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- PDB-6fkj: Tubulin-TUB075 complex -

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Basic information

Entry
Database: PDB / ID: 6fkj
TitleTubulin-TUB075 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-DLW / 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: 2.148 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.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)265,66427
Polymers261,6316
Non-polymers4,03221
Water10,629590
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23820 Å2
ΔGint-157 kcal/mol
Surface area80480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.670, 157.562, 180.100
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) / 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 , 10 types, 611 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-DLW / (5~{S})-2-[(~{E})-~{N}-(2-ethoxyphenyl)-~{C}-methyl-carbonimidoyl]-3-oxidanyl-5-phenyl-cyclohex-2-en-1-one / KNI-10075


Mass: 349.423 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H23NO3
#10: 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
#11: 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
#12: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#13: 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
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 590 / 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: 56.66 %
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: 2.148→49.45 Å / Num. obs: 161351 / % possible obs: 99.5 % / Redundancy: 12.5 % / Biso Wilson estimate: 42.5 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.114 / Rpim(I) all: 0.034 / Rrim(I) all: 0.118 / Net I/σ(I): 16.6
Reflection shellResolution: 2.15→2.21 Å / Redundancy: 8.9 % / Rmerge(I) obs: 2.429 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 11396 / CC1/2: 0.3 / Rpim(I) all: 0.884 / Rrim(I) all: 2.577 / % possible all: 96.3

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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: 2.148→49.445 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.11 / Phase error: 22.25
RfactorNum. reflection% reflection
Rfree0.2064 15592 5.01 %
Rwork0.1747 --
obs0.1763 161351 99.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.148→49.445 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17381 0 250 590 18221
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00418026
X-RAY DIFFRACTIONf_angle_d0.71924431
X-RAY DIFFRACTIONf_dihedral_angle_d16.18510773
X-RAY DIFFRACTIONf_chiral_restr0.0462650
X-RAY DIFFRACTIONf_plane_restr0.0043164
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1478-2.17220.35334730.33518999X-RAY DIFFRACTION90
2.1722-2.19770.35655020.33249482X-RAY DIFFRACTION96
2.1977-2.22450.33655030.31279569X-RAY DIFFRACTION96
2.2245-2.25270.31865100.30039684X-RAY DIFFRACTION98
2.2527-2.28230.34385170.30059708X-RAY DIFFRACTION98
2.2823-2.31360.30695110.28369818X-RAY DIFFRACTION99
2.3136-2.34670.30065240.27049838X-RAY DIFFRACTION99
2.3467-2.38170.27665180.253910015X-RAY DIFFRACTION100
2.3817-2.41890.27925240.24759946X-RAY DIFFRACTION100
2.4189-2.45860.25655280.22889902X-RAY DIFFRACTION100
2.4586-2.5010.25245270.22869956X-RAY DIFFRACTION100
2.501-2.54640.26055210.22489937X-RAY DIFFRACTION100
2.5464-2.59540.25035170.21069910X-RAY DIFFRACTION100
2.5954-2.64840.24495270.20419961X-RAY DIFFRACTION100
2.6484-2.7060.22715140.19549939X-RAY DIFFRACTION100
2.706-2.76890.25355340.19719933X-RAY DIFFRACTION100
2.7689-2.83810.23055230.1929951X-RAY DIFFRACTION100
2.8381-2.91490.22195230.19019922X-RAY DIFFRACTION100
2.9149-3.00060.21945300.18459988X-RAY DIFFRACTION100
3.0006-3.09750.19655180.16739923X-RAY DIFFRACTION100
3.0975-3.20820.22865240.17749933X-RAY DIFFRACTION100
3.2082-3.33660.21295240.17639918X-RAY DIFFRACTION100
3.3366-3.48840.20255270.16559983X-RAY DIFFRACTION100
3.4884-3.67220.18385240.15489896X-RAY DIFFRACTION100
3.6722-3.90220.17525190.14359952X-RAY DIFFRACTION100
3.9022-4.20340.17165310.13839972X-RAY DIFFRACTION100
4.2034-4.62610.1595130.12439907X-RAY DIFFRACTION100
4.6261-5.29490.15355240.1299942X-RAY DIFFRACTION100
5.2949-6.66840.20685280.1639929X-RAY DIFFRACTION100
6.6684-49.45830.15535340.14619924X-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)
11.0767-0.0232-0.20913.46861.27632.4461-0.03450.08810.1577-0.37430.3545-0.4148-0.63660.4595-0.28510.4747-0.11930.08320.4706-0.18080.431631.465586.1552.783
21.61160.14580.263.29371.18133.40780.0339-0.13290.05920.4293-0.00420.1692-0.1938-0.115-0.02030.40740.01690.09150.3239-0.09390.350316.779386.47570.4654
30.90410.0107-1.02022.72962.62665.28060.0774-0.0881-0.14520.58830.4149-0.40210.58930.7021-0.48790.45460.1402-0.07420.4291-0.12860.42829.275962.212562.3317
41.6392-0.2495-0.15292.80091.14162.58890.02410.13570.2378-0.30140.0563-0.0328-0.49190.1344-0.06540.3075-0.0270.02840.351-0.08910.362421.123461.066421.1524
51.4688-0.34120.35831.41280.9813.4436-0.0498-0.0907-0.00010.0715-0.12660.2312-0.0939-0.65750.12550.29680.02180.05190.4435-0.14290.42336.903659.77238.553
61.3891-0.9449-1.0065.21994.2545.56020.0049-0.1931-0.08560.7910.0509-0.00030.8090.2395-0.02840.350.014-0.04630.3091-0.0280.326122.661237.565831.3945
71.3322-0.16850.05832.1550.12451.7234-0.04590.2060.1536-0.27960.0955-0.0703-0.13180.1387-0.0530.2696-0.06570.03790.3324-0.02930.297420.248932.64-11.5978
81.0381-0.55980.31391.49921.1472.1088-0.0187-0.0680.0594-0.0019-0.14940.26780.0474-0.40530.16610.2187-0.06010.02780.3076-0.0390.31942.552431.11533.4804
91.529-0.5541-0.54912.25121.87983.19330.03990.0055-0.16940.34490.0951-0.15480.46170.2178-0.20850.38310.0312-0.02280.2751-0.03650.355122.555610.82762.1748
102.8733-0.1667-0.69092.61190.10552.2905-0.00230.6134-0.0092-0.42690.1119-0.17760.15870.0575-0.14810.57-0.07240.11220.6599-0.15950.350223.82132.4662-39.8812
111.6626-0.4808-0.69922.09770.54352.0512-0.07760.4692-0.2652-0.19930.04790.22360.3107-0.44170.05770.4604-0.1080.01210.5191-0.11960.357.1131-0.6352-25.1056
122.8287-1.1939-1.84212.39341.55072.8789-0.34490.2279-0.69530.09330.1559-0.18110.89940.39670.03970.82780.05240.08970.529-0.2210.636128.2547-17.923-25.0345
134.8152-2.70060.78392.8009-2.36954.2791-0.1844-0.58460.33951.57940.2518-0.8167-0.15080.8322-0.26821.0946-0.0473-0.00060.6207-0.19170.499524.627595.355683.9716
140.14630.86741.06471.5511.90463.6329-0.0312-0.10860.28130.14660.8907-0.7044-0.02151.2843-0.79150.39120.00890.0180.9436-0.46350.846243.503155.756535.0406
150.2487-1.1082-0.97074.69223.70653.6494-0.16260.0375-0.12670.22650.3038-0.29690.65550.672-0.46860.60850.09640.15590.7295-0.2870.71342.88636.114-19.806
162.38592.5308-0.86876.57761.32921.6875-0.65150.4564-0.6697-0.1470.02-0.10031.5479-0.46110.2841.0462-0.16250.21870.591-0.1710.54996.244554.591669.5989
171.09170.42650.09493.5035-0.82583.1764-0.2176-0.9931-0.76960.534-0.2483-0.83370.91241.86290.44420.97440.37980.00231.31940.33560.833414.88357.3976104.8715
182.99610.272-2.47131.47050.45252.8438-0.7253-0.1253-0.90420.35170.2480.0251.2037-0.03220.07391.04630.05720.19550.39470.08090.6664-1.814353.694693.18
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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  • 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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