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- PDB-7cpd: Crystal structure of T2R-TTL-(+)-6-Br-JP18 complex -

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Basic information

Entry
Database: PDB / ID: 7cpd
TitleCrystal structure of T2R-TTL-(+)-6-Br-JP18 complex
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
  • Tubulin tyrosine ligase
KeywordsCEll CYCLE/INHIBITOR / CELL 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-G9U / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin tyrosine ligase / Tubulin alpha-1B chain / Tubulin beta-2B chain / Stathmin-4
Similarity search - Component
Biological speciesHomo sapiens (human)
Gallus gallus (chicken)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.506 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-Br-JP18 complex
Authors: Jiang, H. / Luo, C.
History
DepositionAug 6, 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)269,23320
Polymers266,0846
Non-polymers3,15014
Water6,125340
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: assay for oligomerization
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20770 Å2
ΔGint-133 kcal/mol
Surface area78680 Å2
Unit cell
Length a, b, c (Å)104.782, 156.552, 182.591
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.) Homo sapiens (human) / Gene: STMN4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9H169
#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 , 8 types, 354 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.: 3 / 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-G9U / (6R)-6-[(6-bromanyl-1H-indol-3-yl)methyl]-6,7,8,9-tetrahydrobenzo[7]annulen-5-one


Mass: 368.267 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H18BrNO / 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#12: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 340 / 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: 2.81 Å3/Da / Density % sol: 56.29 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.7
Details: 6-10% PEG 4k, 4-10% glycerol, 30 mM MgCl2, 100 mM MES/Imidazole pH 6.5-6.9
PH range: 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: 2.506→49.89 Å / Num. obs: 102800 / % possible obs: 99.4 % / Redundancy: 13 % / Biso Wilson estimate: 35.09 Å2 / CC1/2: 0.995 / Rmerge(I) obs: 0.089 / Net I/σ(I): 26.4
Reflection shellResolution: 2.506→2.596 Å / Num. unique obs: 8435 / CC1/2: 0.813

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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: 2.506→49.886 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 24.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.24 5063 5.04 %
Rwork0.183 95434 -
obs0.1859 100497 97.03 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 140.32 Å2 / Biso mean: 50.1375 Å2 / Biso min: 17.26 Å2
Refinement stepCycle: final / Resolution: 2.506→49.886 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16725 0 295 340 17360
Biso mean--49.09 45.49 -
Num. residues----2116
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00817938
X-RAY DIFFRACTIONf_angle_d0.9424389
X-RAY DIFFRACTIONf_chiral_restr0.0512674
X-RAY DIFFRACTIONf_plane_restr0.0063163
X-RAY DIFFRACTIONf_dihedral_angle_d16.51710777
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.5061-2.53460.30711340.233243676
2.5346-2.56440.29441560.2345268483
2.5644-2.59570.30691440.2204288089
2.5957-2.62860.321380.2203295991
2.6286-2.66320.28441490.2179307094
2.6632-2.69960.26751900.2171310496
2.6996-2.73820.28891790.2099316798
2.7382-2.77910.26291850.2176316598
2.7791-2.82250.28711650.21223256100
2.8225-2.86880.29531600.2153318999
2.8688-2.91820.26561610.2091316797
2.9182-2.97130.28931490.21533269100
2.9713-3.02840.27361820.21483208100
3.0284-3.09020.28151940.20243280100
3.0902-3.15740.25481830.19833218100
3.1574-3.23080.28281690.21163236100
3.2308-3.31160.26641840.2053252100
3.3116-3.40110.28341690.20043275100
3.4011-3.50120.25341830.18883238100
3.5012-3.61420.22851550.1813283100
3.6142-3.74330.23311680.1758325299
3.7433-3.89310.19981700.1652323499
3.8931-4.07020.22091790.15613263100
4.0702-4.28470.19551850.15623298100
4.2847-4.5530.22641810.14663296100
4.553-4.90430.18551650.14273309100
4.9043-5.39730.21161800.16083327100
5.3973-6.1770.24561630.1791326397
6.177-7.77770.23091730.18133378100
7.7777-49.880.19051700.1706347898
Refinement TLS params.Method: refined / Origin x: -17.3482 Å / Origin y: 43.5741 Å / Origin z: -26.133 Å
111213212223313233
T0.1134 Å2-0.0267 Å20.0029 Å2-0.2442 Å20.0403 Å2--0.3038 Å2
L0.2452 °20.0423 °2-0.1961 °2-0.756 °2-0.7176 °2--1.3454 °2
S-0.0234 Å °-0.0037 Å °0.0198 Å °-0.075 Å °0.1067 Å °0.0256 Å °0.0535 Å °-0.0767 Å °-0.0611 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 437
2X-RAY DIFFRACTION1allB2 - 438
3X-RAY DIFFRACTION1allC1 - 440
4X-RAY DIFFRACTION1allD1 - 441
5X-RAY DIFFRACTION1allE6 - 141
6X-RAY DIFFRACTION1allF1 - 378
7X-RAY DIFFRACTION1allG1
8X-RAY DIFFRACTION1allG2
9X-RAY DIFFRACTION1allH4
10X-RAY DIFFRACTION1allI1 - 3
11X-RAY DIFFRACTION1allJ1 - 3
12X-RAY DIFFRACTION1allK1 - 3
13X-RAY DIFFRACTION1allL1 - 2
14X-RAY DIFFRACTION1allM1
15X-RAY DIFFRACTION1allS1 - 380

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