[English] 日本語
Yorodumi
- PDB-5s5n: Tubulin-Z165170770-complex -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5s5n
TitleTubulin-Z165170770-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-methyl-4-sulfamoylbenzamide / 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: 2.9 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)264,97523
Polymers261,6316
Non-polymers3,34417
Water1,65792
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.610, 159.430, 179.480
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

-
Components

-
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

-
Non-polymers , 8 types, 109 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-W0Y / N-methyl-4-sulfamoylbenzamide


Mass: 214.242 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10N2O3S / 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.: 92 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
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

-
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: 2.9→63.62 Å / Num. obs: 66075 / % possible obs: 97.4 % / Redundancy: 6.684 % / Biso Wilson estimate: 83.625 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.149 / Rrim(I) all: 0.162 / Χ2: 0.812 / Net I/σ(I): 9.98 / Num. measured all: 441656 / Scaling rejects: 398
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
2.9-2.987.0362.5170.8434833495449510.4912.71899.9
2.98-3.066.9831.8391.1333623481948150.621.98899.9
3.06-3.156.9781.3521.5232771469846960.7541.461100
3.15-3.246.9251.091.931607456645640.8251.179100
3.24-3.356.7660.8222.3529960442944280.8880.891100
3.35-3.476.1120.8012.6426005429742550.8690.87799
3.47-3.66.5090.5843.5327012416141500.9370.63599.7
3.6-3.746.4240.4214.1919061399229670.9540.45774.3
3.74-3.916.6110.3545.4721201385932070.9740.38583.1
3.91-4.16.970.2158.5625470366036540.9910.23299.8
4.1-4.326.9430.15211.424281349734970.9940.164100
4.32-4.596.7950.10414.9422497331333110.9970.11299.9
4.59-4.96.4820.09116.7720309313431330.9970.099100
4.9-5.296.1840.0916.5118058292329200.9970.09899.9
5.29-5.86.5960.09117.4617816270227010.9970.099100
5.8-6.486.9470.08219.3216972244324430.9970.088100
6.48-7.496.730.05725.814792219821980.9980.061100
7.49-9.176.1870.03536.8711459185318520.9990.03899.9
9.17-12.975.8990.02451.4186841472147210.026100
12.97-63.626.0920.02159.92524587086110.02299

-
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

5lxt


Resolution: 2.9→63.62 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 34.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2735 3303 5.01 %
Rwork0.222 62686 -
obs0.2245 65989 97.28 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 228.97 Å2 / Biso mean: 102.87 Å2 / Biso min: 51.88 Å2
Refinement stepCycle: final / Resolution: 2.9→63.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17400 0 220 92 17712
Biso mean--93.81 77.74 -
Num. residues----2197
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.9-2.940.42691430.409626492792100
2.94-2.990.43261370.38726262763100
2.99-3.030.44661240.363426452769100
3.03-3.080.39281460.356326702816100
3.08-3.130.38411460.330126202766100
3.13-3.190.36691410.330826592800100
3.19-3.250.38861420.312426342776100
3.25-3.320.36841370.303226522789100
3.32-3.390.37621410.288926652806100
3.39-3.470.33861310.29862636276798
3.47-3.560.27121480.269826142762100
3.56-3.650.30911300.25812533266398
3.68-3.760.30011030.25161826192998
3.76-3.880.33131310.24472542267397
3.9-4.020.24661010.23282184228597
4.02-4.180.24961220.20626922814100
4.18-4.370.25461280.197527152843100
4.37-4.60.21361560.170126682824100
4.6-4.890.23171360.169626722808100
4.89-5.270.22811490.181927082857100
5.27-5.80.2061460.198827202866100
5.8-6.640.25961560.215727242880100
6.64-8.360.21951630.187427462909100
8.36-63.620.26591460.172128863032100
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.1465-0.8353-0.15846.59631.59413.1382-0.12680.30430.0023-0.66990.2993-0.1779-0.39320.2213-0.18260.819-0.13250.06171.0884-0.09540.641832.342290.658550.3724
23.6616-1.5351-2.2937.5894-2.79234.338-0.1165-0.5997-0.36631.14250.2312-0.38530.631.1360.05520.6428-0.0514-0.00090.687-0.17960.45630.167975.282758.5671
32.30880.2622-0.44584.20890.12417.0201-0.0545-0.17850.10690.1346-0.0620.4246-0.1051-0.63130.10750.5965-0.02430.1090.8425-0.18890.576117.246585.779966.3419
41.2714-1.37560.65756.84151.7321.851-0.4794-0.35320.06611.18410.64580.09820.1699-0.0533-0.16730.88850.01250.17141.3225-0.20870.678919.193584.510372.8489
51.48480.81581.76776.33344.03459.3281-0.2136-0.1643-0.15680.87780.4124-0.16881.01640.9552-0.15930.79040.2249-0.03580.7232-0.1250.72632.497963.29161.3269
65.7966-2.8277-2.21697.57432.36817.66430.24090.71020.3413-0.6553-0.2558-0.1369-1.0617-0.56820.07490.55580.0285-0.05020.7947-0.01160.488616.336970.784518.7565
72.01790.79980.60653.71.04194.70440.0657-0.03740.1258-0.127-0.145-0.0978-0.19670.13670.08010.49690.10770.00640.8236-0.10150.457620.349356.726824.8602
85.9691-3.70130.45554.8756-0.81382.0246-0.1804-0.36570.09550.53180.09020.48680.0746-1.14030.0690.86960.14950.09871.5424-0.28630.75396.258961.236342.3841
90.6925-1.8781-2.19166.62774.11838.1082-0.3232-0.3408-0.11461.35940.05880.24761.26210.21980.21280.6431-0.0588-0.04440.8308-0.04410.55820.970242.063730.4764
101.7967-1.7041-0.3544.8461-0.10112.89270.01510.44680.0129-0.1756-0.0708-0.0882-0.10310.09550.06080.5018-0.13290.03290.8762-0.05060.561220.074433.468-12.1441
111.6376-0.9571-0.00272.52471.12782.7486-0.06790.0108-0.05370.0981-0.04850.1696-0.0136-0.46880.10810.5515-0.15830.08540.8507-0.05790.53577.653526.58643.1017
125.0813-2.9030.49794.74530.90336.4681-0.04760.9140.2393-0.82440.21140.0773-0.5055-0.4497-0.13860.8238-0.22270.15271.2717-0.10470.779516.94439.9434-43.9511
131.81690.0316-0.43442.14850.02933.3541-0.37150.9784-0.4633-0.42780.1325-0.22410.5588-0.30460.18390.9424-0.08490.18491.3134-0.3530.738622.4658-1.9984-34.1842
140.77950.6914-1.14544.3091.19193.0258-0.2114-0.4511-0.088-0.74380.55770.56120.20911.0164-0.31731.0523-0.21880.08311.3358-0.36530.83640.8796-5.3181-24.4057
152.7108-1.1084-0.2912.1056-1.24854.3601-0.36640.0204-0.2784-0.11060.51830.16620.2224-0.9269-0.16460.8204-0.23570.14261.2509-0.24260.75648.4037-1.3089-20.7855
167.1-1.5644-5.40693.7451.31884.1026-0.4317-0.291-0.94180.65370.06170.24110.91040.76250.35070.82280.4365-0.0341.3022-0.33390.885130.0831-16.8905-24.4242
175.8253-1.8368-3.65887.42381.4343.51710.3676-0.55310.15191.9056-0.04730.3596-0.25750.8406-0.2351.0838-0.1323-0.23341.4062-0.0380.651127.980594.608480.8814
18-0.27760.01660.16915.3966.08736.60570.1756-0.1073-0.09820.48390.1168-0.58070.60630.2524-0.70560.97860.06690.06551.5422-0.48491.000942.927828.4853.875
195.60472.033-0.87375.0850.54971.0671-0.74750.3172-0.8608-0.94820.5892-0.00371.2508-0.54260.15451.771-0.28410.32151.6412-0.16710.89496.546256.037369.3468
206.7608-1.35215.64595.4962-3.88216.9190.0808-0.94650.46360.3874-0.2367-0.5142-0.53330.40820.15811.0442-0.120.00471.4630.06930.841616.93765.4585102.2163
218.20631.02333.04965.3845-0.0423.707-0.2106-0.5589-0.91440.7180.1344-0.97360.78131.32040.06981.42050.32780.1731.07830.02720.780112.091853.3409104.9957
222.67052.32810.67752.20570.02474.8954-0.22370.5871-0.54880.32280.3019-0.38911.00060.2633-0.10031.57790.12220.38691.0546-0.12930.9086-1.968251.259799.0921
235.32470.1320.58221.32083.40838.8309-0.7310.1598-0.7957-0.15770.68190.1030.9663-0.54750.05571.529-0.09060.22770.7436-0.00050.74541.280359.588187.3606
244.0339-2.9295-1.30682.41272.23796.1686-0.12751.07490.1458-0.288-0.09070.0033-0.4133-0.88590.05970.8302-0.34870.19411.0051-0.05710.7866-7.17565.217179.0207
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more