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- PDB-8a0l: Tubulin-CW1-complex -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 8a0l
TitleTubulin-CW1-complex
Components
  • (Tubulin beta-2B ...) x 2
  • Stathmin-4
  • Tubulin alpha-1B chain
KeywordsCELL CYCLE / TUBULIN FOLD / CYTOSKELETON / MICROTUBULE
Function / homology
Function and homology information


tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / tubulin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein modification process / spindle microtubule / structural constituent of cytoskeleton ...tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / tubulin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein modification process / spindle microtubule / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron projection development / microtubule cytoskeleton / nervous system development / mitotic cell cycle / growth cone / microtubule / neuron projection / protein heterodimerization activity / nucleotide binding / GTPase activity / 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. / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / 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-KLC / 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: 1.9981 Å
AuthorsProta, A.E. / Diaz, J.F. / Steinmetz, M.O. / Oliva, M.A.
Funding support Spain, European Union, Switzerland, 6items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2019-104545RBI00/AEI/10.13039/501100011033 Spain
European Commission2020/2094European Union
H2020 Marie Curie Actions of the European Commission860070 TubInTrainEuropean Union
Swiss National Science Foundation31003A_166608 Switzerland
European CommissionHPRN-CT-2000-18European Union
European CommissionHPRN-CT-2000-00014European Union
CitationJournal: Structure / Year: 2023
Title: Chemical modulation of microtubule structure through the laulimalide/peloruside site.
Authors: Estevez-Gallego, J. / Alvarez-Bernad, B. / Pera, B. / Wullschleger, C. / Raes, O. / Menche, D. / Martinez, J.C. / Lucena-Agell, D. / Prota, A.E. / Bonato, F. / Bargsten, K. / Cornelus, J. / ...Authors: Estevez-Gallego, J. / Alvarez-Bernad, B. / Pera, B. / Wullschleger, C. / Raes, O. / Menche, D. / Martinez, J.C. / Lucena-Agell, D. / Prota, A.E. / Bonato, F. / Bargsten, K. / Cornelus, J. / Gimenez-Abian, J.F. / Northcote, P. / Steinmetz, M.O. / Kamimura, S. / Altmann, K.H. / Paterson, I. / Gago, F. / Van der Eycken, J. / Diaz, J.F. / Oliva, M.A.
History
DepositionMay 28, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 14, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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 beta-2B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,16723
Polymers261,6316
Non-polymers3,53617
Water11,133618
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.630, 156.559, 179.318
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 , 2 types, 3 molecules ACE

#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
#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

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Tubulin beta-2B ... , 2 types, 3 molecules BDF

#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
#4: Protein Tubulin beta-2B chain


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 , 9 types, 635 molecules

#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine 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.: 4 / 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-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


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


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#11: Chemical ChemComp-KLC / (3~{S},4~{R},8~{S},10~{S},12~{S},14~{S})-14-[(~{Z},4~{R})-4-(hydroxymethyl)hex-2-en-2-yl]-4,12-dimethoxy-9,9-dimethyl-3,8,10-tris(oxidanyl)-1-oxacyclotetradecan-2-one


Mass: 460.601 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H44O8 / Feature type: SUBJECT OF INVESTIGATION
#12: 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
#13: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 618 / 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: 6.7
Details: 11% PEG 4K, 10% 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 / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Mar 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9981→47.507 Å / Num. obs: 198578 / % possible obs: 100 % / Redundancy: 13.473 % / Biso Wilson estimate: 50.54 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.129 / Rrim(I) all: 0.134 / Χ2: 0.778 / Net I/σ(I): 14.7
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
2-2.0513.1734.2290.6319153514550145400.1814.39899.9
2.05-2.1113.3153.1320.9118839614156141490.313.257100
2.11-2.1712.582.3831.1817373213817138100.4252.48599.9
2.17-2.2413.1341.8291.6117611513414134090.5911.903100
2.24-2.3114.0311.4572.1118199212974129710.721.511100
2.31-2.3914.3191.122.8418004212576125740.821.161100
2.39-2.4814.2290.8393.817347712196121920.8930.87100
2.48-2.5814.1350.6514.8316491311669116670.9310.675100
2.58-2.713.9850.4966.3415740511258112550.9580.514100
2.7-2.8313.7350.3668.3314766810752107510.9760.38100
2.83-2.9813.1640.25711.3713485210247102440.9860.267100
2.98-3.1612.5580.16816.22121836970597020.9940.176100
3.16-3.3813.3450.11822.86121822913091290.9970.123100
3.38-3.6514.2610.08133.05121719853785350.9980.084100
3.65-413.9080.05843.24109411786878670.9990.06100
4-4.4713.4610.04551.1596086713971380.9990.047100
4.47-5.1612.9820.03956.3982070632263220.9990.041100
5.16-6.3211.5250.04349.9862201539953970.9990.045100
6.32-8.9413.2650.03361.68562424243424010.03599.9
8.94-47.50712.5550.02770.58304202444242310.02899.1

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
XSCALEdata scaling
PDB_EXTRACT3.28data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5LXT

5lxt


Resolution: 1.9981→47.507 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2259 --
Rwork0.1878 --
obs-198578 99.8 %
Refinement stepCycle: final / Resolution: 1.9981→47.507 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17388 0 215 618 18221
Biso mean--60.01 57.31 -
Num. residues----2197
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9981-2.02080.38213110.3909591695
2.0208-2.04460.34193300.34156232100
2.0446-2.06950.36173250.3296229100
2.0695-2.09570.36123310.31746267100
2.0957-2.12330.34283280.31036212100
2.1233-2.15240.3393260.29636237100
2.1524-2.18310.31643300.28256275100
2.1831-2.21570.29663300.26826237100
2.2157-2.25030.29153280.25286224100
2.2503-2.28720.28543290.2496264100
2.2872-2.32670.29523310.23376289100
2.3267-2.3690.2443260.21956222100
2.369-2.41460.26483320.21856287100
2.4146-2.46380.24893280.20626229100
2.4638-2.51740.25273310.2056271100
2.5174-2.5760.26283300.19756292100
2.576-2.64040.22523280.19586264100
2.6404-2.71180.24893320.19996271100
2.7118-2.79150.23373300.19486286100
2.7915-2.88160.25213310.2046292100
2.8816-2.98460.23653320.26310100
2.9846-3.10410.23613300.18966287100
3.1041-3.24530.2373330.1856305100
3.2453-3.41640.20453340.18716338100
3.4164-3.63040.22453320.17546325100
3.6304-3.91050.22673350.16026350100
3.9105-4.30380.19583340.15416364100
4.3038-4.92610.18093380.13796410100
4.9261-6.20420.1933390.17016450100
6.2042-47.5070.18883520.17496673100
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)
11.1848-0.0983-0.3612.65061.20542.9665-0.01490.0830.1342-0.19370.2532-0.261-0.44720.2974-0.20920.4055-0.0280.04010.3794-0.11590.380828.634785.182153.735
21.2601-0.2285-0.23222.87530.87032.95150.1987-0.07150.01910.5477-0.11430.18740.0729-0.0364-0.05580.51720.00440.04540.3839-0.11050.408918.541384.147371.6981
30.64770.07260.13452.5371.41761.9753-0.0007-0.11150.01690.63760.07610.00860.28290.0762-0.0610.53790.0570.0190.4035-0.06880.370123.253276.258869.6784
41.6399-0.27-0.35722.17211.06262.44550.070.15880.1096-0.1356-0.06780.0643-0.3461-0.1113-0.02180.27040.00350.01910.3341-0.0650.311919.073459.241621.8611
51.9069-0.72-0.58691.84450.79121.43610.00760.1278-0.002-0.0131-0.17270.31690.0159-0.4320.13320.3898-0.0140.03870.4856-0.15640.40649.496559.110738.2046
60.3698-0.00640.16291.7891.18192.4612-0.0022-0.07860.03230.4209-0.07860.12040.2191-0.22770.05930.2961-0.03420.03710.3292-0.05120.347215.219449.894138.3565
71.2549-0.2199-0.11371.98290.28481.5963-0.00290.11190.1017-0.17350.0736-0.0756-0.10580.1069-0.06720.2426-0.05960.03630.3268-0.04260.300920.505732.5124-11.976
80.8648-0.42750.14271.26730.83961.4349-0.0029-0.02610.0370.0722-0.03570.06810.1041-0.21630.03480.2429-0.05770.03610.3106-0.03230.33668.013225.383.1254
92.6497-0.39350.5511.8150.34762.2069-0.11710.66410.119-0.30880.11350.06070.0677-0.0697-0.00980.49-0.10120.02670.7227-0.05780.363315.864312.2584-41.9082
102.1654-1.0897-0.59172.2727-0.19720.78940.15320.9629-0.2-0.54770.0682-0.33860.44620.4357-0.17940.6995-0.04620.12540.995-0.31650.559429.76870.6242-46.988
110.94230.3527-0.34551.8950.4221.0265-0.11780.1445-0.0649-0.2590.2459-0.53510.08310.2554-0.10210.52450.02670.06850.6531-0.24240.540530.13772.177-35.3141
121.2439-0.4643-0.14720.5056-0.29920.8968-0.03170.3947-0.4725-0.11280.2114-0.36440.63440.1553-0.18760.7431-0.03180.02490.6039-0.26350.575721.8749-8.8787-32.5171
131.2911-0.0374-0.59321.0468-0.4021.3537-0.02340.3666-0.0703-0.31630.04020.12340.1816-0.46730.01330.4312-0.05910.00550.5721-0.14770.393311.84591.628-32.3041
142.52580.07550.42811.13370.47841.12330.31450.49660.0242-0.1794-0.13680.17510.4455-0.4014-0.14040.5277-0.0809-0.0250.6394-0.10280.42616.6958-3.0157-26.075
150.98460.2757-0.03890.9310.24752.0342-0.05070.2363-0.3801-0.09930.12330.20310.6176-0.4329-0.0120.5549-0.1225-0.00420.4981-0.13610.48948.9344-3.4737-21.3086
162.11960.1543-0.96881.02490.25952.0488-0.1846-0.0501-0.62220.23810.1705-0.34371.07280.5946-0.08840.98870.1986-0.01350.6075-0.24040.827930.9625-17.6003-25.4651
171.4605-0.7758-0.41371.64220.3470.7270.0031-0.2072-0.00720.79530.3819-0.31140.14660.6662-0.34050.9730.0296-0.10150.583-0.19250.60827.724192.22581.5821
180.2273-0.2893-0.29710.80290.71890.9133-0.07550.0472-0.07610.42670.5301-0.39810.6170.7957-0.46060.43370.06940.00890.6793-0.26160.646443.417327.88523.9036
190.2386-0.3485-0.16850.48110.41460.21820.0164-0.041-0.32950.543-0.2034-0.02582.2582-0.6846-0.09871.8412-0.45930.16310.7729-0.17180.69058.303355.26974.6157
201.95750.01191.17911.1091-0.51590.93160.3985-0.38410.37530.1737-0.498-0.18630.11870.3720.18071.3281-0.0005-0.17081.46440.03791.063116.261463.4547108.8946
210.88060.2285-0.31471.29070.38881.4797-0.2541-0.0799-0.5460.24870.3320.14570.8980.3588-0.0821.50380.10460.11221.03580.20621.04223.65348.1091102.2588
221.332-0.4722-0.80021.1799-0.50411.5375-0.39980.0722-0.4951-0.06340.64980.13650.7906-0.3446-0.25681.2379-0.25170.18110.8111-0.01940.7645-0.982258.783787.4954
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 243 )A1 - 243
2X-RAY DIFFRACTION2chain 'A' and (resid 244 through 311 )A244 - 311
3X-RAY DIFFRACTION3chain 'A' and (resid 312 through 437 )A312 - 437
4X-RAY DIFFRACTION4chain 'B' and (resid 2 through 238 )B2 - 238
5X-RAY DIFFRACTION5chain 'B' and (resid 239 through 311 )B239 - 311
6X-RAY DIFFRACTION6chain 'B' and (resid 312 through 438 )B312 - 438
7X-RAY DIFFRACTION7chain 'C' and (resid 1 through 199 )C1 - 199
8X-RAY DIFFRACTION8chain 'C' and (resid 200 through 440 )C200 - 440
9X-RAY DIFFRACTION9chain 'D' and (resid 1 through 64 )D1 - 64
10X-RAY DIFFRACTION10chain 'D' and (resid 65 through 127 )D65 - 127
11X-RAY DIFFRACTION11chain 'D' and (resid 128 through 160 )D128 - 160
12X-RAY DIFFRACTION12chain 'D' and (resid 161 through 215 )D161 - 215
13X-RAY DIFFRACTION13chain 'D' and (resid 216 through 259 )D216 - 259
14X-RAY DIFFRACTION14chain 'D' and (resid 260 through 295 )D260 - 295
15X-RAY DIFFRACTION15chain 'D' and (resid 296 through 399 )D296 - 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 83 )F1 - 83
20X-RAY DIFFRACTION20chain 'F' and (resid 84 through 146 )F84 - 146
21X-RAY DIFFRACTION21chain 'F' and (resid 147 through 283 )F147 - 283
22X-RAY DIFFRACTION22chain 'F' and (resid 284 through 379 )F284 - 379

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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

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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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