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- PDB-6fjm: tubulin-Disorazole Z complex -

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Basic information

Entry
Database: PDB / ID: 6fjm
Titletubulin-Disorazole Z 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 / Disorazole Z / 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: 2.1 Å
AuthorsMenchon, G. / Prota, A.E. / Lucena Agell, D. / Bucher, P. / Jansen, R. / Irschik, H. / Mueller, R. / Paterson, I. / Diaz, J.F. / Altmann, K.-H. / Steinmetz, M.O.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_166608 Switzerland
CitationJournal: Nat Commun / Year: 2018
Title: A fluorescence anisotropy assay to discover and characterize ligands targeting the maytansine site of tubulin.
Authors: Menchon, G. / Prota, A.E. / Lucena-Agell, D. / Bucher, P. / Jansen, R. / Irschik, H. / Muller, R. / Paterson, I. / Diaz, J.F. / Altmann, K.H. / Steinmetz, M.O.
History
DepositionJan 22, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 30, 2018Provider: repository / Type: Initial release
Revision 1.1Jun 13, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 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)265,41325
Polymers261,6316
Non-polymers3,78219
Water15,331851
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22830 Å2
ΔGint-184 kcal/mol
Surface area80890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.390, 157.630, 179.630
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 , 8 types, 870 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.: 7 / 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-DKN / Disorazole Z


Mass: 746.799 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H46N2O12
#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.: 851 / 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: 2.83 Å3/Da / Density % sol: 56.56 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 6.7
Details: 10 % PEG 4k, 16 % glycerol, 30 mM MgCl2, 30 mM CaCl2, and 100 mM 2-(N-morpholino)ethanesulfonic acid/imidazole

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00004 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Oct 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00004 Å / Relative weight: 1
ReflectionResolution: 2.1→55.974 Å / Num. obs: 172635 / % possible obs: 100 % / Redundancy: 12.1 % / Biso Wilson estimate: 46.1 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.105 / Rrim(I) all: 0.107 / Net I/σ(I): 18.5
Reflection shellResolution: 2.1→2.15 Å / Redundancy: 7.9 % / Rmerge(I) obs: 3.126 / Mean I/σ(I) obs: 0.68 / CC1/2: 0.243 / Rrim(I) all: 3.354 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(dev_2863: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4I4T

4i4t


Resolution: 2.1→55.974 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.76
RfactorNum. reflection% reflection
Rfree0.2129 8641 5.01 %
Rwork0.1789 --
obs0.1807 172624 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.1→55.974 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17402 0 229 864 18495
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00418076
X-RAY DIFFRACTIONf_angle_d0.62124525
X-RAY DIFFRACTIONf_dihedral_angle_d11.6610830
X-RAY DIFFRACTIONf_chiral_restr0.0432672
X-RAY DIFFRACTIONf_plane_restr0.0043183
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.12390.38673150.36365353X-RAY DIFFRACTION100
2.1239-2.14890.35622600.34075397X-RAY DIFFRACTION100
2.1489-2.17510.3732650.33515460X-RAY DIFFRACTION100
2.1751-2.20260.34272790.31715382X-RAY DIFFRACTION100
2.2026-2.23160.34692820.30255437X-RAY DIFFRACTION100
2.2316-2.26220.3322920.29045409X-RAY DIFFRACTION100
2.2622-2.29450.32433160.28665377X-RAY DIFFRACTION100
2.2945-2.32870.30822690.27065476X-RAY DIFFRACTION100
2.3287-2.36510.30862870.25955418X-RAY DIFFRACTION100
2.3651-2.40390.27732760.24685405X-RAY DIFFRACTION100
2.4039-2.44540.28792820.2395436X-RAY DIFFRACTION100
2.4454-2.48980.27642970.22655432X-RAY DIFFRACTION100
2.4898-2.53770.31262820.22555451X-RAY DIFFRACTION100
2.5377-2.58950.26512940.215397X-RAY DIFFRACTION100
2.5895-2.64580.27012880.20665448X-RAY DIFFRACTION100
2.6458-2.70740.26552980.20425436X-RAY DIFFRACTION100
2.7074-2.77510.26512810.19825472X-RAY DIFFRACTION100
2.7751-2.85010.24342820.19155440X-RAY DIFFRACTION100
2.8501-2.9340.25572810.19555445X-RAY DIFFRACTION100
2.934-3.02870.22972780.18935489X-RAY DIFFRACTION100
3.0287-3.13690.21282870.18015450X-RAY DIFFRACTION100
3.1369-3.26250.24073230.18235465X-RAY DIFFRACTION100
3.2625-3.41090.20512930.16865453X-RAY DIFFRACTION100
3.4109-3.59070.1812940.15885507X-RAY DIFFRACTION100
3.5907-3.81570.18083000.14895459X-RAY DIFFRACTION100
3.8157-4.11020.15812890.13645525X-RAY DIFFRACTION100
4.1102-4.52370.14522950.12645541X-RAY DIFFRACTION100
4.5237-5.17780.14922750.12955558X-RAY DIFFRACTION100
5.1778-6.5220.21292650.1745670X-RAY DIFFRACTION100
6.522-55.99430.19133160.16845795X-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)
11.0913-0.0464-0.52243.87571.57563.09870.00080.08040.1648-0.5250.3352-0.4626-0.66570.4268-0.29170.5046-0.10340.09170.4879-0.1590.463631.643486.348352.6994
22.08940.14270.52453.6991.36444.40270.0242-0.14860.09320.4282-0.07060.3076-0.2258-0.18470.02380.41150.0190.09710.3618-0.09660.397517.143286.615570.4496
31.14140.4603-0.35633.23642.38675.69390.0147-0.0871-0.1380.67430.2717-0.2720.70920.5618-0.30540.50640.1288-0.05190.4397-0.10820.467829.540562.356962.2631
42.3291-0.3254-0.56383.41080.88522.9120.11490.11460.3056-0.3187-0.02550.0183-0.62920.0382-0.08050.37160.00380.01870.3715-0.07130.358821.490361.116321.1239
51.7752-0.63390.3621.5160.67563.8551-0.1503-0.09170.00190.1763-0.06980.356-0.2031-0.86650.19130.39480.03860.05350.5669-0.16840.50367.32559.832138.558
61.0433-0.9701-0.91964.45254.04385.84750.0215-0.1981-0.04850.7613-0.00380.04080.67940.3211-0.0160.4278-0.0003-0.01970.4005-0.03150.371622.690138.065832.0658
71.13-0.0961-0.14862.25720.16421.8593-0.00360.15310.1342-0.27970.0468-0.0607-0.16820.1093-0.0290.2938-0.06280.02830.3585-0.03160.331320.026232.6638-11.5312
81.4304-0.4170.53921.55771.06622.5803-0.0099-0.1030.15880.0066-0.17980.2576-0.0138-0.46680.16950.2599-0.04790.03260.3775-0.04840.38952.488531.07993.7023
92.8113-1.7771-2.43764.11414.74956.8755-0.0255-0.0392-0.05940.42050.2046-0.09420.60570.2886-0.17130.3620.0324-0.03480.2749-0.00890.339222.508110.80322.2942
102.3424-0.6961-0.08342.3471-0.16341.9918-0.11880.5891-0.0983-0.58140.1811-0.2240.22670.2162-0.05730.5991-0.07690.09660.6782-0.16860.390324.04332.5385-39.6965
111.7272-0.1277-0.61231.90470.78532.572-0.09140.4007-0.1872-0.21750.03230.20190.4091-0.37610.04630.4894-0.09780.01710.4765-0.11230.37267.3364-0.6879-24.9789
123.4184-1.1654-2.59812.44732.19425.9973-0.23580.0664-0.63440.22930.1212-0.11171.03450.52630.08020.78560.11180.02960.4679-0.17310.632627.8663-17.7748-24.7267
135.1116-2.91621.43573.8402-3.86845.6854-0.3205-0.25280.11180.84280.3914-0.75410.06360.4497-0.14451.153-0.034-0.0340.6584-0.1940.613425.506695.273483.6284
143.06283.28473.34133.45172.923.67640.0432-0.27430.39550.35440.407-0.34360.30540.6339-0.77220.36070.05210.00310.733-0.25820.645743.586455.448734.185
151.2259-2.2093-1.68628.28914.86263.11110.00240.111-0.22730.27580.2521-0.56390.49880.5039-0.33410.4820.08290.12740.7979-0.26160.726642.75276.1282-19.9104
163.62322.1337-0.90047.10411.35854.0912-0.53440.5762-0.6417-0.27360.1369-0.12851.3988-0.55730.30521.0338-0.14270.19450.5947-0.13870.54886.467954.724269.5421
173.0194-0.0863-0.20343.5367-1.55014.2394-0.059-0.909-0.52170.5444-0.4901-0.93110.56391.75180.4150.88080.2168-0.08261.23520.22930.786715.135857.4736104.8557
182.9640.6462-2.02171.41310.49852.5213-0.497-0.0488-0.66820.23610.256-0.10581.0412-0.1269-0.05080.97320.02420.14530.41880.05010.6568-1.532753.703993.1684
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 2 through 205)
5X-RAY DIFFRACTION5chain 'B' and (resid 206 through 381)
6X-RAY DIFFRACTION6chain 'B' and (resid 382 through 440)
7X-RAY DIFFRACTION7chain 'C' and (resid 1 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 441)
13X-RAY DIFFRACTION13chain 'E' and (resid 7 through 28)
14X-RAY DIFFRACTION14chain 'E' and (resid 45 through 89)
15X-RAY DIFFRACTION15chain 'E' and (resid 90 through 144)
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 384)

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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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