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- PDB-6y4m: Structure of Tubulin Tyrosine Ligase in Complex with Tb111 -

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Basic information

Entry
Database: PDB / ID: 6y4m
TitleStructure of Tubulin Tyrosine Ligase in Complex with Tb111
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 / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins ...tubulin-tyrosine ligase activity / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Hedgehog 'off' state / Cilium Assembly / Intraflagellar transport / COPI-dependent Golgi-to-ER retrograde traffic / Carboxyterminal post-translational modifications of tubulin / RHOH GTPase cycle / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / PKR-mediated signaling / The role of GTSE1 in G2/M progression after G2 checkpoint / Aggrephagy / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Separation of Sister Chromatids / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / COPI-mediated anterograde transport / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / tubulin binding / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / protein modification process / spindle microtubule / structural constituent of cytoskeleton / microtubule cytoskeleton organization / microtubule cytoskeleton / neuron projection development / mitotic cell cycle / growth cone / microtubule / neuron projection / nucleotide binding / GTPase activity / GTP binding / Golgi apparatus / metal ion binding / cytoplasm
Similarity search - Function
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. ...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. / 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
Similarity search - Domain/homology
PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / (2~{R})-1-methylpiperidine-2-carboxylic acid / Chem-O9H / Chem-OH5 / TRIETHYLENE GLYCOL / VALINE / Tubulin tyrosine ligase / Tubulin beta chain ...PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / (2~{R})-1-methylpiperidine-2-carboxylic acid / Chem-O9H / Chem-OH5 / 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: 3.34 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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 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)265,37723
Polymers261,4476
Non-polymers3,93017
Water59433
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23440 Å2
ΔGint-109 kcal/mol
Surface area80600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.961, 152.590, 185.989
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
12B
22D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 4381 - 438
21CC1 - 4381 - 438
12BB1 - 4311 - 431
22DD1 - 4311 - 431

NCS ensembles :
ID
1
2

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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 , 12 types, 50 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.: 4 / 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-O9H / [(1~{R},3~{R})-1-acetyloxy-1-[4-methanoyl-5-(2-phenylmethoxyethyl)-2,3-dihydro-1,3-thiazol-2-yl]-4-methyl-pentan-3-yl]-methyl-azanium


Mass: 421.573 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H33N2O4S
#12: Chemical ChemComp-OH5 / (2~{S},4~{R})-4-azanyl-2-methyl-5-phenyl-pentanoic acid


Mass: 207.269 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H17NO2
#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-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
#16: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 33 / 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: 2.82 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.03 M calcium chloride, 0.03 M magnesium chloride, 0.10 M MES pH 6.50, 3.20% w/v PEG 4000, 5.00% 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: 0.979 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 6, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.34→30 Å / Num. obs: 43404 / % possible obs: 99.5 % / Redundancy: 4.2 % / CC1/2: 0.975 / Rmerge(I) obs: 0.216 / Rpim(I) all: 0.114 / Rrim(I) all: 0.245 / Net I/σ(I): 5.1
Reflection shellResolution: 3.34→3.52 Å / Rmerge(I) obs: 0.683 / Num. unique obs: 6256 / CC1/2: 0.617 / Rpim(I) all: 0.353 / Rrim(I) all: 0.772

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
REFMAC5.8.0238refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 3.34→29.9 Å / Cor.coef. Fo:Fc: 0.919 / Cor.coef. Fo:Fc free: 0.902 / SU B: 65.786 / SU ML: 0.454 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.524
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2341 2168 5 %RANDOM
Rwork0.2071 ---
obs0.2085 41185 99.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 184.33 Å2 / Biso mean: 82.208 Å2 / Biso min: 2.4 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20 Å2-0 Å2
2---1.04 Å2-0 Å2
3----0.39 Å2
Refinement stepCycle: final / Resolution: 3.34→29.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17452 0 255 21 17728
Biso mean--72.25 36.76 -
Num. residues----2206
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0020.01318133
X-RAY DIFFRACTIONr_bond_other_d0.0010.01716348
X-RAY DIFFRACTIONr_angle_refined_deg1.1941.65224587
X-RAY DIFFRACTIONr_angle_other_deg1.0581.57437998
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.51352203
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.29222.586994
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.631153048
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.70715114
X-RAY DIFFRACTIONr_chiral_restr0.0370.22339
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.0220291
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023818
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A133690.1
12C133690.1
21B137280.07
22D137280.07
LS refinement shellResolution: 3.34→3.425 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 154 -
Rwork0.296 2958 -
all-3112 -
obs--99.62 %
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)
10.9820.17510.24093.3713-1.282.37090.0438-0.0053-0.15760.01830.15470.02280.4657-0.2032-0.19850.1842-0.0354-0.06640.50750.13320.1461-25.1455-4.368662.5453
21.9726-0.10540.08832.6918-1.53732.5859-0.074-0.0785-0.3174-0.0707-0.0113-0.13820.30930.16310.08530.04760.03060.01830.36740.06460.0673-15.611820.095929.8778
31.6022-0.5488-0.00892.1152-0.57351.6182-0.1540.1038-0.0602-0.11350.094-0.12730.02660.08320.060.0605-0.09360.01280.42270.01710.016-13.016648.8703-3.5842
43.0247-0.13780.58621.8044-0.16142.3263-0.30980.70070.3626-0.27440.1745-0.012-0.44230.16960.13530.5015-0.2726-0.15070.77650.27870.2077-17.541580.6411-30.8211
50.3729-0.49440.67362.0879-2.45543.4211-0.1953-0.01960.03610.44780.35670.1502-0.5921-0.7162-0.16140.25260.0141-0.04570.69420.1930.4027-39.492137.635120.5592
61.66490.55461.36791.84751.11714.0675-0.2087-0.34990.62970.4440.15110.1252-0.6375-0.44050.05760.69710.1534-0.17540.6587-0.03690.5697-4.980824.809392.3281
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 439
2X-RAY DIFFRACTION2B1 - 431
3X-RAY DIFFRACTION3C1 - 440
4X-RAY DIFFRACTION4D1 - 431
5X-RAY DIFFRACTION5E50 - 187
6X-RAY DIFFRACTION6F1 - 381

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