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- PDB-3e22: Tubulin-colchicine-soblidotin: Stathmin-like domain complex -

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Basic information

Entry
Database: PDB / ID: 3.0E+22
TitleTubulin-colchicine-soblidotin: Stathmin-like domain complex
Components
  • Stathmin-4
  • Tubulin alpha-1C chain
  • Tubulin beta-2B chain
KeywordsCELL CYCLE / alpha-tubulin / beta-tubulin / colchicine / gtpase / microtubule / soblidotin / stathmin / tubulin
Function / homology
Function and homology information


Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / COPI-dependent Golgi-to-ER retrograde traffic ...Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / Intraflagellar transport / Carboxyterminal post-translational modifications of tubulin / Sealing of the nuclear envelope (NE) by ESCRT-III / Kinesins / Resolution of Sister Chromatid Cohesion / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / COPI-dependent Golgi-to-ER retrograde traffic / COPI-independent Golgi-to-ER retrograde traffic / COPI-mediated anterograde transport / RHO GTPases activate IQGAPs / RHO GTPases Activate Formins / MHC class II antigen presentation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Aggrephagy / The role of GTSE1 in G2/M progression after G2 checkpoint / Separation of Sister Chromatids / Recruitment of NuMA to mitotic centrosomes / Hedgehog 'off' state / positive regulation of axon guidance / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / microtubule-based process / tubulin binding / 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 / hydrolase activity / protein heterodimerization activity / GTPase activity / GTP binding / Golgi apparatus / metal ion binding / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix hairpin bin / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix hairpin bin / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / 60s Ribosomal Protein L30; Chain: A; / 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 / Helix non-globular / Special / Helix Hairpins / Rossmann fold / 2-Layer Sandwich / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-LOC / SOBLIDOTIN / Stathmin-4 / Tubulin alpha-1C chain / Tubulin beta-2B chain
Similarity search - Component
Biological speciesRATTUS NORVEGICUS (Norway rat)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.8 Å
AuthorsCormier, A. / Marchand, M. / Ravelli, R.B. / Knossow, M. / Gigant, B.
CitationJournal: Embo Rep. / Year: 2008
Title: Structural insight into the inhibition of tubulin by vinca domain peptide ligands
Authors: Cormier, A. / Marchand, M. / Ravelli, R.B. / Knossow, M. / Gigant, B.
History
DepositionAug 5, 2008Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 21, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin alpha-1C chain
B: Tubulin beta-2B chain
C: Tubulin alpha-1C chain
D: Tubulin beta-2B chain
E: Stathmin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,31114
Polymers216,8295
Non-polymers3,4829
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17370 Å2
ΔGint-101 kcal/mol
Surface area64090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)324.093, 324.093, 53.280
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31A
41C
51A
61C
12B
22D
32B
42D
52B
62D
72B
82D

NCS domain segments:

Refine code: 1

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ARGARGALAALAAA2 - 2402 - 240
211ARGARGALAALACC2 - 2402 - 240
321VALVALVALVALAA260 - 324260 - 324
421VALVALVALVALCC260 - 324260 - 324
531GLNGLNMGMGAA - G358 - 601358
631GLNGLNMGMGCC - L358 - 601358
112ARGARGMETMETBB2 - 1722 - 170
212ARGARGMETMETDD2 - 1722 - 170
322THRTHRPHEPHEBB180 - 214178 - 212
422THRTHRPHEPHEDD180 - 214178 - 212
532ASPASPLEULEUBB226 - 387224 - 377
632ASPASPLEULEUDD226 - 387224 - 377
742GLNGLNLOCLOCBB - I394 - 700384
842GLNGLNLOCLOCDD - N394 - 700384

NCS ensembles :
ID
1
2

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Components

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Protein , 3 types, 5 molecules ACBDE

#1: Protein Tubulin alpha-1C chain / tubulin alpha chain


Mass: 50088.262 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: brain / References: UniProt: Q3ZCJ7
#2: Protein Tubulin beta-2B chain / tubulin beta chain


Mass: 49969.797 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Bos taurus (domestic cattle) / Organ: brain / References: UniProt: Q6B856
#3: Protein Stathmin-4 / Stathmin-like protein B3 / RB3


Mass: 16712.967 Da / Num. of mol.: 1 / Fragment: RB3 stathmin-like domain 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) RATTUS NORVEGICUS (Norway rat) / Gene: STMN4 / Plasmid: PET-8C / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P63043

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Non-polymers , 5 types, 9 molecules

#4: 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
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: 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
#7: Chemical ChemComp-LOC / N-[(7S)-1,2,3,10-tetramethoxy-9-oxo-6,7-dihydro-5H-benzo[d]heptalen-7-yl]ethanamide / COLCHICINE


Mass: 399.437 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H25NO6
#8: Chemical ChemComp-TZT / SOBLIDOTIN / TZT-1027


Mass: 701.979 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H67N5O6

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Details

Sequence detailsTHERE IS ONE COMPLEX IN THE ASYMMETRIC UNIT, WHICH CONSISTS OF TWO ALPHA-BETA TUBULIN HETERODIMERS ...THERE IS ONE COMPLEX IN THE ASYMMETRIC UNIT, WHICH CONSISTS OF TWO ALPHA-BETA TUBULIN HETERODIMERS (CHAINS A-B AND C-D), AND ONE STATHMIN-LIKE DOMAIN OF RB3 (RB3-SLD) WHICH CORRESPONDS TO STAHMIN RESIDUES 5 TO 145 WITH THE ADDITION OF ONE ACETYLATED ALANINE AT THE N-TERMINUS. THE NUMBERING OF RB3-SLD IS ACCORDING TO THE STATHMIN SEQUENCE. ALPHA- TUBULIN AND BETA-TUBULIN HAVE BEEN ALIGNED AS IN NOGALES ET AL., NATURE VOL 391,199-203. IN THIS ALIGNMENT, RESIDUES 45-46 AND 361-368 OF ALPHA-TUBULIN ARE MISSING IN BETA- TUBULIN. THERE ARE SEVERAL EXPRESSED TUBULIN ISOTYPES IN MAMMALIAN BRAIN. WE USED THE BOS TAURUS TUBULIN SEQUENCE OF THE MOST ABUNDANT ISOTYPES (ALPHA: ISOTYPE 1, GI:73586894, BETA: ISOTYPE 2, GI:51491829) BUT WITH THE ILE TO VAL SUBSTITUTION AT POSITION 318 ON BETA TUBULIN.

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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: 3.73 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG, PIPES buffer, The crystal of tubulin-colchicine:RB3-SLD complex was soaked with a 2.0mM soblidotin solution for 24 hours., pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9786 / Wavelength: 0.9786 Å
DetectorType: ADSC / Detector: CCD / Date: Jul 3, 2003 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 3.8→35 Å / Num. all: 32732 / Num. obs: 32732 / % possible obs: 98.3 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rsym value: 0.063 / Net I/σ(I): 20
Reflection shellResolution: 3.8→3.87 Å / Mean I/σ(I) obs: 2.3 / Rsym value: 0.469 / % possible all: 94.9

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.1.24refinement
ADSCQuantumdata collection
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SA0

1sa0


Resolution: 3.8→20 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.89 / SU B: 53.956 / SU ML: 0.711 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.792 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2948 1598 5.1 %RANDOM
Rwork0.229 ---
all0.2313 32176 --
obs0.2313 31414 97.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 95.446 Å2
Baniso -1Baniso -2Baniso -3
1-3.54 Å21.77 Å20 Å2
2--3.54 Å20 Å2
3----5.31 Å2
Refinement stepCycle: LAST / Resolution: 3.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13924 0 230 0 14154
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.02114488
X-RAY DIFFRACTIONr_angle_refined_deg1.9531.95919704
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.22251799
X-RAY DIFFRACTIONr_chiral_restr0.1330.22173
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211139
X-RAY DIFFRACTIONr_nbd_refined0.2960.27786
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2120.2613
X-RAY DIFFRACTIONr_metal_ion_refined0.2360.22
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.4470.250
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1010.22
X-RAY DIFFRACTIONr_mcbond_it0.1391.58994
X-RAY DIFFRACTIONr_mcangle_it0.252214425
X-RAY DIFFRACTIONr_scbond_it0.33935494
X-RAY DIFFRACTIONr_scangle_it0.5484.55279
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A2881tight positional0.070.05
2B3110tight positional0.050.05
1A2881tight thermal0.090.5
2B3110tight thermal0.070.5
LS refinement shellResolution: 3.8→3.895 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.456 104
Rwork0.399 2023
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)
15.4545-2.72180.90445.5892-0.4043.08910.0578-0.3505-0.71720.31190.15650.69140.3816-0.4366-0.21430.21940.1041-0.16120.26690.10360.3962165.62963.23550.924
27.596-2.59650.74634.65040.32224.47780.00260.36960.2634-0.27770.2569-0.379-0.36070.2414-0.25950.63070.4849-0.30.4693-0.10050.4373202.8245.24639.401
38.6959-4.5196-0.46517.3235-0.57942.24740.63010.54790.6557-0.7279-0.1027-0.5708-0.30510.0449-0.52740.96070.4676-0.24080.8128-0.63311.0335239.22722.89632.274
47.1984-2.34560.65195.5995-1.04896.26750.09620.1782-0.4693-0.8056-0.3392-0.09460.22930.51490.2431.05590.4726-0.03810.7198-0.57681.0483270.343-4.75929.985
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 437
2X-RAY DIFFRACTION1E4 - 64
3X-RAY DIFFRACTION2B2 - 438
4X-RAY DIFFRACTION2E65 - 89
5X-RAY DIFFRACTION3C2 - 437
6X-RAY DIFFRACTION3E90 - 115
7X-RAY DIFFRACTION4D2 - 438
8X-RAY DIFFRACTION4E116 - 141

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