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- PDB-5s54: Tubulin-Z2856434816-complex -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5s54
TitleTubulin-Z2856434816-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 / Chem-WLS / 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: 2.4 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)264,55521
Polymers261,6316
Non-polymers2,92415
Water4,522251
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.330, 157.150, 179.170
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 , 7 types, 266 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-WLS / 1-(pyridin-4-yl)-N-[(thiophen-2-yl)methyl]methanamine


Mass: 204.291 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H12N2S / Feature type: SUBJECT OF INVESTIGATION
#10: 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
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 251 / 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: 2.4→71.96 Å / Num. obs: 115397 / % possible obs: 99.9 % / Redundancy: 6.801 % / Biso Wilson estimate: 72.888 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.095 / Rrim(I) all: 0.103 / Χ2: 1.006 / Net I/σ(I): 10.58 / Num. measured all: 784868 / Scaling rejects: 125
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
2.4-2.467.0172.2370.7259103844684230.3852.41499.7
2.46-2.536.9151.8030.9256969826682380.4851.94899.7
2.53-2.66.7831.3721.2654112799779780.5981.48599.8
2.6-2.686.4581.0981.5750359781077980.651.19599.8
2.68-2.776.6460.8562.1150249756975610.7540.92999.9
2.77-2.877.0840.6362.9651643729872900.8650.68699.9
2.87-2.987.0740.4723.9750077708270790.9190.509100
2.98-3.16.9880.3245.5747657682568200.9560.3599.9
3.1-3.246.950.2437.2345312652565200.9740.26299.9
3.24-3.396.7310.1749.5542114626062570.9850.188100
3.39-3.586.4620.12612.2938625598059770.9910.13799.9
3.58-3.796.8320.09616.2338404562356210.9950.103100
3.79-4.067.0560.07620.2437727534853470.9960.082100
4.06-4.386.9360.06423.634430496449640.9970.07100
4.38-4.86.7420.05327.630877458245800.9980.058100
4.8-5.376.270.05226.6526059416141560.9980.05799.9
5.37-6.26.8240.05527.1625318371037100.9970.059100
6.2-7.596.8020.04930.4721452315631540.9980.05399.9
7.59-10.736.150.0436.4615239248324780.9980.04499.8
10.73-71.966.3220.03641.429142145414460.9990.03999.4

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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: 2.4→71.96 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 30.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2504 5755 4.99 %
Rwork0.2057 109613 -
obs0.208 115368 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 228.23 Å2 / Biso mean: 85.5649 Å2 / Biso min: 41.98 Å2
Refinement stepCycle: final / Resolution: 2.4→71.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17169 0 186 251 17606
Biso mean--83.44 68.01 -
Num. residues----2172
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 (%)
2.4-2.430.39871680.35193642381099
2.43-2.460.3761880.344736243812100
2.46-2.490.37041900.337735983788100
2.49-2.520.35012010.336435553756100
2.52-2.550.36482050.330636363841100
2.55-2.590.37512030.330835783781100
2.59-2.620.44961830.344236333816100
2.62-2.660.34141760.315736283804100
2.66-2.70.35161610.296736213782100
2.7-2.750.34162100.298436223832100
2.75-2.790.33671830.279336143797100
2.79-2.850.36811710.265436553826100
2.85-2.90.32542050.263336473852100
2.9-2.960.31861780.261236433821100
2.96-3.020.32871840.251136173801100
3.02-3.090.33661890.258736643853100
3.09-3.170.3071660.25636363802100
3.17-3.260.32341930.244836593852100
3.26-3.350.26391490.236536843833100
3.35-3.460.27621940.224336493843100
3.46-3.590.24322130.214836283841100
3.59-3.730.26162210.202336483869100
3.73-3.90.24351670.19536723839100
3.9-4.10.20322170.181836423859100
4.1-4.360.2471990.173636893888100
4.36-4.70.19882110.148936543865100
4.7-5.170.17572230.158536803903100
5.17-5.920.23011970.186137363933100
5.92-7.450.25541790.199637953974100
7.46-71.960.21072310.16413864409599
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)
11.448-0.864-0.16836.35081.65782.8090.05150.16770.3063-0.60610.2654-0.4912-0.90280.3594-0.32970.7673-0.12120.17940.6105-0.14460.666132.131589.232750.5893
22.56220.4042-1.07695.0924-0.00221.94820.1909-0.2941-0.01880.3977-0.08310.01070.05850.2959-0.08410.62570.0654-0.01250.6676-0.15670.611130.068373.782858.8678
31.7179-0.96720.05344.80480.17335.01910.30860.0070.30960.3718-0.00630.3965-0.5947-0.1433-0.23270.62790.07960.14870.5698-0.13460.782117.166384.08466.6789
41.9341-0.88890.04086.46821.35513.1680.0291-0.330.32491.10450.14120.0976-0.1949-0.043-0.18890.74270.01750.19160.7308-0.15030.667419.094882.832373.0826
50.76661.36261.01566.27074.34543.12480.0354-0.1022-0.1510.46960.34-0.41860.53420.7293-0.42920.50540.1721-0.08260.6471-0.1450.718632.542561.772261.4942
67.1457-1.5056-0.63195.53550.72716.39790.07830.25890.8322-0.6287-0.00980.2412-1.1513-0.1836-0.0510.66930.02390.0080.44980.0040.587715.639869.79119.0165
72.60110.05030.01012.67011.8224.1656-0.03870.08060.0779-0.18370.0751-0.0112-0.3556-0.0339-0.04040.45770.01720.01960.5526-0.09260.564319.990655.906725.1495
84.9252-2.15691.48033.9037-0.33644.0223-0.10150.0115-0.14540.2917-0.02810.6403-0.2954-1.30680.1150.61130.09960.09650.9698-0.20370.68576.020259.759242.5586
91.5041-1.3679-1.17464.73083.13036.3907-0.1747-0.3114-0.16170.69820.29710.06340.79070.3462-0.1480.4622-0.0040.0080.5832-0.03750.644420.879841.163431.0778
102.4799-0.5311-0.42583.50810.36012.5470.00570.22390.136-0.28710.085-0.1211-0.36150.139-0.07880.5344-0.10810.05760.5883-0.05330.51320.194832.7221-12.1137
111.3668-0.77070.03232.12831.12872.3345-0.0371-0.09450.10180.0856-0.04190.1636-0.0675-0.29670.08040.4066-0.07330.03430.4694-0.04550.51337.875525.66013.064
125.8706-2.7197-0.12998.8234-0.01542.282-0.00570.88520.2542-0.69780.2060.2618-0.0413-0.2125-0.18730.7115-0.16620.06651.0020.04790.518417.25129.2329-44.3123
133.07720.2885-0.38561.8820.00712.9827-0.10150.5772-0.1198-0.46040.2466-0.28370.2360.1607-0.1340.7498-0.08650.10640.8185-0.25220.617222.8086-2.6684-34.3624
145.2126-3.9310.1867.3759-1.2540.36960.27850.55-0.7521-0.4481-0.22031.00010.5374-0.3755-0.04270.8289-0.2194-0.01090.9664-0.2420.7611.9302-6.619-25.2446
152.9394-0.9230.08122.35250.02273.7358-0.25950.2613-0.22170.19290.27870.19930.3457-0.5039-0.02250.7435-0.1890.05130.6884-0.12580.62848.7308-2.0239-21.015
165.19340.1747-3.05962.4404-0.36834.3676-0.3929-0.0342-0.85780.04320.2813-0.19680.87190.8145-0.02711.01580.14740.00560.6753-0.26740.879930.4127-17.4185-24.544
172.2748-0.2365-0.29812.430.53432.27380.132-0.51370.19970.78210.072-0.2306-0.77750.6676-0.20861.5668-0.1928-0.08581.2767-0.25281.120827.494692.652981.4295
18-0.0208-0.1849-0.57564.5655.02945.6893-0.1972-0.01410.00610.77271.0042-0.71260.98121.3954-0.93130.72510.12720.00521.0004-0.31440.94243.020827.83283.8589
194.0061.3961-2.15845.73230.17654.8844-0.56870.5838-0.5099-0.28260.396-0.18461.6198-0.22870.11721.0927-0.14930.13890.7106-0.17570.676.646754.155869.4953
207.770.99735.58636.3936-2.487.635-0.1114-0.34590.35660.6932-0.2489-0.9282-0.42091.22430.33270.9150.1536-0.09550.9893-0.03040.819116.82463.8123102.4174
215.99060.75133.78954.9844-2.09246.64560.3566-0.2762-0.86010.766-0.2073-0.94260.90511.6979-0.09851.34470.39570.031.00590.07340.976812.171651.7152105.1972
224.60742.6192-2.44795.7888-2.01054.5208-0.34210.1659-0.4980.6540.4105-0.0581.0192-0.3288-0.10431.18130.07280.15530.58460.01070.7549-5.881854.241996.875
233.3450.1272-2.58840.26641.06497.2487-0.29750.09-0.46870.16430.407-0.06711.1562-0.0916-0.13231.01460.05790.0130.53020.02590.67741.324957.633287.4322
246.32430.63991.30485.17080.15256.6401-0.2110.1330.04720.77490.49580.08321.0833-0.2422-0.31510.7775-0.00060.02180.7158-0.06010.8233-4.758259.346983.0705
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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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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