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- PDB-9lnv: Crystal structure of T2R-TTL-YQVB6 Complex -

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Basic information

Entry
Database: PDB / ID: 9lnv
TitleCrystal structure of T2R-TTL-YQVB6 Complex
Components
  • Detyrosinated tubulin alpha-1B chain
  • Stathmin-4
  • Tubulin beta chain
  • Tubulin tyrosine ligase
KeywordsSTRUCTURAL PROTEIN / tubule inhibitor
Function / homology
Function and homology information


tubulin-tyrosine ligase / regulation of metaphase plate congression / 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 ...tubulin-tyrosine ligase / regulation of metaphase plate congression / 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 / MHC class II antigen presentation / Recruitment of NuMA to mitotic centrosomes / COPI-mediated anterograde transport / regulation of microtubule polymerization or depolymerization / microtubule-based process / positive regulation of mitotic cell cycle / post-translational protein modification / spindle microtubule / structural constituent of cytoskeleton / microtubule cytoskeleton organization / mitotic cell cycle / microtubule cytoskeleton / growth cone / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / 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. ...: / 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
: / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin beta chain / Tubulin--tyrosine ligase / Stathmin-4 / Tubulin alpha-1B chain
Similarity search - Component
Biological speciesSus scrofa (pig)
Mus musculus (house mouse)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.67 Å
AuthorsWu, C.Y. / Wang, Y.X. / Chen, Q.F.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of T2R-TTL-YQVB6 Complex
Authors: Wu, C.Y. / Wang, Y.X. / Chen, Q.F.
History
DepositionJan 22, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Detyrosinated tubulin alpha-1B chain
C: Detyrosinated tubulin alpha-1B chain
D: Tubulin beta chain
E: Stathmin-4
F: Tubulin tyrosine ligase
B: Tubulin beta chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)264,19515
Polymers261,3056
Non-polymers2,8909
Water27015
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.211, 156.467, 184.705
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 ACDBEF

#1: Protein Detyrosinated tubulin alpha-1B chain


Mass: 50041.273 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: TUBA1B / Production host: Escherichia coli (E. coli) / References: UniProt: Q2XVP4
#2: Protein Tubulin beta chain


Mass: 49999.887 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Gene: TUBB2B, LOC100624785 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8D1UIR5
#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.) Mus musculus (house mouse) / Gene: Stmn4 / Production host: Escherichia coli (E. coli) / References: UniProt: P63042
#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: A0A8V0Z8P0

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Non-polymers , 6 types, 24 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.: 2 / 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-A1EPR / 10'-fluorovinblastine


Mass: 828.965 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C46H57FN4O9 / Feature type: SUBJECT OF INVESTIGATION
#9: 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
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationN

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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: 2.92 Å3/Da / Density % sol: 57.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 6% PEG, 5% glycerol, 0.1 M MES, 30 mM CaCl2, 30 mM MgCl2, pH 6.7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97861 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97861 Å / Relative weight: 1
ReflectionResolution: 2.67→119.39 Å / Num. obs: 87167 / % possible obs: 99.96 % / Redundancy: 13.2 % / CC1/2: 0.959 / Net I/σ(I): 4.2
Reflection shellResolution: 2.67→2.72 Å / Num. unique obs: 4276 / CC1/2: 0.481

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Processing

Software
NameVersionClassification
PHENIX(???)refinement
xia2data reduction
XDSdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.67→91.42 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2877 4386 5.04 %
Rwork0.2179 --
obs0.2214 86972 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.67→91.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17256 0 184 15 17455
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d17.2886653
X-RAY DIFFRACTIONf_chiral_restr0.0532681
X-RAY DIFFRACTIONf_plane_restr0.0083161
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.67-2.70.38951610.28672685X-RAY DIFFRACTION99
2.7-2.730.38481370.28032728X-RAY DIFFRACTION99
2.73-2.770.36161500.27962697X-RAY DIFFRACTION99
2.77-2.80.36131520.27172718X-RAY DIFFRACTION100
2.8-2.840.31721320.26952737X-RAY DIFFRACTION100
2.84-2.880.40151400.26812704X-RAY DIFFRACTION100
2.88-2.920.36581560.26952737X-RAY DIFFRACTION100
2.92-2.960.36771360.27322716X-RAY DIFFRACTION100
2.96-3.010.35241470.26542737X-RAY DIFFRACTION100
3.01-3.060.33731500.26652689X-RAY DIFFRACTION100
3.06-3.110.36121380.26592777X-RAY DIFFRACTION100
3.11-3.170.39671490.26582702X-RAY DIFFRACTION100
3.17-3.230.34391560.25452713X-RAY DIFFRACTION100
3.23-3.290.31851380.24092773X-RAY DIFFRACTION100
3.29-3.360.33741240.2382752X-RAY DIFFRACTION100
3.36-3.440.32781470.22942736X-RAY DIFFRACTION100
3.44-3.530.30111420.22942750X-RAY DIFFRACTION100
3.53-3.620.27571440.21752752X-RAY DIFFRACTION99
3.62-3.730.31661410.2182749X-RAY DIFFRACTION100
3.73-3.850.26531420.21232757X-RAY DIFFRACTION100
3.85-3.990.27721600.19332715X-RAY DIFFRACTION100
3.99-4.150.231630.18782758X-RAY DIFFRACTION100
4.15-4.340.23161390.17632776X-RAY DIFFRACTION100
4.34-4.560.22541400.16872786X-RAY DIFFRACTION100
4.57-4.850.22891300.16442803X-RAY DIFFRACTION100
4.85-5.230.27461600.18492754X-RAY DIFFRACTION100
5.23-5.750.2511500.1942795X-RAY DIFFRACTION100
5.75-6.580.27471650.21812805X-RAY DIFFRACTION100
6.58-8.290.26911350.20842852X-RAY DIFFRACTION100
8.29-91.420.23611620.22052933X-RAY DIFFRACTION98

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