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- PDB-9gmy: Tubulin in complex with an oxathiane analog of zampanolide -

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Basic information

Entry
Database: PDB / ID: 9gmy
TitleTubulin in complex with an oxathiane analog of zampanolide
Components
  • Stathmin-4
  • Tubulin alpha-1B chain
  • Tubulin beta-2B chain
  • Tubulin tyrosine ligase
KeywordsCELL CYCLE / tubulin / microtubule stabilizing agents / zampanolide
Function / homology
Function and homology information


tubulin-tyrosine ligase / regulation of metaphase plate congression / 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 ...tubulin-tyrosine ligase / regulation of metaphase plate congression / 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 / positive regulation of mitotic cell cycle / post-translational protein modification / spindle microtubule / 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 / GTPase activity / ubiquitin protein ligase binding / GTP binding / Golgi apparatus / metal ion binding / cytoplasm / cytosol
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 / 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 (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsOliva, M.A. / Diaz, J.F. / Altmann, K.H.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)CNS2023-145079 Spain
CitationJournal: To Be Published
Title: Tubulin in complex with an oxathiane analog of zampanolide
Authors: Oliva, M.A. / Diaz, J.F. / Altmann, K.H.
History
DepositionAug 30, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 10, 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: 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)271,08326
Polymers266,9126
Non-polymers4,17120
Water23,3111294
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area23240 Å2
ΔGint-171 kcal/mol
Surface area78130 Å2
Unit cell
Length a, b, c (Å)104.907, 158.35, 178.836
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
32B
42D

NCS domain segments:

Beg auth comp-ID: ARG / Beg label comp-ID: ARG

Dom-IDComponent-IDEns-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111VALVALAA2 - 4372 - 437
211VALVALCC2 - 4372 - 437
322ALAALABB2 - 4382 - 428
422ALAALADD2 - 4382 - 428

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4

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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 (domestic 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 (domestic 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: 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 , 11 types, 1314 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.: 3 / Source method: obtained synthetically / Formula: Ca
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#10: 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
#11: 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
#12: Chemical ChemComp-A1IM9 / (2Z,4E)-N-[(S)-[(1R,2E,5S,8E,10Z,17S)-3,11-dimethyl-7,13-bis(oxidanylidene)-6,21-dioxa-19-thiabicyclo[15.3.1]henicosa-2,8,10-trien-5-yl]-oxidanyl-methyl]hexa-2,4-dienamide


Mass: 503.651 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H37NO6S / Feature type: SUBJECT OF INVESTIGATION
#13: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#14: 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
#15: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1294 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 2.78 Å3/Da / Density % sol: 55.8 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 0.1 M Mes/0.1M Imidazole, 0.03M CaCl2/MgCl2, 5 mM L-Tyr, 2.5% glycerol, 4.6% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Mar 3, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.97→49.306 Å / Num. obs: 209850 / % possible obs: 99.9 % / Redundancy: 9.4 % / Biso Wilson estimate: 38.629 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.064 / Rpim(I) all: 0.021 / Rrim(I) all: 0.067 / Net I/av σ(I): 8.6 / Net I/σ(I): 18.8
Reflection shellResolution: 1.97→2 Å / Redundancy: 8.1 % / Rmerge(I) obs: 1.386 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 10323 / CC1/2: 0.539 / Rpim(I) all: 0.507 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→49.306 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.957 / SU B: 7.118 / SU ML: 0.097 / Cross valid method: FREE R-VALUE / ESU R: 0.126 / ESU R Free: 0.125
Details: Hydrogens have been used if present in the input file
RfactorNum. reflection% reflection
Rfree0.2024 10427 4.971 %
Rwork0.1602 199310 -
all0.162 --
obs-209737 99.93 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 49.186 Å2
Baniso -1Baniso -2Baniso -3
1-0.723 Å20 Å20 Å2
2--0.257 Å2-0 Å2
3----0.98 Å2
Refinement stepCycle: LAST / Resolution: 1.97→49.306 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16991 0 259 1294 18544
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01218094
X-RAY DIFFRACTIONr_bond_other_d0.0010.01616690
X-RAY DIFFRACTIONr_angle_refined_deg2.2981.83624613
X-RAY DIFFRACTIONr_angle_other_deg0.7811.75938519
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.72952235
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.1295138
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg11.483529
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.744103055
X-RAY DIFFRACTIONr_dihedral_angle_other_3_deg1.62101
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.56910867
X-RAY DIFFRACTIONr_chiral_restr0.1150.22686
X-RAY DIFFRACTIONr_chiral_restr_other0.1320.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0221545
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024234
X-RAY DIFFRACTIONr_nbd_refined0.2420.23753
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.215753
X-RAY DIFFRACTIONr_nbtor_refined0.1870.28952
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.210063
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2170.21259
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1330.25
X-RAY DIFFRACTIONr_metal_ion_refined0.1240.28
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2040.226
X-RAY DIFFRACTIONr_nbd_other0.1860.267
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1640.227
X-RAY DIFFRACTIONr_mcbond_it3.1812.6978818
X-RAY DIFFRACTIONr_mcbond_other3.1812.6978819
X-RAY DIFFRACTIONr_mcangle_it3.9854.82311083
X-RAY DIFFRACTIONr_mcangle_other3.9874.82111072
X-RAY DIFFRACTIONr_scbond_it5.0753.2039276
X-RAY DIFFRACTIONr_scbond_other5.0753.2039276
X-RAY DIFFRACTIONr_scangle_it7.1035.6513516
X-RAY DIFFRACTIONr_scangle_other7.1035.6513517
X-RAY DIFFRACTIONr_lrange_it9.09230.19320821
X-RAY DIFFRACTIONr_lrange_other9.10229.20120465
X-RAY DIFFRACTIONr_ncsr_local_group_10.1330.0513407
X-RAY DIFFRACTIONr_ncsr_local_group_20.1230.0513894
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.13310.05007
12AX-RAY DIFFRACTIONLocal ncs0.13310.05007
23AX-RAY DIFFRACTIONLocal ncs0.123050.05007
24AX-RAY DIFFRACTIONLocal ncs0.123050.05007
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.97-2.0210.2987970.276146230.277154330.9360.94599.91580.26
2.021-2.0760.2767640.249141480.25149170.9490.95999.96650.226
2.076-2.1360.2587680.208138550.211146240.9570.97299.99320.181
2.136-2.2020.226900.182134120.184141040.9680.97899.98580.156
2.202-2.2740.2296920.174130620.177137590.9680.98199.96370.147
2.274-2.3540.2176230.154126530.156132870.9720.98699.91720.129
2.354-2.4420.1876420.145122300.147128820.9780.98799.92240.122
2.442-2.5420.2025880.143117210.146123300.9750.98899.82970.122
2.542-2.6550.1866390.137112420.14118930.9790.98999.89910.118
2.655-2.7840.2055290.152108070.154113490.9730.98799.88550.133
2.784-2.9340.2045420.148102990.151108550.9750.98799.8710.134
2.934-3.1110.25020.15497500.156102520.9750.9861000.143
3.111-3.3250.2064630.16391820.16596460.9770.98699.98960.155
3.325-3.590.214920.16885280.1790200.9770.9861000.164
3.59-3.9310.1833970.15279190.15383180.9820.98999.9760.152
3.931-4.3910.173700.1372010.13275710.9840.991000.135
4.391-5.0640.1483310.12663810.12767140.9870.99299.97020.134
5.064-6.1850.2482620.17854590.18157210.9730.9851000.186
6.185-8.6790.2122040.17643030.17745110.9790.98599.91130.187
8.679-49.3060.2261320.19725350.19926770.970.97699.62640.213
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)
10.91860.0411-0.30492.09190.69291.38780.0524-0.00570.09850.12420.00960.0761-0.17520.0016-0.0620.12690.00710.01860.0979-0.08470.089125.517983.560560.6867
20.9789-0.2080.02931.49730.89561.9456-0.0078-0.02590.13980.0356-0.06830.1884-0.2054-0.20460.0760.06260.0101-0.00110.1442-0.08790.139316.168357.260629.2673
30.9259-0.25920.10251.29280.49941.2137-0.01030.03210.0672-0.00310.02080.084-0.0495-0.0561-0.01060.0094-0.01670.01760.0637-0.0390.06213.336229.1098-3.7337
41.42410.0249-0.29121.05860.13691.5856-0.06830.2832-0.0804-0.16770.1004-0.06250.1230.0011-0.03210.1385-0.03010.00880.1835-0.1240.09717.5143-1.5808-32.1879
50.1301-0.1224-0.10121.96721.97162.2405-0.03310.0156-0.02340.21410.2643-0.2360.22430.3668-0.23120.1059-0.00990.02290.2581-0.10280.257139.951241.797919.4393
61.12780.1538-1.18071.0277-0.40562.9463-0.1211-0.0655-0.31260.01250.1147-0.10610.42640.18260.00650.32770.01370.00990.11750.00520.25194.095356.774591.0152
Refinement TLS groupSelection: ALL

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