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- PDB-5s67: Tubulin-Z1896597864-complex -

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Basic information

Entry
Database: PDB / ID: 5s67
TitleTubulin-Z1896597864-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 / 1-(6-methoxypyridin-2-yl)-N-methylmethanamine / 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: 2.1 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)264,69922
Polymers261,6316
Non-polymers3,06716
Water7,368409
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.900, 158.960, 179.980
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, 425 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-X1M / 1-(6-methoxypyridin-2-yl)-N-methylmethanamine


Mass: 152.194 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H12N2O / 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.: 409 / 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: 2.1→62.75 Å / Num. obs: 172579 / % possible obs: 98.4 % / Redundancy: 6.664 % / Biso Wilson estimate: 57.823 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.087 / Rrim(I) all: 0.094 / Χ2: 1.023 / Net I/σ(I): 11.66 / Num. measured all: 1150032 / Scaling rejects: 313
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
2.1-2.155.952.7080.637610212831127910.2452.97399.7
2.15-2.216.3452.0450.887943812546125190.372.2399.8
2.21-2.286.2842.4530.776499512218103430.3742.67484.7
2.28-2.357.0651.1941.638315211798117690.6321.28899.8
2.35-2.427.0280.9052.158074311505114890.7560.97799.9
2.42-2.516.9050.6712.857664511108111000.840.72599.9
2.51-2.66.7660.5123.687279210770107580.8960.55599.9
2.6-2.716.5010.44.586698910309103040.9290.435100
2.71-2.836.7740.296.2767345995399420.9640.31499.9
2.83-2.977.0520.218.5966839948494780.9820.22799.9
2.97-3.136.9660.14212.0363075906190550.9910.15399.9
3.13-3.326.850.10315.8458749858585770.9950.11299.9
3.32-3.556.4710.07719.5252146806580590.9970.08499.9
3.55-3.836.670.06124.5645736753468570.9980.06691
3.83-4.26.860.04831.0147790697169660.9980.05299.9
4.2-4.76.7880.03936.6842773630563010.9990.04299.9
4.7-5.426.2420.03736.6634994561056060.9990.04199.9
5.42-6.646.8570.03937.4832674476547650.9990.042100
6.64-9.396.420.03244.3724042375337450.9990.03599.8
9.39-62.756.0390.02751.6813013217021550.9990.0399.3

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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: 2.1→62.75 Å / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.32 / Phase error: 28.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2378 8543 4.95 %
Rwork0.2102 163896 -
obs0.2116 172439 98.35 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 201.71 Å2 / Biso mean: 69.3772 Å2 / Biso min: 33.47 Å2
Refinement stepCycle: final / Resolution: 2.1→62.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17439 0 195 409 18043
Biso mean--64.51 58.09 -
Num. residues----2203
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 (%)
2.1-2.120.39853020.376154805782100
2.12-2.150.36222570.355755065763100
2.15-2.180.37622980.348154585756100
2.18-2.20.35512830.332554875770100
2.2-2.230.31722790.316355155794100
2.23-2.260.57081830.54633657384066
2.26-2.290.33372460.30585480572699
2.29-2.330.30293020.29855205822100
2.33-2.370.31952670.287954795746100
2.37-2.40.32782660.279955485814100
2.4-2.450.31232810.268455295810100
2.45-2.490.31032800.261354965776100
2.49-2.540.29332850.260755295814100
2.54-2.590.28472780.241755035781100
2.59-2.650.28213290.248355105839100
2.65-2.710.27613030.249254885791100
2.71-2.780.28822990.252255185817100
2.78-2.850.28262790.243755545833100
2.85-2.930.27493120.245355105822100
2.93-3.030.26452740.241755405814100
3.03-3.140.2953170.234854985815100
3.14-3.260.26752810.233255915872100
3.26-3.410.26553230.225755185841100
3.41-3.590.26213080.212655785886100
3.59-3.820.22682480.20274931517988
3.82-4.110.20972880.179255885876100
4.11-4.520.17682880.160956645952100
4.52-5.180.17232830.153756175900100
5.18-6.520.22172990.193457196018100
6.52-62.750.17143050.16365885619099
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)
11.3856-0.1620.0554.1490.77792.8521-0.03120.11630.1808-0.49110.3468-0.3963-0.85350.3404-0.320.6903-0.1520.15670.4989-0.13860.462432.260290.048250.6088
24.2497-0.8898-2.80734.6362-0.88922.60440.0649-0.18580.0270.33830.0069-0.13150.15140.1983-0.05590.44910.0363-0.00840.4277-0.13610.402130.062774.684558.9528
32.0540.27730.43313.21531.02244.59080.10020.05130.06970.2122-0.06310.267-0.1427-0.181-0.04360.43370.01970.06740.3263-0.09280.431317.152485.209166.6591
41.2991-1.04640.1256.55511.64592.7326-0.0653-0.16380.15130.76760.07260.1847-0.102-0.0177-0.00870.4996-0.02470.10270.4352-0.08240.477519.01983.982173.1233
52.25860.49621.46625.24743.88528.89270.1537-0.1025-0.07590.66670.3916-0.58470.78990.6496-0.51720.49160.101-0.05320.3857-0.10080.553132.419262.74261.6785
65.9234-1.8535-0.97158.16311.345.45540.11120.1920.8136-0.2594-0.08170.2667-1.0384-0.13250.0080.5091-0.00390.00490.4473-0.00060.491316.083370.346619.1629
72.2457-0.0087-0.09682.1861.30433.27240.01480.0530.0960.0133-0.04450.0052-0.2080.02790.00990.3374-0.00530.01630.4198-0.0770.43220.178356.325725.2789
84.1896-1.82371.90014.1055-0.53523.898-0.1927-0.271-0.10490.12040.04150.572-0.1283-1.17320.14930.46720.02790.05680.6624-0.15720.52015.820560.669542.3523
90.9295-1.5373-0.73074.64322.95774.5544-0.0535-0.2129-0.07530.7170.14140.0040.70110.3136-0.08940.3468-0.04510.00210.4407-0.04850.455420.747941.723531.3252
101.5185-0.26280.11222.24890.19272.1245-0.06440.16790.1341-0.23980.1115-0.0237-0.18640.0947-0.04570.3599-0.06560.02570.4148-0.02970.397320.080633.4494-12.1637
111.1991-0.6353-0.04371.90280.87831.783-0.0123-0.02610.04860.1124-0.06370.13010.0547-0.23870.0770.2921-0.06250.03080.359-0.02210.37597.645726.38353.0268
124.5826-1.93960.15916.85470.67362.1224-0.05940.69610.1756-0.69850.05560.1105-0.103-0.2807-0.00710.6152-0.07890.02750.7847-0.01920.322317.202810.1157-44.1559
131.49850.0573-0.16271.18390.27852.4697-0.03990.4559-0.1619-0.32690.1165-0.22840.30330.0991-0.07490.6071-0.0240.06270.6088-0.16450.487622.6699-1.9575-34.3886
142.5631-1.5341-0.87895.81681.01871.2210.0050.7787-0.4438-0.5016-0.27740.71410.4178-0.78630.13370.6884-0.1481-0.01110.898-0.22910.62271.2688-5.7174-25.5506
152.2129-0.6229-0.74461.64410.74432.838-0.19820.3518-0.31920.00130.12450.25320.2926-0.3280.09940.5168-0.12540.01930.4401-0.12380.47768.5359-1.3018-20.9966
163.4486-0.0888-2.04272.71870.66663.5139-0.42970.0579-0.85470.03690.0938-0.28310.77240.32470.07970.78840.12360.02010.5705-0.2080.838230.135-16.8719-24.7006
173.8079-1.62960.67425.42260.91821.76230.1671-0.34160.34991.10960.1849-0.4826-0.22890.2466-0.39450.9185-0.1128-0.02430.6479-0.18820.546327.799893.524881.6031
180.1155-0.1162-0.35644.91084.93385.6076-0.1233-0.0215-0.00650.67790.5726-0.41340.78920.9545-0.57250.4630.11360.01680.8087-0.22390.715142.934928.2543.9804
193.20912.0855-1.23116.14421.01364.1308-0.58520.3826-0.6433-0.39080.212-0.4571.3415-0.20390.28370.9882-0.13870.13980.597-0.14620.6486.491255.36269.9131
206.19450.3153.12514.2412-1.86122.8866-0.2327-0.66920.26150.6625-0.093-1.1284-0.36571.43290.35020.75950.0143-0.15610.99840.01730.755816.794865.2909102.7537
214.31230.24032.23784.2781-0.65746.32-0.2184-0.4148-0.30090.8582-0.1911-0.91580.48211.68480.36020.96060.2647-0.01430.97650.20890.827111.977953.3397106
221.84730.7055-1.31273.2907-0.41061.9956-0.4223-0.0563-0.65810.46530.2001-0.29110.9160.02420.14111.13880.08070.16140.50360.0850.8579-1.835750.752999.7898
232.8180.0403-1.88520.87040.69345.1272-0.32620.1597-0.53050.01040.207-0.00830.8696-0.03680.06850.7999-0.01780.05970.4380.01150.59771.235159.009787.8667
246.6844-3.7817-3.23773.72231.13832.941-0.11020.6697-0.1925-0.08050.36530.2311-0.4533-1.2337-0.21980.5293-0.1506-0.03610.66120.02330.6665-8.157763.791779.6527
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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Yorodumi

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  • 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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