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- PDB-5s50: Tubulin-Z57299526-complex -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5s50
TitleTubulin-Z57299526-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
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / N-[(furan-2-yl)methyl]-1H-benzimidazol-2-amine / 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: 3.1 Å
AuthorsMuehlethaler, T. / Gioia, D. / Prota, A.E. / Sharpe, M.E. / Cavalli, A. / Steinmetz, M.O.
Funding supportEuropean Union, Italy, Switzerland, 4items
OrganizationGrant numberCountry
iNEXT/Horizon 2020PID2692European Union
NEON/Regione LombardiaID239047 Italy
Swiss National Science Foundation31003A_166608 Switzerland
Swiss National Science Foundation31030A_192566 Switzerland
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Comprehensive Analysis of Binding Sites in Tubulin.
Authors: Muhlethaler, T. / Gioia, D. / Prota, A.E. / Sharpe, M.E. / Cavalli, A. / Steinmetz, M.O.
History
DepositionNov 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2021Provider: repository / Type: Initial release
Revision 1.1Mar 6, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)264,97323
Polymers261,6316
Non-polymers3,34217
Water41423
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.030, 158.020, 180.880
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, 40 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-WZD / N-[(furan-2-yl)methyl]-1H-benzimidazol-2-amine


Mass: 213.235 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H11N3O / 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.: 23 / 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: Diamond / Beamline: I04-1 / Wavelength: 0.91587 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 14, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 3.1→79.01 Å / Num. obs: 54710 / % possible obs: 99.8 % / Redundancy: 6.71 % / Biso Wilson estimate: 106.964 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.088 / Rrim(I) all: 0.096 / Χ2: 0.981 / Net I/σ(I): 14.78 / Num. measured all: 367126 / Scaling rejects: 181
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
3.1-3.186.9562.2730.8427658398639760.4052.45699.7
3.18-3.276.9021.7141.1227167394839360.5341.85399.7
3.27-3.366.7161.2611.5225446379837890.6721.36799.8
3.36-3.476.3420.9052.0423193366336570.7620.98799.8
3.47-3.586.6280.6982.6923807360335920.8580.75899.7
3.58-3.716.6320.5013.7722649343934150.910.54399.3
3.71-3.857.1380.3355.6524054338133700.9680.36199.7
3.85-47.0860.2367.8522726321232070.9830.25599.8
4-4.186.9920.16210.9621640309630950.990.175100
4.18-4.386.9030.11514.1420460296929640.9950.12499.8
4.38-4.626.7820.0819.4819098282428160.9970.08799.7
4.62-4.96.4880.06921.8717361267926760.9980.07599.9
4.9-5.246.1230.06522.615553254225400.9970.07199.9
5.24-5.666.4510.06423.8515167235323510.9980.06999.9
5.66-6.26.9720.05727.4515144217421720.9980.06299.9
6.2-6.936.8450.04732.813751200820090.9990.051100
6.93-86.5520.03342.3211511175717570.9990.036100
8-9.85.9770.02357.0989481503149710.02599.6
9.8-13.866.2540.0268.377517120312020.9990.02299.9
13.86-79.016.2060.01973.4242767076890.9990.02197.5

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Processing

Software
NameVersionClassificationNB
PHENIX1.18.2_3874refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIX1.18.2_3874phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5lxt
Resolution: 3.1→79.01 Å / SU ML: 0.53 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 32.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2697 2691 4.92 %
Rwork0.2076 52002 -
obs0.2107 54693 99.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 302.01 Å2 / Biso mean: 136.4036 Å2 / Biso min: 70.27 Å2
Refinement stepCycle: final / Resolution: 3.1→79.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17416 0 226 23 17665
Biso mean--126.08 109.65 -
Num. residues----2201
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.1-3.160.4031490.380527172866100
3.16-3.220.42991260.355326992825100
3.22-3.280.39451430.34126822825100
3.28-3.350.38981430.311127172860100
3.35-3.430.35431270.295727092836100
3.43-3.520.32931410.285626782819100
3.52-3.610.35121520.284427182870100
3.61-3.720.3681150.30912716283199
3.72-3.840.31061640.230926902854100
3.84-3.980.25561380.22527112849100
3.98-4.140.23941300.205927342864100
4.14-4.320.26041420.201927402882100
4.32-4.550.22441280.183427372865100
4.55-4.840.23471320.173227482880100
4.84-5.210.2641520.18127552907100
5.21-5.730.29871300.19627772907100
5.73-6.560.2721740.208227562930100
6.57-8.270.2741420.185728122954100
8.27-79.010.21991630.16652906306999
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)
12.10280.53330.72245.42310.57223.18220.03060.58460.3488-0.92050.3436-0.6973-0.85560.3381-0.4171.2377-0.22130.27031.0705-0.29431.179931.95889.957750.5076
22.86-1.3441-2.3048.16111.05366.5159-0.0697-0.6264-0.07960.96330.4178-0.37050.62861.6696-0.22421.0323-0.01710.05521.1274-0.28141.083629.85474.528758.772
32.63870.99171.11385.1502-0.12487.85050.1856-0.09560.12940.00450.06130.3088-0.64-0.3749-0.30060.87310.09570.15630.9198-0.26990.99516.59384.782566.4548
41.8774-1.1976-0.0838.82032.40512.7255-0.5759-0.33690.04521.6560.85070.20910.30220.182-0.24811.19780.10670.15191.1569-0.24891.064318.69283.686973.014
51.92491.51060.98113.69523.17548.73070.0155-0.71880.11750.70260.7118-0.4041.24471.5708-0.8751.09620.3068-0.13121.3931-0.42641.328832.206162.442661.4774
67.0187-2.7209-0.26558.36391.64817.57050.20410.27530.8161-1.0692-0.28340.2566-1.443-0.59630.05771.08230.08750.02641.0859-0.07911.067315.869270.367118.7907
72.197-0.7632-1.07093.84181.73746.67140.06360.12150.1858-0.3418-0.0097-0.0041-0.4512-0.1525-0.04050.6680.06470.02670.7145-0.17720.881720.059856.534825.0495
85.9219-4.20172.93095.6403-0.40724.8481-0.1117-0.660.25480.0674-0.05920.4114-0.0243-1.55170.13650.93560.0440.12451.4448-0.42391.06075.418460.393441.9849
90.9734-1.6483-2.30035.43833.78035.9107-0.3087-0.19490.05811.18750.12390.12961.01830.34820.17570.9756-0.09170.03240.9718-0.11381.074220.829842.24631.2014
103.6137-0.99450.17766.0550.10953.89150.0040.46530.2261-0.3140.0265-0.2614-0.19660.2697-0.0510.8019-0.20270.06430.9117-0.01780.814620.515532.8187-11.9071
112.9147-1.66830.42613.9841.08684.7347-0.0522-0.0863-0.08110.07460.01680.29240.131-0.44360.01190.7745-0.21760.13060.8642-0.05270.92358.149625.9723.3015
128.1845-2.63930.29746.3905-1.42133.6503-0.07830.92540.1885-1.16260.12880.27470.1378-0.4266-0.00861.5044-0.47350.10181.7683-0.16041.120717.25648.8173-44.0146
133.4846-0.451-1.30862.82780.41582.9438-0.51051.3522-0.6033-0.56420.3451-0.13510.4027-0.30120.14691.242-0.2830.12691.4388-0.33980.944822.9601-2.7456-33.8648
143.1975-3.2694-1.87726.5736-0.3192.87081.16830.6646-1.0228-0.8336-0.13531.10620.45070.5769-0.87891.7442-0.2568-0.15381.9463-0.52211.40260.8645-6.6392-25.2596
153.8671-0.97610.93112.927-2.08293.6038-0.3916-0.3249-0.22940.36760.72210.1568-0.3462-0.6714-0.38021.4299-0.30640.0891.4406-0.28111.21698.9182-2.1937-20.4433
166.1662-0.6868-4.71883.58370.49316.1733-0.332-0.6023-1.268-0.15160.39940.01370.6511.2083-0.23291.65050.14210.06051.3474-0.42071.639130.7795-17.5069-23.7971
177.8281-2.8794-3.4156.80254.08175.4252-0.623-1.10760.91331.93030.499-0.44141.06311.09820.01991.55270.0654-0.24611.5225-0.31811.27327.240593.404981.7045
180.40420.0084-0.34864.45444.93844.8961-0.3943-0.09560.05121.22560.7251-0.12171.39051.3639-0.22361.37460.13090.04461.2086-0.31571.308943.234328.17274.1861
196.08391.5708-1.43935.80410.99994.6515-0.54340.6858-0.5106-0.4580.8305-0.1650.746-0.5524-0.26791.8502-0.32580.26871.5032-0.16061.37566.327454.88769.4291
208.5379-0.96753.21684.1584-2.38294.94360.3719-0.44340.8983-0.1013-0.0166-0.1285-1.2860.0052-0.44031.5373-0.02610.0271.48420.0731.082516.590764.2945102.393
212.81131.15030.80382.93980.16974.0151-0.1672-0.4944-0.7850.38220.3757-0.35111.13980.6602-0.021.89650.37370.1711.2891-0.08251.265411.619752.4809105.4119
222.44631.6127-0.43812.68260.86323.8738-0.42390.4204-1.01070.44890.328-0.51871.1650.06690.04211.95050.15240.36561.1754-0.0821.563-2.064549.909799.1505
233.56260.4784-0.08411.74040.53146.1749-0.29650.1761-0.7453-0.24390.70210.11170.9465-0.5385-0.34932.1649-0.07050.42721.0712-0.04781.23890.992958.317387.3867
244.8658-1.9525-1.94744.07481.73729.02760.08180.88740.9443-0.4150.14990.7396-0.69750.5455-0.37431.3728-0.250.20921.2246-0.14831.4028-7.933163.521179.2127
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 160 )A1 - 160
2X-RAY DIFFRACTION2chain 'A' and (resid 161 through 199 )A161 - 199
3X-RAY DIFFRACTION3chain 'A' and (resid 200 through 311 )A200 - 311
4X-RAY DIFFRACTION4chain 'A' and (resid 312 through 401 )A312 - 401
5X-RAY DIFFRACTION5chain 'A' and (resid 402 through 438 )A402 - 438
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 88 )B1 - 88
7X-RAY DIFFRACTION7chain 'B' and (resid 89 through 259 )B89 - 259
8X-RAY DIFFRACTION8chain 'B' and (resid 260 through 372 )B260 - 372
9X-RAY DIFFRACTION9chain 'B' and (resid 373 through 438 )B373 - 438
10X-RAY DIFFRACTION10chain 'C' and (resid 1 through 197 )C1 - 197
11X-RAY DIFFRACTION11chain 'C' and (resid 198 through 440 )C198 - 440
12X-RAY DIFFRACTION12chain 'D' and (resid 1 through 88 )D1 - 88
13X-RAY DIFFRACTION13chain 'D' and (resid 89 through 273 )D89 - 273
14X-RAY DIFFRACTION14chain 'D' and (resid 274 through 311 )D274 - 311
15X-RAY DIFFRACTION15chain 'D' and (resid 312 through 399 )D312 - 399
16X-RAY DIFFRACTION16chain 'D' and (resid 400 through 441 )D400 - 441
17X-RAY DIFFRACTION17chain 'E' and (resid 6 through 46 )E6 - 46
18X-RAY DIFFRACTION18chain 'E' and (resid 47 through 143 )E47 - 143
19X-RAY DIFFRACTION19chain 'F' and (resid 1 through 66 )F1 - 66
20X-RAY DIFFRACTION20chain 'F' and (resid 67 through 140 )F67 - 140
21X-RAY DIFFRACTION21chain 'F' and (resid 141 through 207 )F141 - 207
22X-RAY DIFFRACTION22chain 'F' and (resid 208 through 297 )F208 - 297
23X-RAY DIFFRACTION23chain 'F' and (resid 298 through 354 )F298 - 354
24X-RAY DIFFRACTION24chain 'F' and (resid 355 through 382 )F355 - 382

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