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- PDB-9k7e: Crystal structure of T2R-TTL-taccalonolide Y8 complex -

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Basic information

Entry
Database: PDB / ID: 9k7e
TitleCrystal structure of T2R-TTL-taccalonolide Y8 complex
Components
  • Detyrosinated tubulin alpha-1B chain
  • Stathmin-4
  • Tubulin beta-2B chain
  • Tubulin--tyrosine ligase
KeywordsSTRUCTURAL PROTEIN / tubulin / inhibitor
Function / homology
Function and homology information


tubulin-tyrosine ligase / tubulin-tyrosine ligase activity / positive regulation of axon guidance / 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 / tubulin-tyrosine ligase activity / positive regulation of axon guidance / 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 / microtubule depolymerization / 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 / tubulin binding / spindle microtubule / structural constituent of cytoskeleton / microtubule cytoskeleton organization / neuron migration / neuron projection development / mitotic cell cycle / microtubule cytoskeleton / growth cone / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / neuron projection / protein heterodimerization activity / GTPase activity / GTP binding / Golgi apparatus / ATP binding / 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. / 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
Similarity search - Domain/homology
: / PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Tubulin--tyrosine ligase / Stathmin-4 / Tubulin alpha-1B chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciesSus scrofa (pig)
Bos taurus (domestic cattle)
Rattus norvegicus (Norway rat)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsYu, Q.W. / Wang, Y.X.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Crystal structure of T2R-TTL-taccalonolide Y8 complex
Authors: Yu, Q.W. / Wang, Y.X.
History
DepositionOct 23, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 5, 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
B: Tubulin beta-2B chain
C: Detyrosinated 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)258,74819
Polymers255,3866
Non-polymers3,36313
Water724
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)104.830, 157.190, 181.650
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 ACBDEF

#1: Protein Detyrosinated tubulin alpha-1B chain


Mass: 48966.324 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-2B chain


Mass: 48391.410 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: TUBB2B / Production host: Escherichia coli (E. coli) / References: UniProt: Q6B856
#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: 43825.914 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gallus gallus (chicken) / Production host: Escherichia coli (E. coli) / References: UniProt: A0A8C9FGJ1, tubulin-tyrosine ligase

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Non-polymers , 8 types, 17 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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#7: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#8: Chemical ChemComp-A1EE1 / (4~{R})-5-(4-hydroxyphenyl)-3-(4-methylphenyl)-4-phenyl-2,4-dihydropyrrolo[3,4-c]pyrazol-6-one


Mass: 381.427 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H19N3O2
#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: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#11: 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 / Feature type: SUBJECT OF INVESTIGATION / Comment: AMP-PCP, energy-carrying molecule analogue*YM
#12: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 4 / 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: 2.93 Å3/Da / Density % sol: 58.05 %
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: SSRF / Beamline: BL18U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.45→52.43 Å / Num. obs: 110769 / % possible obs: 100 % / Redundancy: 13.5 % / CC1/2: 0.995 / Net I/σ(I): 10.4
Reflection shellResolution: 2.45→2.51 Å / Num. unique obs: 8089 / CC1/2: 0.712

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Processing

Software
NameVersionClassification
PHENIX(1.21_5207: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→52.43 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2673 1999 1.81 %
Rwork0.2137 --
obs0.2147 110666 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.45→52.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17175 0 181 4 17360
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_dihedral_angle_d16.8676566
X-RAY DIFFRACTIONf_chiral_restr0.052624
X-RAY DIFFRACTIONf_plane_restr0.0083116
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.45-2.510.41911420.31297680X-RAY DIFFRACTION100
2.51-2.580.31451400.27797643X-RAY DIFFRACTION100
2.58-2.660.31841420.25317710X-RAY DIFFRACTION100
2.66-2.740.30891410.25367659X-RAY DIFFRACTION100
2.74-2.840.30711420.2577730X-RAY DIFFRACTION100
2.84-2.950.33551420.26267700X-RAY DIFFRACTION100
2.95-3.090.3761410.25857717X-RAY DIFFRACTION100
3.09-3.250.29491430.24357705X-RAY DIFFRACTION100
3.25-3.450.28091420.23457742X-RAY DIFFRACTION100
3.45-3.720.2541430.21987754X-RAY DIFFRACTION100
3.72-4.090.26431430.18697806X-RAY DIFFRACTION100
4.09-4.690.22871440.16797808X-RAY DIFFRACTION100
4.69-5.90.21521460.18947891X-RAY DIFFRACTION100
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)
11.32940.51741.04991.66070.19431.21970.0936-0.1589-0.220.39560.154-0.23360.9050.4174-0.25150.85740.1908-0.14770.5435-0.11950.559929.205-97.1482-53.955
20.99250.5577-0.66772.3237-0.31.6460.0626-0.5313-0.00970.2548-0.1581-0.2350.7290.2103-0.01170.68760.1256-0.11430.5978-0.03040.544428.4697-87.0892-42.7304
30.75420.1161-0.08172.35461.19191.62020.0394-0.0477-0.0351-0.0290.3984-0.50460.18320.6163-0.36670.42160.069-0.08130.6474-0.26680.607335.1272-78.039-55.1774
41.07630.2932-0.74141.6133-0.32212.22310.2012-0.02170.0088-0.16650.02060.04110.22130.2707-0.19870.4491-0.008-0.06740.4313-0.12940.46320.954-84.4111-64.6996
50.8039-0.47330.35531.310.70581.69640.2142-0.1025-0.0326-0.4331-0.22920.68250.2602-0.3834-0.03410.5914-0.0377-0.15820.4805-0.08740.5319.1829-84.4584-71.8739
60.7011-0.01080.11652.01081.05031.92790.0210.07650.0342-0.42140.1321-0.0207-0.03780.2594-0.14350.4725-0.01550.00060.4542-0.10960.433822.9814-76.7315-69.9046
72.3403-0.81010.27173.09280.45722.6346-0.3352-0.387-0.55880.51280.51860.19950.35680.152-0.17370.3571-0.03070.01340.4462-0.0550.491415.824-64.4008-21.6862
82.86820.79520.68982.0057-0.12061.75550.4494-0.4194-0.62390.638-0.35080.03560.6676-0.0874-0.12110.665-0.0503-0.06380.4337-0.00810.622116.3949-72.3688-17.8687
90.91710.51790.12261.91910.04661.63360.0814-0.2873-0.09420.3230.0789-0.32140.34660.3283-0.15650.42940.0732-0.06810.5871-0.08220.509729.0327-56.3987-14.5689
100.94370.82090.63752.31320.95032.3952-0.02210.01140.0430.0355-0.03390.0670.0809-0.08880.04290.2774-0.008-0.00820.4148-0.10880.418917.1009-53.9206-26.7439
111.67860.1141-0.53910.2145-0.11711.9280.16530.0645-0.26190.0895-0.21190.3270.2285-0.01840.04160.3974-0.0307-0.0350.3789-0.17040.526819.2134-61.8214-39.6965
122.25451.23151.04071.77570.7830.5674-0.0581-0.40240.20480.3625-0.21140.48020.361-1.61070.13210.5028-0.16330.08420.9342-0.20630.7703-4.1274-62.879-34.4663
131.68950.3424-0.3571.12490.21811.3619-0.07740.11880.0252-0.1167-0.00920.14420.1041-0.5390.10260.5021-0.0539-0.03440.603-0.14650.53346.4581-61.0198-44.6153
140.39040.70280.20461.90831.12821.6025-0.14930.10950.0738-0.5904-0.05620.6846-0.3782-0.13110.19460.4063-0.0104-0.06730.4428-0.08380.499215.1396-42.3121-34.0303
150.64810.1370.06071.81052.11023.2046-0.06140.15210.1699-0.56230.1752-0.3012-0.78610.757-0.12480.4349-0.03850.05810.4437-0.04060.458625.3416-38.2152-30.9732
160.93050.0368-0.06261.93960.20481.3247-0.0554-0.2012-0.03390.22450.0899-0.0240.08280.0528-0.0380.33650.0619-0.01790.3972-0.02110.343317.9659-31.490111.3249
170.80190.25190.25581.14960.78031.595-0.0856-0.0175-0.0491-0.07190.00380.0792-0.0871-0.1420.07540.27070.0743-0.02240.3103-0.04430.33848.2199-26.4507-4.24
181.7136-0.28790.58031.51440.6040.5575-0.6394-1.29210.10520.65370.74210.37720.0517-0.5571-0.04090.80630.3339-0.04691.2051-0.15980.469917.4451-4.936340.3152
192.17720.47710.16362.161-0.41791.4878-0.1054-1.0342-0.18220.58060.1767-0.0256-0.0946-0.2498-0.01360.73670.1710.02061.0495-0.0320.481917.1672-11.121445.7407
200.64170.1464-0.24992.24120.32311.4129-0.2878-0.73380.27760.79340.3657-0.7793-0.30040.6349-0.06120.87970.1841-0.27251.0892-0.24910.724933.81671.317143.7876
211.81050.0467-0.03051.1589-0.67931.8798-0.3269-0.49890.40810.72660.3155-0.3375-0.38920.0422-0.02860.660.1567-0.15490.6518-0.21610.459926.83411.189634.0002
220.4188-0.05590.43571.10990.07572.2369-0.3618-0.49040.2990.3210.27040.0582-0.6332-0.38810.06560.84960.265-0.1210.8265-0.30080.612915.38410.087733.8717
230.6712-0.3692-0.30.29140.1092.1707-0.0785-0.24040.06730.09510.07330.12870.07530.06140.02670.50970.0393-0.05590.5551-0.13090.487317.9936-6.990722.8699
240.20090.19510.37370.74920.30061.409-0.4769-0.4240.61120.23550.33770.419-0.5886-0.94140.16650.75310.2496-0.03711.0174-0.20580.65184.75916.031523.3995
251.4263-0.28970.2391.4279-0.08592.38-0.2419-0.35140.13920.13530.16850.0173-0.4047-0.38870.07750.5610.1677-0.07980.5779-0.13610.49679.18853.056520.7647
261.8840.3558-0.39560.98770.03591.0867-0.1598-0.04470.6893-0.0030.1043-0.1795-0.43010.60070.01110.87710.0304-0.19590.4856-0.26710.819230.427616.830523.8452
271.44090.33290.00121.86510.93811.36750.04680.0337-0.1364-0.5560.0904-0.1298-0.12720.836-0.10180.85880.03430.02950.8169-0.1740.644427.5727-92.3247-82.2846
280.28060.43890.73470.08430.28560.2569-0.19020.0677-0.0312-0.61890.4367-0.2149-0.75460.7054-0.24170.5927-0.06790.00140.7503-0.23060.665642.723-28.5281-5.2158
291.5913-0.24641.47831.3311-0.14922.0217-0.5335-0.21340.39810.14110.138-0.0454-1.0376-0.24070.30090.96820.0745-0.14870.5151-0.14570.68326.1907-54.6627-69.8233
302.0673-0.4228-0.13352.1161-1.99742.0417-0.16670.36420.2286-0.77790.1896-0.33530.21390.4125-0.00160.7951-0.1142-0.05090.7560.01760.56111.2464-65.5718-97.3549
311.8689-0.9648-0.5692.1268-0.71010.7869-0.10120.48070.259-1.1697-0.0424-0.6643-0.56580.630.1790.9919-0.24150.16541.4720.2740.976420.7769-55.7047-108.7561
321.0971-0.31160.85890.6966-0.65922.393-0.53030.13380.60440.09890.0471-0.1085-1.2299-0.0260.42881.0166-0.091-0.2920.51680.17380.816-1.6426-53.0885-97.0154
331.26510.30351.2950.76250.15191.3019-0.39140.16950.508-0.21570.2455-0.6689-0.4813-0.45380.071.5331-0.215-0.2690.95260.35341.41396.4996-40.6752-105.7248
341.53010.64111.43260.73750.3382.6464-0.36960.18710.5131-0.27750.15550.1751-0.63360.04290.07390.8814-0.0803-0.15540.47760.07640.6608-2.0515-57.7407-95.0829
351.90430.15510.85821.0449-0.63112.8274-0.3816-0.41990.51260.18260.45080.2913-0.7114-0.6202-0.04670.8480.2068-0.10110.606-0.03190.7958-7.4319-56.2885-79.819
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 72 )
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 102 )
3X-RAY DIFFRACTION3chain 'A' and (resid 103 through 199 )
4X-RAY DIFFRACTION4chain 'A' and (resid 200 through 273 )
5X-RAY DIFFRACTION5chain 'A' and (resid 274 through 311 )
6X-RAY DIFFRACTION6chain 'A' and (resid 312 through 437 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 27 )
8X-RAY DIFFRACTION8chain 'B' and (resid 28 through 86 )
9X-RAY DIFFRACTION9chain 'B' and (resid 87 through 126 )
10X-RAY DIFFRACTION10chain 'B' and (resid 127 through 241 )
11X-RAY DIFFRACTION11chain 'B' and (resid 242 through 271 )
12X-RAY DIFFRACTION12chain 'B' and (resid 272 through 293 )
13X-RAY DIFFRACTION13chain 'B' and (resid 294 through 363 )
14X-RAY DIFFRACTION14chain 'B' and (resid 364 through 391 )
15X-RAY DIFFRACTION15chain 'B' and (resid 392 through 428 )
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 223 )
17X-RAY DIFFRACTION17chain 'C' and (resid 224 through 440 )
18X-RAY DIFFRACTION18chain 'D' and (resid 1 through 28 )
19X-RAY DIFFRACTION19chain 'D' and (resid 29 through 86 )
20X-RAY DIFFRACTION20chain 'D' and (resid 87 through 125 )
21X-RAY DIFFRACTION21chain 'D' and (resid 126 through 178 )
22X-RAY DIFFRACTION22chain 'D' and (resid 179 through 236 )
23X-RAY DIFFRACTION23chain 'D' and (resid 237 through 264 )
24X-RAY DIFFRACTION24chain 'D' and (resid 265 through 309 )
25X-RAY DIFFRACTION25chain 'D' and (resid 310 through 391 )
26X-RAY DIFFRACTION26chain 'D' and (resid 392 through 431 )
27X-RAY DIFFRACTION27chain 'E' and (resid 6 through 46 )
28X-RAY DIFFRACTION28chain 'E' and (resid 47 through 141 )
29X-RAY DIFFRACTION29chain 'F' and (resid 1 through 66 )
30X-RAY DIFFRACTION30chain 'F' and (resid 67 through 96 )
31X-RAY DIFFRACTION31chain 'F' and (resid 97 through 183 )
32X-RAY DIFFRACTION32chain 'F' and (resid 184 through 223 )
33X-RAY DIFFRACTION33chain 'F' and (resid 224 through 257 )
34X-RAY DIFFRACTION34chain 'F' and (resid 258 through 339 )
35X-RAY DIFFRACTION35chain 'F' and (resid 340 through 380 )

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