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- PDB-6gj4: Tubulin-6j complex -

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Basic information

Entry
Database: PDB / ID: 6gj4
TitleTubulin-6j 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 / cytosol / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Rossmann fold - #11480 / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Helix hairpin bin / 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 / Tubulin-tyrosine ligase/Tubulin polyglutamylase / Tubulin-tyrosine ligase family / TTL domain profile. / Helix hairpin bin / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / 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; / 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 / 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-EZW / 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: 2.4 Å
AuthorsBrindisi, M. / Ulivieri, C. / Alfano, G. / Gemma, S. / Balaguer, F.d.A. / Khan, T. / Grillo, A. / Chemi, G. / Menchon, G. / Prota, A.E. ...Brindisi, M. / Ulivieri, C. / Alfano, G. / Gemma, S. / Balaguer, F.d.A. / Khan, T. / Grillo, A. / Chemi, G. / Menchon, G. / Prota, A.E. / Olieric, N. / Agell, D.L. / Barasoain, I. / Diaz, J.F. / Nebbioso, A. / Conte, M.R. / Lopresti, L. / Magnano, S. / Amet, R. / Kinsella, P. / Zisterer, D.M. / Ibrahim, O. / O'Sullivan, J. / Morbidelli, L. / Spaccapelo, R. / Baldari, C. / Butini, S. / Novellino, E. / Campiani, G. / Altucci, L. / Steinmetz, M.O. / Brogi, S.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Swiss National Science Foundation31003A_166608 Switzerland
CitationJournal: Eur J Med Chem / Year: 2018
Title: Structure-activity relationships, biological evaluation and structural studies of novel pyrrolonaphthoxazepines as antitumor agents.
Authors: Brindisi, M. / Ulivieri, C. / Alfano, G. / Gemma, S. / de Asis Balaguer, F. / Khan, T. / Grillo, A. / Chemi, G. / Menchon, G. / Prota, A.E. / Olieric, N. / Lucena-Agell, D. / Barasoain, I. / ...Authors: Brindisi, M. / Ulivieri, C. / Alfano, G. / Gemma, S. / de Asis Balaguer, F. / Khan, T. / Grillo, A. / Chemi, G. / Menchon, G. / Prota, A.E. / Olieric, N. / Lucena-Agell, D. / Barasoain, I. / Diaz, J.F. / Nebbioso, A. / Conte, M. / Lopresti, L. / Magnano, S. / Amet, R. / Kinsella, P. / Zisterer, D.M. / Ibrahim, O. / O'Sullivan, J. / Morbidelli, L. / Spaccapelo, R. / Baldari, C. / Butini, S. / Novellino, E. / Campiani, G. / Altucci, L. / Steinmetz, M.O. / Brogi, S.
History
DepositionMay 16, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 5, 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.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

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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)265,30321
Polymers261,6316
Non-polymers3,67215
Water3,693205
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21810 Å2
ΔGint-136 kcal/mol
Surface area79960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.970, 157.810, 181.220
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, 220 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.: 2 / 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-EZW / 5-(quinolin-5-yl)naphtho[2,3-b]pyrrolo[1,2-d][1,4]oxazepin-4-yl acetate


Mass: 418.443 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H18N2O3
#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-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.: 205 / 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: 2.87 Å3/Da / Density % sol: 57.12 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 6.7
Details: 10% PEG 4K, 12.5% GLYCEROL, 30 MM MAGNESIUM CHLORIDE, 30 MM CALCIUM CHLORIDE, 0.1M MES / 0.1M IMIDAZOLE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00001 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Dec 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00001 Å / Relative weight: 1
ReflectionResolution: 2.4→48.022 Å / Num. obs: 117973 / % possible obs: 100 % / Redundancy: 6.7 % / CC1/2: 0.996 / Rmerge(I) obs: 0.146 / Rpim(I) all: 0.064 / Rrim(I) all: 0.158 / Net I/σ(I): 8.7
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 6.7 % / Rmerge(I) obs: 2.499 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 8642 / CC1/2: 0.346 / Rpim(I) all: 1.105 / Rrim(I) all: 2.706 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 4i4t

4i4t


Resolution: 2.4→48.022 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 27.74
RfactorNum. reflection% reflection
Rfree0.2406 5775 4.9 %
Rwork0.1968 --
obs0.199 117973 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.4→48.022 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17202 0 234 205 17641
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00317823
X-RAY DIFFRACTIONf_angle_d0.62824168
X-RAY DIFFRACTIONf_dihedral_angle_d11.66710628
X-RAY DIFFRACTIONf_chiral_restr0.0432629
X-RAY DIFFRACTIONf_plane_restr0.0043123
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.42730.39031910.36333718X-RAY DIFFRACTION100
2.4273-2.45580.38352020.35943681X-RAY DIFFRACTION100
2.4558-2.48580.37951950.33373667X-RAY DIFFRACTION100
2.4858-2.51720.36071810.31863700X-RAY DIFFRACTION100
2.5172-2.55040.35911810.30613745X-RAY DIFFRACTION100
2.5504-2.58530.33821890.29893676X-RAY DIFFRACTION100
2.5853-2.62220.32951920.28653735X-RAY DIFFRACTION100
2.6222-2.66140.3281830.28153664X-RAY DIFFRACTION100
2.6614-2.70290.30551960.2733739X-RAY DIFFRACTION100
2.7029-2.74730.32622040.2653686X-RAY DIFFRACTION100
2.7473-2.79460.29351790.25923726X-RAY DIFFRACTION100
2.7946-2.84540.30772040.25413680X-RAY DIFFRACTION100
2.8454-2.90020.31551770.24663705X-RAY DIFFRACTION100
2.9002-2.95930.31321860.25383747X-RAY DIFFRACTION100
2.9593-3.02370.33221920.25393709X-RAY DIFFRACTION100
3.0237-3.0940.30011940.23093733X-RAY DIFFRACTION100
3.094-3.17140.2732010.2213713X-RAY DIFFRACTION100
3.1714-3.25710.30041980.22283701X-RAY DIFFRACTION100
3.2571-3.35290.28641870.21833736X-RAY DIFFRACTION100
3.3529-3.46110.25131950.20783727X-RAY DIFFRACTION100
3.4611-3.58480.23612050.20173735X-RAY DIFFRACTION100
3.5848-3.72830.23411730.19013765X-RAY DIFFRACTION100
3.7283-3.89790.22951910.1713752X-RAY DIFFRACTION100
3.8979-4.10330.20841890.16223759X-RAY DIFFRACTION100
4.1033-4.36020.19331890.15353778X-RAY DIFFRACTION100
4.3602-4.69660.16621930.13733768X-RAY DIFFRACTION100
4.6966-5.16870.20391790.1493794X-RAY DIFFRACTION100
5.1687-5.91550.23552090.17573821X-RAY DIFFRACTION100
5.9155-7.44840.2011930.18273858X-RAY DIFFRACTION100
7.4484-48.0320.18412270.1643980X-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)
11.4154-0.2984-0.71764.65561.00712.730.090.12430.2141-0.38340.2439-0.4929-0.58560.4143-0.34040.5495-0.09440.11170.5982-0.17930.563231.660686.552353.0303
21.94250.21270.71774.01791.10823.90940.0085-0.11710.13670.54280.10220.2947-0.35110.0408-0.10050.56050.0110.15050.4678-0.1280.534617.745786.617271.1856
31.5342-0.6879-0.49324.94561.78544.36480.1044-0.1119-0.18710.61970.1857-0.20120.66050.3878-0.32310.45430.0693-0.06070.5825-0.15930.561329.093663.496761.0553
41.7596-0.3614-0.50473.18740.70332.1720.07230.20210.254-0.32850.0084-0.1171-0.44160.0592-0.09440.3980.01010.01650.495-0.06720.432521.48561.366621.0547
52.1272-0.1438-0.08071.96010.6073.26120.0128-0.01240.0060.088-0.0730.339-0.0796-0.65040.05860.37840.06310.04640.517-0.1380.5057.091960.208238.3437
61.9929-0.6139-0.51474.93414.12536.9146-0.0347-0.2146-0.13110.7548-0.05320.02970.75680.45880.09520.45810.0154-0.05990.419-0.00460.382422.518937.856231.3844
71.5765-0.427-0.15242.94010.44051.9115-0.02090.20820.1157-0.37310.0499-0.1016-0.20860.1074-0.04360.3703-0.06840.02470.436-0.04320.36219.667332.6522-11.592
81.4459-0.18820.49171.86261.00233.151-0.0075-0.05190.0464-0.0234-0.15270.3004-0.0107-0.44370.15250.3278-0.0490.03890.4499-0.05860.45652.169931.15133.6426
92.4824-1.3286-1.92563.0393.92065.38690.09440.1877-0.02450.33360.1049-0.17350.49730.1819-0.19540.45240.06-0.03310.3932-0.0260.43122.193710.75532.2226
102.0473-0.31420.18332.5857-0.40252.6397-0.20270.7653-0.1689-0.55430.3196-0.20230.17910.0711-0.10250.6641-0.15030.09960.9453-0.23290.53624.01092.1031-39.7775
111.85610.0119-0.41812.03540.03433.1691-0.1570.6077-0.2761-0.15590.25970.2130.353-0.6441-0.08520.5154-0.12760.00970.7337-0.13210.50327.4068-1.0697-24.9546
124.3605-1.1398-2.49772.43540.04743.0958-0.25950.1916-0.70430.02480.1143-0.16811.11380.37740.13180.85740.06890.05460.6364-0.28630.798427.8812-18.1297-24.4031
133.087-1.35280.67482.0598-1.72252.0549-0.0523-0.38150.10451.22240.0733-0.0347-0.45751.2111-0.19681.5535-0.14740.11170.9054-0.19660.675925.992994.772684.8482
143.25652.94833.49642.89343.13053.69710.1806-0.40290.38820.55420.173-0.35850.57310.4045-0.70670.530.03270.0160.7969-0.24770.813443.683455.878534.7434
150.5853-1.071-1.33842.3141.99472.2425-0.0787-0.0899-0.33580.22280.0987-0.2440.46420.3044-0.27450.67940.05370.10040.8596-0.25320.886642.23067.3469-18.3927
164.89741.7545-0.84845.1359-0.28193.4851-0.29410.6973-0.9649-0.0732-0.03490.01851.75-0.52350.07431.0857-0.17590.17070.6932-0.19170.7126.480554.701569.9989
173.58340.2054-1.28774.6323-2.10446.6975-0.0551-0.6836-0.50520.7047-0.3165-1.06220.34071.5950.37480.93340.1674-0.11731.05540.14550.912115.135858.0162105.3188
182.7240.8869-1.57310.9891-0.08272.1396-0.36350.0445-0.73460.21380.2270.02051.1002-0.3042-0.02411.10250.00660.15520.56870.07280.7772-1.999354.056893.0362
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 437)
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 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 1 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 6 through 28)
14X-RAY DIFFRACTION14chain 'E' and (resid 44 through 89)
15X-RAY DIFFRACTION15chain 'E' and (resid 90 through 140)
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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