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- PDB-5s5g: Tubulin-Z1129283193-complex -

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Open data


ID or keywords:

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Basic information

Entry
Database: PDB / ID: 5s5g
TitleTubulin-Z1129283193-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-(4-methylpyridin-3-yl)acetamide / 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: 2.69 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)264,69722
Polymers261,6316
Non-polymers3,06516
Water6,666370
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)104.645, 157.922, 179.187
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, 386 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-SZY / N-(4-methylpyridin-3-yl)acetamide


Mass: 150.178 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10N2O / 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.: 370 / 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: Dec 13, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91587 Å / Relative weight: 1
ReflectionResolution: 2.93→72.26 Å / Num. obs: 65335 / % possible obs: 99.5 % / Redundancy: 6.795 % / Biso Wilson estimate: 55.051 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.178 / Rrim(I) all: 0.193 / Χ2: 0.868 / Net I/σ(I): 7.72 / Num. measured all: 443945 / Scaling rejects: 18
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
2.93-36.9910.8512.2132654478146710.7660.91897.7
3-3.097.1130.6692.8133039464846450.8440.72199.9
3.09-3.187.0430.5433.3431862454445240.8960.58699.6
3.18-3.277.0450.4563.9231140444044200.9180.49299.5
3.27-3.386.9490.3734.6629687428042720.9420.40399.8
3.38-3.56.8280.3115.4728187413541280.9490.33699.8
3.5-3.636.4290.263625852402940210.9590.28699.8
3.63-3.786.5970.2346.8525372384938460.970.25499.9
3.78-3.956.8620.1888.4125512372037180.9780.20399.9
3.95-4.147.0770.1659.5625110355235480.9820.17899.9
4.14-4.376.9870.14710.5523734339933970.9860.15999.9
4.37-4.636.8460.12911.8522003321632140.9860.13999.9
4.63-4.956.7110.12612.1520166300730050.9840.13799.9
4.95-5.356.1740.12711.217528284028390.9840.138100
5.35-5.866.3690.12911.0916750263126300.9860.141100
5.86-6.556.9820.12911.6516498236323630.9860.139100
6.55-7.566.7620.11613.1114274211221110.9890.125100
7.56-9.266.3330.10315.0311367179917950.9860.11299.8
9.26-13.15.8730.09216.598433144414360.990.10199.4
13.1-72.266.3520.08317.4747778497520.9920.0988.6

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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

5lxt


Resolution: 2.69→72.26 Å / SU ML: 0.42 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2712 1949 2.41 %
Rwork0.2175 78868 -
obs0.2188 80817 97.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 192.48 Å2 / Biso mean: 51.956 Å2 / Biso min: 15.36 Å2
Refinement stepCycle: final / Resolution: 2.69→72.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17416 0 193 370 17979
Biso mean--43.43 35.68 -
Num. residues----2200
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.69-2.760.39561340.37165345547993
2.76-2.830.41021330.35525393552695
2.83-2.920.3711380.34065505564396
2.92-3.010.42181310.29955485561696
3.01-3.120.31071370.27825557569497
3.12-3.240.26671380.2645613575197
3.24-3.390.34141370.24715602573998
3.39-3.570.31041400.23045651579198
3.57-3.790.26931380.22795580571897
3.79-4.080.25561430.17715706584999
4.08-4.490.22021430.15715771591499
4.5-5.150.20711430.155767591099
5.15-6.480.23221450.19275853599899
6.48-72.260.20081490.1776040618999
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)
10.84630.04490.24073.39880.8462.0623-0.02370.20990.2291-0.62720.3698-0.2952-0.76750.2733-0.25020.5481-0.12020.14840.365-0.13930.393732.175589.733650.3728
21.3284-0.2673-1.37784.6874-0.10282.51230.4362-0.2223-0.18830.5874-0.2308-0.33070.25210.212-0.13140.31970.025-0.0350.305-0.15810.31430.186674.350358.6531
31.57450.154-0.2584.26121.02124.17460.0842-0.05050.07330.2911-0.04540.3558-0.3171-0.1868-0.05520.30520.02380.06030.2547-0.09210.3317.248284.635666.466
40.7978-0.1020.28483.43620.92252.6585-0.0464-0.1999-0.00950.99420.09090.3251-0.0996-0.0096-0.04850.4284-0.01790.10630.3616-0.10370.318319.202683.403672.8952
51.88140.39850.13383.55012.20232.6540.1207-0.0914-0.00430.71680.3875-0.34090.83591.0365-0.32970.39890.1326-0.0720.3208-0.11150.419232.673462.375561.2941
64.7365-1.4375-0.51255.55480.50922.36890.16070.15880.6453-0.368-0.19450.4241-1.0005-0.22760.13480.51410.02940.00590.2895-0.03060.415216.043470.116618.9932
71.53480.04140.50712.36961.40673.59130.0431-0.09940.1601-0.0249-0.11390.0781-0.304-0.0654-0.0220.2322-0.00650.02580.2771-0.09270.281920.292256.167525.1262
83.622-1.60770.66632.9512-0.392.1567-0.1207-0.02930.02220.1749-0.09320.563-0.2346-0.96420.13740.36980.07390.05160.6228-0.18920.4375.929660.287542.1787
90.643-0.8311-0.53623.56321.96413.76820.0008-0.178-0.01260.5750.05690.05720.45380.2645-0.04160.2338-0.0308-0.02920.2764-0.04360.313521.090841.398930.7332
101.1796-0.666-0.05663.42010.35071.3866-0.09630.16150.0755-0.19990.1735-0.0237-0.10190.0291-0.05920.1981-0.06580.02230.2709-0.04580.246720.118833.0111-12.0307
111.196-0.6406-0.13751.79930.90821.4604-0.0166-0.00090.01410.0961-0.0560.12250.0548-0.20070.04630.1944-0.04970.04860.2407-0.02490.24717.818325.99153.1668
124.0775-1.7606-0.60366.03821.75094.4563-0.09920.99890.251-0.80990.2272-0.002-0.1156-0.4158-0.07680.4359-0.1020.04760.6579-0.03340.276717.23389.6301-43.9558
131.30460.0842-0.18031.8960.33252.6266-0.10020.442-0.1726-0.17240.1349-0.1110.33490.0973-0.00740.3651-0.01690.06710.5176-0.19420.36422.7387-2.3342-34.1299
141.29390.1250.13473.06061.54862.36470.11760.257-0.6512-0.32-0.17560.87630.5774-0.69550.030.4794-0.13530.02480.6284-0.2050.51651.2968-5.983-25.2617
152.0476-0.86990.0152.55360.13812.4051-0.17110.3797-0.2063-0.1440.13410.12350.4255-0.42360.15990.4538-0.12550.04120.3814-0.11730.34738.6707-1.6772-20.7886
160.96620.64560.60052.5258-0.41450.7829-0.41140.2217-0.8630.2604-0.16890.06490.64760.3030.13510.59630.03910.02330.4365-0.26380.59930.2651-17.2204-24.3552
172.4265-2.5481-1.02114.89573.36913.6409-0.1498-0.32790.06221.41430.2653-0.43650.62660.6478-0.17690.9238-0.1308-0.01620.5489-0.23280.515827.880693.100481.3425
180.3108-0.1944-0.30860.21490.0598-0.0184-0.0007-0.0281-0.07080.44980.5936-0.69010.66650.8689-0.49930.42120.10830.01740.6976-0.27440.589743.009428.08753.9555
191.53270.5863-1.20973.70070.61531.3028-0.5770.7315-0.504-0.49180.3167-0.07321.3544-0.65220.08431.0836-0.28010.2270.6356-0.17490.52266.664754.840969.4517
203.8076-0.1743.85543.5616-2.21916.58040.0234-0.33320.31360.543-0.3339-0.8495-0.35541.78690.25020.640.0256-0.10590.9933-0.00320.593915.982864.68102.4799
214.9820.84632.14683.706-0.35333.38730.0093-0.5161-0.67510.5842-0.2125-0.96711.14671.39360.1760.90310.339-0.00360.87330.12770.728512.096452.2181105.0815
221.90310.8798-0.35751.2161-0.22421.2742-0.40360.069-0.91140.31330.2643-0.23721.15910.0229-0.30011.1870.15270.22210.35930.08630.8361-1.89149.994599.1042
232.62890.8695-1.43431.37860.09411.1294-0.48130.1618-0.4139-0.2020.3117-0.10710.7946-0.20550.07060.7021-0.07710.13040.33970.01690.41811.322658.344387.3526
244.5465-1.85460.28421.7744-1.37122.70550.2950.93030.0055-0.38590.29660.5843-0.4881-0.955-0.43420.4574-0.1198-0.01590.65560.08950.5588-7.006163.871378.9765
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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