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- PDB-7cpq: crystal structure of T2R-TTL-(+)-6-Cl-JP18 complex -

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Basic information

Entry
Database: PDB / ID: 7cpq
Titlecrystal structure of T2R-TTL-(+)-6-Cl-JP18 complex
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
  • Tubulin tyrosine ligase
KeywordsCELL CYCLE / inhibitor / complex
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 / 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 ...tubulin-tyrosine ligase activity / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / 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 / neuron projection development / microtubule cytoskeleton / nervous system development / mitotic cell cycle / growth cone / microtubule / neuron projection / protein heterodimerization activity / nucleotide binding / GTPase activity / GTP binding / Golgi apparatus / metal ion binding / cytosol / 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
Chem-G9X / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / IMIDAZOLE / 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 (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.595 Å
AuthorsJiang, H. / Luo, C.
Funding support1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)
CitationJournal: To Be Published
Title: crystal structure of T2R-TTL-(+)-6-Cl-JP18 complex
Authors: Jiang, H. / Luo, C.
History
DepositionAug 7, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 11, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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 tyrosine ligase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)269,16925
Polymers266,0846
Non-polymers3,08519
Water1,29772
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22180 Å2
ΔGint-142 kcal/mol
Surface area76810 Å2
Unit cell
Length a, b, c (Å)104.877, 156.616, 182.624
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+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) Bos taurus (cattle) / 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 (cattle) / References: UniProt: Q6B856
#3: Protein Stathmin-4 / / Stathmin-like protein B3 / RB3


Mass: 22125.301 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: 43549.625 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, 91 molecules

#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine 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.: 3 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-G9X / (6R)-6-[(6-chloranyl-1H-indol-3-yl)methyl]-6,7,8,9-tetrahydrobenzo[7]annulen-5-one


Mass: 323.816 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H18ClNO / Feature type: SUBJECT OF INVESTIGATION
#9: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine 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: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#11: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#12: Chemical ChemComp-IMD / IMIDAZOLE / Imidazole


Mass: 69.085 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H5N2
#13: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 56.36 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 6-10% PEG 4k, 4-10% glycerol, 30 mM MgCl2, 100 mM MES/Imidazole pH 6.5-6.9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.9875 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 6, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9875 Å / Relative weight: 1
ReflectionResolution: 2.594→49.91 Å / Num. obs: 92838 / % possible obs: 99.4 % / Redundancy: 12.9 % / Biso Wilson estimate: 46.77 Å2 / CC1/2: 0.987 / Rmerge(I) obs: 0.2 / Net I/σ(I): 23
Reflection shellResolution: 2.594→2.688 Å / Num. unique obs: 7549 / CC1/2: 0.708

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4O2B

4o2b


Resolution: 2.595→49.904 Å / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 27.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2666 4654 5.14 %
Rwork0.2196 85907 -
obs0.222 90561 96.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 181.06 Å2 / Biso mean: 45.0715 Å2 / Biso min: 24.08 Å2
Refinement stepCycle: final / Resolution: 2.595→49.904 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16458 0 300 72 16830
Biso mean--44.01 39.45 -
Num. residues----2082
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117932
X-RAY DIFFRACTIONf_angle_d0.86924372
X-RAY DIFFRACTIONf_chiral_restr0.0542673
X-RAY DIFFRACTIONf_plane_restr0.0053163
X-RAY DIFFRACTIONf_dihedral_angle_d16.88110778
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.595-2.62420.38731080.297212772
2.6242-2.6550.35951230.2959244084
2.655-2.68740.32481480.2927257589
2.6874-2.72140.36051320.288267192
2.7214-2.75720.31561550.2884278594
2.7572-2.7950.34491570.2831279896
2.795-2.83490.33451470.2813285398
2.8349-2.87720.34511620.2814287899
2.8772-2.92220.33991470.2772290399
2.9222-2.97010.34251390.2785292499
2.9701-3.02130.30491600.2762290299
3.0213-3.07620.30191760.2757289999
3.0762-3.13540.33461710.263289699
3.1354-3.19940.33851830.2581291099
3.1994-3.26890.35471420.265284697
3.2689-3.34490.26351540.2479290299
3.3449-3.42860.28641730.23952933100
3.4286-3.52130.28361780.22762928100
3.5213-3.62480.27971590.21682972100
3.6248-3.74180.24571830.212903100
3.7418-3.87550.24631700.20142926100
3.8755-4.03060.23681370.18792999100
4.0306-4.21390.22651610.18772942100
4.2139-4.4360.22431750.1827293399
4.436-4.71370.21941340.1666294297
4.7137-5.07730.21191500.1775293698
5.0773-5.58770.2341620.19773008100
5.5877-6.39480.28821520.21193022100
6.3948-8.05130.21731610.19513051100
8.0513-49.90.19681550.1761310397
Refinement TLS params.Method: refined / Origin x: -17.464 Å / Origin y: 43.389 Å / Origin z: -23.189 Å
111213212223313233
T0.2108 Å2-0.0182 Å20.0031 Å2-0.3284 Å20.0094 Å2--0.3798 Å2
L0.2356 °20.0196 °2-0.1274 °2-0.8201 °2-0.7859 °2--1.3591 °2
S-0.0171 Å °0.0049 Å °0.0165 Å °-0.0614 Å °0.0736 Å °0.012 Å °0.0415 Å °-0.0403 Å °-0.0514 Å °
Refinement TLS groupSelection details: all

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