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- PDB-7z7d: Tubulin-Todalam-Vinblastine-complex -

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Basic information

Entry
Database: PDB / ID: 7z7d
TitleTubulin-Todalam-Vinblastine-complex
Components
  • (Tubulin beta-2B ...) x 2
  • Stathmin-4
  • Tubulin alpha-1B chain
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 / cellular response to interleukin-4 / tubulin binding / 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 / cellular response to interleukin-4 / tubulin binding / 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
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. / 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. / 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
Chem-4I2 / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-VLB / 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 Å
AuthorsMuehlethaler, T. / Milanos, L. / Ortega, J.A. / Blum, T.B. / Gioia, D. / Roy, B. / Prota, A.E. / Cavalli, A. / Steinmetz, M.O.
Funding supportEuropean Union, Switzerland, 3items
OrganizationGrant numberCountry
European Union (EU)ID239047 NEONEuropean Union
Swiss National Science Foundation31003A_166608 Switzerland
Swiss National Science Foundation310030_192566 Switzerland
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2022
Title: Rational Design of a Novel Tubulin Inhibitor with a Unique Mechanism of Action.
Authors: Muhlethaler, T. / Milanos, L. / Ortega, J.A. / Blum, T.B. / Gioia, D. / Roy, B. / Prota, A.E. / Cavalli, A. / Steinmetz, M.O.
History
DepositionMar 15, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2022Provider: repository / Type: Initial release
Revision 1.1May 4, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Jun 22, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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 beta-2B chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)265,73523
Polymers261,6316
Non-polymers4,10317
Water15,421856
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: equilibrium centrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.286, 157.296, 182.526
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 , 2 types, 3 molecules ACE

#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
#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

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Tubulin beta-2B ... , 2 types, 3 molecules BDF

#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
#4: Protein Tubulin beta-2B chain


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 , 9 types, 873 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.: 4 / 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-VLB / (2ALPHA,2'BETA,3BETA,4ALPHA,5BETA)-VINCALEUKOBLASTINE / VINBLASTINE


Mass: 810.974 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H58N4O9 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-4I2 / N-(4-{2-[3-(trifluoromethyl)anilino]-1,3-thiazol-4-yl}phenyl)acetamide


Mass: 377.383 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H14F3N3OS / Feature type: SUBJECT OF INVESTIGATION
#12: 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
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 856 / 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: 2.8 Å3/Da / Density % sol: 56.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 2% PEG 4K, 4% glycerol, 30 mM MgCl2, 30 mM CaCl2, 0.1 M MES/Imidazole, 5 mM L-tyrosine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Sep 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→45.6 Å / Num. obs: 405947 / % possible obs: 96.2 % / Redundancy: 4.6 % / Biso Wilson estimate: 40.97 Å2 / CC1/2: 0.998 / CC star: 1 / Rmerge(I) obs: 0.07222 / Rpim(I) all: 0.03566 / Rrim(I) all: 0.08104 / Net I/σ(I): 11.6
Reflection shellResolution: 2→2.08 Å / Rmerge(I) obs: 1.274 / Mean I/σ(I) obs: 1.02 / Num. unique obs: 64331 / CC1/2: 0.386 / CC star: 0.746 / Rpim(I) all: 0.6473 / Rrim(I) all: 1.437

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
XDSdata scaling
PDB_EXTRACT3.28data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 5lxt

5lxt


Resolution: 2→45.6 Å / SU ML: 0.31 / Cross valid method: FREE R-VALUE / σ(F): 1.91 / Phase error: 27.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2357 10029 5.01 %
Rwork0.2038 362008 -
obs0.2054 200577 96.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 150.8 Å2 / Biso mean: 54.6883 Å2 / Biso min: 19.8 Å2
Refinement stepCycle: final / Resolution: 2→45.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17329 0 257 856 18442
Biso mean--44.86 51.55 -
Num. residues----2190
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.020.36116400.3635120591269996
2.02-2.050.38266130.3555117381235194
2.05-2.070.33696060.3367116041221093
2.07-2.10.35186240.3279120351265996
2.1-2.130.32256600.3098123701303099
2.13-2.150.33076490.304123911304099
2.15-2.190.34476490.3031123451299499
2.19-2.220.32146530.2953123641301799
2.22-2.250.32796520.2884123951304799
2.25-2.290.3236510.2782123501300199
2.29-2.330.32046500.2733123241297499
2.33-2.370.34026510.2727123981304999
2.37-2.420.30296520.258123331298599
2.42-2.470.27946450.2454122641290998
2.47-2.520.27386550.2337123111296698
2.52-2.580.28246490.2337122711292097
2.58-2.640.26476470.2227120971274497
2.64-2.710.26286480.2232121221277097
2.71-2.790.27646380.226120271266596
2.79-2.880.28016270.2198119981262595
2.88-2.990.25696140.2209116671228193
2.99-3.110.24676140.2076117141232894
3.11-3.250.25326420.2073120961273897
3.25-3.420.23076400.2051121031274396
3.42-3.630.23096350.1911120671270296
3.63-3.910.22046260.1766119221254895
3.91-4.310.17276320.161117911242394
4.31-4.930.16826150.1455116881230393
4.93-6.210.18946040.17115371214192
6.21-45.60.18256130.1579116271224093

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