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- PDB-6fkl: Tubulin-TUB015 complex -

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Basic information

Entry
Database: PDB / ID: 6fkl
TitleTubulin-TUB015 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 / regulation of microtubule polymerization or depolymerization / microtubule-based process / cytoplasmic microtubule / tubulin binding / cellular response to interleukin-4 / spindle microtubule / protein modification process ...tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / cytoplasmic microtubule / tubulin binding / cellular response to interleukin-4 / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / neuron projection development / mitotic cell cycle / double-stranded RNA binding / microtubule cytoskeleton / growth cone / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / neuron projection / cilium / protein heterodimerization activity / nucleotide binding / GTPase activity / ubiquitin protein ligase binding / GTP binding / Golgi apparatus / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Rossmann fold - #11480 / Helix hairpin bin / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Stathmin family / Stathmin, conserved site / Stathmin superfamily ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Rossmann fold - #11480 / Helix hairpin bin / 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. / ATP-grasp fold, A domain / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / ATP-grasp fold, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / 60s Ribosomal Protein L30; Chain: A; / 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. / Dna Ligase; domain 1 / 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 / Helix non-globular / Special / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / Chem-DLK / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / 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 (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.098 Å
AuthorsProta, A.E. / Steinmetz, M.O. / Priego, E.-M.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_166608 Switzerland
CitationJournal: Sci Rep / Year: 2018
Title: High-affinity ligands of the colchicine domain in tubulin based on a structure-guided design.
Authors: Bueno, O. / Estevez Gallego, J. / Martins, S. / Prota, A.E. / Gago, F. / Gomez-SanJuan, A. / Camarasa, M.J. / Barasoain, I. / Steinmetz, M.O. / Diaz, J.F. / Perez-Perez, M.J. / Liekens, S. / Priego, E.M.
History
DepositionJan 24, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 21, 2018Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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)265,44126
Polymers261,6316
Non-polymers3,81020
Water10,124562
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23340 Å2
ΔGint-165 kcal/mol
Surface area80030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.748, 157.764, 179.971
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 (domestic 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 (domestic cattle) / 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 , 9 types, 582 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.: 5 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: 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
#10: 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
#11: Chemical ChemComp-DLK / 2-{1-[(2-Methoxyphenyl)amino]ethylidene}-5-phenyl-1,3-cyclohexanedione


Mass: 335.396 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H21NO3
#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


Mass: 18.015 Da / Num. of mol.: 562 / Source method: isolated from a natural source / Formula: H2O

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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: 2.84 Å3/Da / Density % sol: 56.72 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 6.7
Details: 5% PEG 4K, 12% glycerol, 30 mM MgCl2, 30 mM CaCl2, 100 mM MES/Imidazole

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00002 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 2, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00002 Å / Relative weight: 1
ReflectionResolution: 2.098→49.44 Å / Num. obs: 171487 / % possible obs: 98.5 % / Redundancy: 12.3 % / Biso Wilson estimate: 39.7 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.033 / Rrim(I) all: 0.114 / Net I/σ(I): 16.7
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 8.5 % / Rmerge(I) obs: 2.142 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 11675 / CC1/2: 0.349 / Rpim(I) all: 0.803 / Rrim(I) all: 2.281 / % possible all: 91.8

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Processing

Software
NameVersionClassification
PHENIX(dev_2863: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4O2B

4o2b


Resolution: 2.098→49.436 Å / SU ML: 0.28 / Cross valid method: FREE R-VALUE / σ(F): 1.28 / Phase error: 23.04
RfactorNum. reflection% reflection
Rfree0.2168 8575 5 %
Rwork0.1784 --
obs0.1803 171487 98.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.098→49.436 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17373 0 235 562 18170
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00318159
X-RAY DIFFRACTIONf_angle_d0.61324666
X-RAY DIFFRACTIONf_dihedral_angle_d14.03810916
X-RAY DIFFRACTIONf_chiral_restr0.0432686
X-RAY DIFFRACTIONf_plane_restr0.0043201
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0979-2.12180.36434800.34829083X-RAY DIFFRACTION85
2.1218-2.14680.32865180.31559840X-RAY DIFFRACTION92
2.1468-2.17290.33965290.31269958X-RAY DIFFRACTION93
2.1729-2.20040.32935190.29619963X-RAY DIFFRACTION94
2.2004-2.22940.2995300.290610107X-RAY DIFFRACTION94
2.2294-2.25990.32465420.281710319X-RAY DIFFRACTION96
2.2599-2.29220.32035450.275810307X-RAY DIFFRACTION97
2.2922-2.32640.30155470.264810410X-RAY DIFFRACTION97
2.3264-2.36280.29075590.251510594X-RAY DIFFRACTION99
2.3628-2.40150.27935600.242110649X-RAY DIFFRACTION100
2.4015-2.44290.26225550.220710710X-RAY DIFFRACTION100
2.4429-2.48740.22585680.205510728X-RAY DIFFRACTION100
2.4874-2.53520.25135610.205510622X-RAY DIFFRACTION100
2.5352-2.58690.24225620.200110668X-RAY DIFFRACTION100
2.5869-2.64320.24355580.200110624X-RAY DIFFRACTION100
2.6432-2.70470.2515680.199410736X-RAY DIFFRACTION100
2.7047-2.77230.24335590.202410648X-RAY DIFFRACTION100
2.7723-2.84720.25315670.198810696X-RAY DIFFRACTION100
2.8472-2.9310.24215660.199110684X-RAY DIFFRACTION100
2.931-3.02560.23915670.186910680X-RAY DIFFRACTION100
3.0256-3.13370.23415620.177510623X-RAY DIFFRACTION100
3.1337-3.25920.2425610.185610714X-RAY DIFFRACTION100
3.2592-3.40750.22555690.178610682X-RAY DIFFRACTION100
3.4075-3.58710.18995640.163810701X-RAY DIFFRACTION100
3.5871-3.81170.18435590.149710639X-RAY DIFFRACTION100
3.8117-4.10590.1885620.142210693X-RAY DIFFRACTION100
4.1059-4.51890.15675670.126510711X-RAY DIFFRACTION100
4.5189-5.17210.1675590.12810628X-RAY DIFFRACTION100
5.1721-6.5140.19575560.160910727X-RAY DIFFRACTION100
6.514-49.44940.17075640.150210642X-RAY DIFFRACTION100
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)
10.8153-0.011-0.20473.15641.29722.2443-0.02740.07560.16-0.34090.3214-0.3615-0.57960.427-0.2540.4511-0.11350.08320.4413-0.16340.414931.591186.255152.6805
21.41440.27810.39662.99920.88693.21340.0639-0.06550.070.4147-0.01690.2223-0.2663-0.1183-0.04670.39490.02020.10280.3052-0.09090.360316.940686.628270.4341
30.84840.2783-0.23232.59261.76264.26350.0714-0.0768-0.17470.58080.2863-0.320.61820.55-0.33210.39090.1192-0.06190.3512-0.12220.397229.446162.310662.3091
41.4866-0.2453-0.15242.48090.72142.34390.0540.11650.2015-0.25920.0404-0.0505-0.45470.1162-0.09120.2789-0.02230.03560.3252-0.08510.321721.178561.127921.1056
51.1366-0.39270.09311.09240.93732.9171-0.0674-0.08590.00980.0681-0.11180.2285-0.1106-0.59950.13980.27630.03010.03970.4307-0.14430.41227.094659.868638.5556
60.7008-0.4839-0.30033.89912.71745.051-0.0037-0.1951-0.05050.73770.0215-0.06070.57780.3462-0.04110.33490.0121-0.04050.3213-0.04440.306522.705137.670431.401
71.1025-0.15320.00581.84650.19631.586-0.03310.18320.127-0.26710.0603-0.0976-0.10370.1527-0.02080.2621-0.05740.03710.3254-0.02960.297120.273132.6046-11.4757
80.9511-0.47850.34671.38740.99491.86090.0041-0.07380.0420.0015-0.14990.25470.0531-0.3870.12380.2009-0.04510.03110.3086-0.03740.31662.44831.29773.4697
91.7223-1.0324-1.1682.70862.60054.19010.0050.0264-0.0810.34610.1154-0.1210.53110.2172-0.12830.32220.0278-0.01780.2535-0.02840.313422.459510.86932.1984
102.9149-0.1952-0.70232.5097-0.54472.20550.04330.56310.0227-0.3540.1246-0.150.12850.0896-0.17140.5382-0.05320.10540.6162-0.15310.336523.89452.4441-39.8025
111.4325-0.4058-0.85851.66770.52522.458-0.09160.4733-0.2075-0.25130.07010.17990.2865-0.39960.01430.4156-0.09190.0120.4583-0.09780.32537.3277-0.5139-24.8135
122.8315-0.8964-1.61512.48081.02713.0565-0.25130.2534-0.7370.01920.0666-0.16350.78960.35480.18020.72690.07680.06930.4737-0.20390.566228.0989-17.9541-25.0411
133.6865-1.11560.52733.2336-4.09056.1897-0.0886-0.43220.2791.54730.1124-0.4679-0.1050.8438-0.13590.9796-0.0396-0.00230.582-0.19110.483824.822995.994783.4315
140.39431.68942.14244.53365.37877.81910.0974-0.13930.13830.22060.6259-0.6830.09050.789-0.74560.30720.01820.01670.8481-0.37310.744943.556855.804434.917
150.3525-1.1664-0.79486.99166.11525.8615-0.09940.0104-0.12270.04110.2912-0.33020.41070.6285-0.32360.5320.06860.16160.6977-0.25410.69242.69196.0811-19.7563
161.89561.639-0.95795.21770.70321.4647-0.61290.5426-0.6719-0.41560.0367-0.19941.7168-0.52490.16681.0605-0.18580.2150.5514-0.16030.51766.392454.725169.5589
171.43020.2704-0.27843.2651-0.6893.3411-0.1766-1.1326-0.66650.5331-0.281-0.84250.66121.87750.4340.86360.3156-0.03871.25260.30820.77715.033457.6408104.7792
183.17840.3735-2.48111.43880.40673.0633-0.705-0.0651-0.8090.2570.27620.0271.1894-0.1199-0.00670.93970.0530.17870.31820.07610.5739-1.643753.787193.1308
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 205)
2X-RAY DIFFRACTION2chain 'A' and (resid 206 through 381)
3X-RAY DIFFRACTION3chain 'A' and (resid 382 through 438)
4X-RAY DIFFRACTION4chain 'B' and (resid 1 through 205)
5X-RAY DIFFRACTION5chain 'B' and (resid 206 through 381)
6X-RAY DIFFRACTION6chain 'B' and (resid 382 through 438)
7X-RAY DIFFRACTION7chain 'C' and (resid 2 through 205)
8X-RAY DIFFRACTION8chain 'C' and (resid 206 through 381)
9X-RAY DIFFRACTION9chain 'C' and (resid 382 through 440)
10X-RAY DIFFRACTION10chain 'D' and (resid 2 through 205)
11X-RAY DIFFRACTION11chain 'D' and (resid 206 through 381)
12X-RAY DIFFRACTION12chain 'D' and (resid 382 through 440)
13X-RAY DIFFRACTION13chain 'E' and (resid 6 through 27)
14X-RAY DIFFRACTION14chain 'E' and (resid 44 through 89)
15X-RAY DIFFRACTION15chain 'E' and (resid 90 through 143)
16X-RAY DIFFRACTION16chain 'F' and (resid 1 through 66)
17X-RAY DIFFRACTION17chain 'F' and (resid 67 through 198)
18X-RAY DIFFRACTION18chain 'F' and (resid 199 through 380)

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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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