.80530.06820.04220.5696-0.26010.706430.398-17.18-24.717
172.0666-0.8534-0.41851.62260.88630.8556-0.1322-0.1920.18720.73290.2554-0.44750.30670.4794-0.11860.9717-0.0295-0.01810.6214-0.17030.565427.5292.68981.976
180.1872-0.1794-0.30980.00240.12540.4354-0.0366-0.0386-0.05020.32190.5189-0.55520.46230.6958-0.51320.47470.06960.03050.7884-0.2570.71642.99228.8454.982
192.1860.2732-2.06572.06670.48233.0184-0.33640.37-0.6134-0.1162-0.0256-0.13830.8936-0.41530.32460.9208-0.08050.13030.5811-0.10770.65366.15654.76669.849
201.40520.53570.7841.0164-0.97792.4732-0.0002-0.6679-0.07150.3947-0.369-0.801-0.23181.410.36350.82060.0058-0.14881.24350.09230.768415.57264.39103.142
212.12670.39330.88171.3774-0.36672.5204-0.0759-0.6338-0.91140.4887-0.3033-0.62030.7861.61390.31841.05320.21820.03421.25940.3741.025310.97951.931105.777
221.10990.7791-0.90420.8824-0.08651.5583-0.3856-0.0191-0.74040.19370.1366-0.12410.8566-0.02610.11221.13210.08860.22670.49450.09870.8617-2.88750.09299.144
232.5073-0.135-1.39760.79090.5722.3648-0.27620.0229-0.45440.03070.2322-0.06430.51330.01230.02350.7927-0.03010.08260.47490.00520.56040.99558.23187.874
242.8034-0.0525-0.02361.4006-0.18814.0743-0.09490.1478-0.53370.06410.00490.22820.1574-0.16070.09740.6427-0.03220.04970.6370.01030.723-3.97160.36783.714
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 1:160 )A1 - 160
2X-RAY DIFFRACTION2( CHAIN A AND RESID 161:199 )A161 - 199
3X-RAY DIFFRACTION3( CHAIN A AND RESID 200:311 )A200 - 311
4X-RAY DIFFRACTION4( CHAIN A AND RESID 312:401 )A312 - 401
5X-RAY DIFFRACTION5( CHAIN A AND RESID 402:437 )A402 - 437
6X-RAY DIFFRACTION6( CHAIN B AND RESID 1:88 )B1 - 88
7X-RAY DIFFRACTION7( CHAIN B AND RESID 89:259 )B89 - 259
8X-RAY DIFFRACTION8( CHAIN B AND RESID 260:372 )B260 - 372
9X-RAY DIFFRACTION9( CHAIN B AND RESID 373:437 )B373 - 437
10X-RAY DIFFRACTION10( CHAIN C AND RESID 1:197 )C1 - 197
11X-RAY DIFFRACTION11( CHAIN C AND RESID 198:440 )C198 - 440
12X-RAY DIFFRACTION12( CHAIN D AND RESID 1:88 )D1 - 88
13X-RAY DIFFRACTION13( CHAIN D AND RESID 89:273 )D89 - 273
14X-RAY DIFFRACTION14( CHAIN D AND RESID 274:311 )D274 - 311
15X-RAY DIFFRACTION15( CHAIN D AND RESID 312:399 )D312 - 399
16X-RAY DIFFRACTION16( CHAIN D AND RESID 400:441 )D400 - 441
17X-RAY DIFFRACTION17( CHAIN E AND RESID 6:46 )E6 - 46
18X-RAY DIFFRACTION18( CHAIN E AND RESID 47:141 )E47 - 141
19X-RAY DIFFRACTION19( CHAIN F AND RESID 1:66 )F1 - 66
20X-RAY DIFFRACTION20( CHAIN F AND RESID 67:140 )F67 - 140
21X-RAY DIFFRACTION21( CHAIN F AND RESID 141:207 )F141 - 207
22X-RAY DIFFRACTION22( CHAIN F AND RESID 208:297 )F208 - 297
23X-RAY DIFFRACTION23( CHAIN F AND RESID 298:354 )F298 - 354
24X-RAY DIFFRACTION24( CHAIN F AND RESID 355:381 )F355 - 381

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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.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

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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