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- PDB-6y4n: Structure of Tubulin Tyrosine Ligase in Complex with Tb116 -

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Basic information

Entry
Database: PDB / ID: 6y4n
TitleStructure of Tubulin Tyrosine Ligase in Complex with Tb116
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta chain
  • Tubulin-Tyrosine Ligase
KeywordsLIGASE / TTL / Tubulin / complex
Function / homology
Function and homology information


tubulin-tyrosine ligase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Resolution of Sister Chromatid Cohesion / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle ...tubulin-tyrosine ligase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Resolution of Sister Chromatid Cohesion / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / EML4 and NUDC in mitotic spindle formation / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / microtubule depolymerization / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / COPI-mediated anterograde transport / regulation of microtubule polymerization or depolymerization / tubulin binding / spindle microtubule / protein modification process / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / neuron projection development / mitotic cell cycle / microtubule cytoskeleton / growth cone / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / neuron projection / nucleotide binding / GTPase activity / GTP binding / Golgi apparatus / metal ion binding / cytoplasm
Similarity search - Function
Rossmann fold - #11480 / 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. ...Rossmann fold - #11480 / 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, B domain / D-amino Acid Aminotransferase; Chain A, domain 1 / 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 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / (2~{R})-1-methylpiperidine-2-carboxylic acid / Chem-O9K / Chem-O9N / benzyl hydrogen carbonate / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / VALINE ...PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / (2~{R})-1-methylpiperidine-2-carboxylic acid / Chem-O9K / Chem-O9N / benzyl hydrogen carbonate / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / VALINE / Tubulin tyrosine ligase / Tubulin beta chain / Stathmin-4 / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Gallus gallus (chicken)
Sus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.852 Å
AuthorsGavrilyuk, J. / Nocek, B. / Rigol, S. / Nicolaou, K.C. / Stoll, V.
CitationJournal: J.Org.Chem. / Year: 2021
Title: Design, Synthesis, and Biological Evaluation of Tubulysin Analogues, Linker-Drugs, and Antibody-Drug Conjugates, Insights into Structure-Activity Relationships, and Tubulysin-Tubulin Binding ...Title: Design, Synthesis, and Biological Evaluation of Tubulysin Analogues, Linker-Drugs, and Antibody-Drug Conjugates, Insights into Structure-Activity Relationships, and Tubulysin-Tubulin Binding Derived from X-ray Crystallographic Analysis.
Authors: Nicolaou, K.C. / Pan, S. / Pulukuri, K.K. / Ye, Q. / Rigol, S. / Erande, R.D. / Vourloumis, D. / Nocek, B.P. / Munneke, S. / Lyssikatos, J. / Valdiosera, A. / Gu, C. / Lin, B. / Sarvaiaya, H. ...Authors: Nicolaou, K.C. / Pan, S. / Pulukuri, K.K. / Ye, Q. / Rigol, S. / Erande, R.D. / Vourloumis, D. / Nocek, B.P. / Munneke, S. / Lyssikatos, J. / Valdiosera, A. / Gu, C. / Lin, B. / Sarvaiaya, H. / Trinidad, J. / Sandoval, J. / Lee, C. / Hammond, M. / Aujay, M. / Taylor, N. / Pysz, M. / Purcell, J.W. / Gavrilyuk, J.
History
DepositionFeb 21, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 31, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 23, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tubulin alpha-1B chain
B: Tubulin beta chain
C: Tubulin alpha-1B chain
D: Tubulin beta chain
E: Stathmin-4
F: Tubulin-Tyrosine Ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,53726
Polymers261,4476
Non-polymers4,09020
Water10,827601
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23690 Å2
ΔGint-113 kcal/mol
Surface area80660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.284, 154.969, 183.433
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) Sus scrofa (pig) / References: UniProt: Q2XVP4
#2: Protein Tubulin beta chain / Beta-tubulin


Mass: 49907.770 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P02554
#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 , 14 types, 621 molecules

#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE


Mass: 523.180 Da / Num. of mol.: 3 / 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.: 1 / 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-O9B / (2~{R})-1-methylpiperidine-2-carboxylic acid


Mass: 143.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H13NO2
#11: Chemical ChemComp-O9K / [(1~{R},3~{R})-1-(4-methanoyl-1,3-thiazol-2-yl)-4-methyl-3-(methylamino)pentyl] ethanoate


Mass: 284.375 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C13H20N2O3S
#12: Chemical ChemComp-O9N / methyl (2~{S},4~{S})-2,4-bis(azanyl)-5-phenyl-pentanoate


Mass: 222.284 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H18N2O2
#13: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#14: Chemical ChemComp-VAL / VALINE


Type: L-peptide linking / Mass: 117.146 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H11NO2
#15: Chemical ChemComp-P6S / benzyl hydrogen carbonate


Mass: 152.147 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8O3
#16: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#17: 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
#18: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 601 / 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: 2.83 Å3/Da / Density % sol: 56.61 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 30 mM calcium chloride, 30 mM magnesium chloride, 0.10 M MES pH 6.0, 2.0% w/v PEG 4000, 5.0% w/v glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.852→78.93 Å / Num. obs: 69959 / % possible obs: 100 % / Redundancy: 6.7 % / Biso Wilson estimate: 79.07 Å2 / Rmerge(I) obs: 0.131 / Rsym value: 0.131 / Net I/σ(I): 11.1
Reflection shellResolution: 2.852→2.901 Å / Redundancy: 6.4 % / Rmerge(I) obs: 0.864 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 3461 / Rsym value: 0.864 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.7 (6-FEB-2020)refinement
XDSdata reduction
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.852→78.929 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.91 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.318
RfactorNum. reflection% reflectionSelection details
Rfree0.22 3527 5.04 %RANDOM
Rwork0.1827 ---
obs0.1846 69959 100 %-
Displacement parametersBiso max: 189.36 Å2 / Biso mean: 70.97 Å2 / Biso min: 25.06 Å2
Baniso -1Baniso -2Baniso -3
1--8.981 Å20 Å20 Å2
2---0.7938 Å20 Å2
3---9.7748 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: final / Resolution: 2.852→78.929 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17464 0 264 589 18317
Biso mean--60.29 53.08 -
Num. residues----2207
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d10628SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes5788HARMONIC5
X-RAY DIFFRACTIONt_it18202HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion2333SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact25894SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d35299HARMONIC20.008
X-RAY DIFFRACTIONt_angle_deg63524HARMONIC20.97
X-RAY DIFFRACTIONt_omega_torsion3.07
X-RAY DIFFRACTIONt_other_torsion15.59
LS refinement shellResolution: 2.852→2.87 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.2587 69 4.93 %
Rwork0.241 1331 -
obs--100 %
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)
10.05920.3338-0.01131.309-0.92131.3493-0.01980.00640.078-0.05280.1589-0.05970.2057-0.1705-0.1391-0.0133-0.0177-0.039-0.04340.0954-0.0508-25.3161-4.320261.951
20.2304-0.1615-0.02960.7934-0.77291.1635-0.0024-0.0297-0.014-0.0868-0.0105-0.02840.09250.02620.0129-0.05390.0063-0.0012-0.01820.0520.0003-15.467620.913329.6166
30.1744-0.0099-0.21680.4963-0.40810.5447-0.10450.0211-0.0377-0.03390.0518-0.0248-0.03630.00590.0527-0.0336-0.05030.0074-0.00150.0190-12.589749.1815-3.7711
40.74480.03330.18680.8328-0.51580.7777-0.27940.31510.0647-0.01560.17350.035-0.15980.19270.10590.0103-0.152-0.08820.07330.152-0.1434-16.936580.4007-31.6036
50.1371-0.27680.4752.3624-2.91043.6232-0.0814-0.0215-0.00890.19780.38390.33-0.2348-0.5442-0.3025-0.08560.0347-0.02870.05680.152-0.0166-39.244538.028120.0263
61.0095-0.07661.15160.06510.43212.5932-0.3075-0.06620.27590.00580.1034-0.0919-0.2539-0.24630.2040.13910.0813-0.152-0.1797-0.0618-0.0129-5.521524.065292.5146
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A1 - 439
2X-RAY DIFFRACTION2{ B|* }B1 - 431
3X-RAY DIFFRACTION3{ C|* }C1 - 440
4X-RAY DIFFRACTION4{ D|* }D1 - 431
5X-RAY DIFFRACTION5{ E|* }E50 - 187
6X-RAY DIFFRACTION6{ F|* }F1 - 381

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