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- PDB-3ut5: Tubulin-Colchicine-Ustiloxin: Stathmin-like domain complex -

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Basic information

Entry
Database: PDB / ID: 3ut5
TitleTubulin-Colchicine-Ustiloxin: Stathmin-like domain complex
Components
  • Stathmin-4
  • Tubulin alpha chain
  • Tubulin beta chain
  • Vinca tetrapeptide
KeywordsSTRUCTURAL PROTEIN/INHIBITOR / Microtubules / Tubulin / Vinca domain / Ustiloxin / Stathmin / STRUCTURAL PROTEIN / STRUCTURAL PROTEIN-INHIBITOR complex
Function / homology
Function and homology information


axonemal microtubule / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / neuron projection arborization / cerebellar cortex morphogenesis / dentate gyrus development / pyramidal neuron differentiation / centrosome cycle / motor behavior ...axonemal microtubule / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / neuron projection arborization / cerebellar cortex morphogenesis / dentate gyrus development / pyramidal neuron differentiation / centrosome cycle / motor behavior / microtubule depolymerization / response to L-glutamate / smoothened signaling pathway / regulation of synapse organization / startle response / locomotory exploration behavior / microtubule polymerization / regulation of microtubule polymerization or depolymerization / response to tumor necrosis factor / condensed chromosome / response to mechanical stimulus / homeostasis of number of cells within a tissue / cellular response to calcium ion / tubulin binding / adult locomotory behavior / intracellular protein transport / neuron migration / synapse organization / visual learning / neuromuscular junction / recycling endosome / cerebral cortex development / structural constituent of cytoskeleton / memory / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / neuron projection development / mitotic cell cycle / gene expression / growth cone / neuron apoptotic process / microtubule / hydrolase activity / neuron projection / protein heterodimerization activity / GTPase activity / protein-containing complex binding / GTP binding / Golgi apparatus / identical protein binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #30 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Stathmin family / Stathmin, conserved site / Stathmin superfamily / Stathmin family / Stathmin family signature 1. / Stathmin family signature 2. / Stathmin-like (SLD) domain profile. / 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
N-{[(3R,4R,7S,10R,11R)-3-ethyl-11,15-dihydroxy-3-methyl-10-(methylamino)-6,9-dioxo-7-(propan-2-yl)-2-oxa-5,8-diazabicyclo[10.3.1]hexadeca-1(16),12,14-trien-4-yl]carbonyl}glycine / GUANOSINE-5'-DIPHOSPHATE / GUANOSINE-5'-TRIPHOSPHATE / Chem-LOC / Tubulin beta chain / Tubulin alpha chain / Stathmin-4
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
Ovis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.73 Å
AuthorsRanaivoson, F.M. / Gigant, B. / Knossow, M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structural plasticity of tubulin assembly probed by vinca-domain ligands.
Authors: Ranaivoson, F.M. / Gigant, B. / Berritt, S. / Joullie, M. / Knossow, M.
History
DepositionNov 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 1, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Other
Revision 1.2Jan 23, 2013Group: Database references
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / pdbx_validate_torsion / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tubulin alpha chain
B: Tubulin beta chain
C: Tubulin alpha chain
D: Tubulin beta chain
E: Stathmin-4
F: Vinca tetrapeptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,99019
Polymers217,7296
Non-polymers3,26113
Water2,468137
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19930 Å2
ΔGint-178 kcal/mol
Surface area68360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.810, 128.870, 254.840
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 , 3 types, 5 molecules ACBDE

#1: Protein Tubulin alpha chain


Mass: 50204.445 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: D0VWZ0
#2: Protein Tubulin beta chain


Mass: 50043.875 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: D0VWY9
#3: Protein Stathmin-4 / Stathmin-like protein B3 / RB3


Mass: 16719.938 Da / Num. of mol.: 1 / Mutation: C58A, F64W
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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Protein/peptide , 1 types, 1 molecules F

#4: Protein/peptide Vinca tetrapeptide


Type: Peptide-like / Class: Inhibitor / Mass: 512.553 Da / Num. of mol.: 1 / Source method: obtained synthetically
References: N-{[(3R,4R,7S,10R,11R)-3-ethyl-11,15-dihydroxy-3-methyl-10-(methylamino)-6,9-dioxo-7-(propan-2-yl)-2-oxa-5,8-diazabicyclo[10.3.1]hexadeca-1(16),12,14-trien-4-yl]carbonyl}glycine

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Non-polymers , 6 types, 150 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.: 2 / Source method: obtained synthetically / Formula: Mg
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#8: 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
#9: 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 / Comment: medication, antiinflammatory*YM
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsInhibitor of microtubule assembly
Has protein modificationY
Sequence detailsAUTHOR STATES THAT FOR ALPHA-TUBULIN (CHAIN A AND CHAIN C), THE BOVINE BRAIN TUBULIN SEQUENCE WAS ...AUTHOR STATES THAT FOR ALPHA-TUBULIN (CHAIN A AND CHAIN C), THE BOVINE BRAIN TUBULIN SEQUENCE WAS USED FOR REFINEMENT BECAUSE THE SEQUENCE OF OVINE BRAIN TUBULIN IS NOT AVAILABLE. FOR BETA-TUBULIN (CHAIN B AND CHAIN D), THERE ARE THREE MAJOR ISOTYPES EXPRESSED IN THE BRAIN. THEY MAINLY USED THE BETA 2B ISOTYPE SEQUENCE (NCBI NP_001003900.1), BUT INTRODUCED POINT MUTATIONS WHEN POSSIBLE TO TAKE INTO ACCOUNT THE ISOTYPE DIVERSITY. SPECIFICALLY, RESIDUE THR 33 IS FOUND IN 75% OF TUBULIN MOLECULES (25% IS SER). IT IS REFINED WITH THR BUT WITH AN 75% OCCUPANCY FOR THE CG2 ATOM. RESIDUE 172: MET (60%) OR VAL (40%), REFINED WITH MET, BUT WITH OCCUPANCY 0.6 FOR SD AND CE ATOMS. RESIDUE 220: A MIX OF THR (75%) AND ALA (25%), REFINED WITH THR, OCCUPANCY 0.75 FOR OG1 AND CG2 ATOMS. AT POSITION 277, A MIX OF SER (75%) AND ALA (25%), REFINED WITH SER BUT WITH OCCUPANCY O.75 FOR OG ATOM. RESIDUE 298: SAME AS ABOVE BUT WITH SER 60% AND ALA 40%, REFINED WITH SER BUT WITH OCCUPANCY O.60 FOR OG ATOM. POSITION 317: THR 25%, ALA 75%, REFINED WITH A THR BUT WITH AN 0.25 OCCUPANCY FOR THE OG1 AND CG2 ATOMS. RESIDUE 318: ILE (60%) OR VAL (40%), REFINED WITH ILE, WITH OCCUPANCY 0.6 FOR CD1 ATOM. RESIDUE 335: THE SAME AS ABOVE BUT WITH ILE 25% AND VAL 75%, REFINED WITH ILE, WITH OCCUPANCY 0.25 FOR CD1 ATOM. RESIDUE 375, A MIX OF ALA (0.75) AND SER (0.25) AT THIS POSITION, REFINED WITH SER, OCCUPANCY 0.25 FOR OG ATOM. THE STATHMIN-4 FRAGMENT (CHAIN E) USED IN THIS STUDY INCLUDES A N-TERMINAL ALA RESIDUE, HAS TWO POINT MUTATIONS (CYS14 TO ALA AND PHE20 TO TRP, STATHMIN NUMBERING).

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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: 2.45 Å3/Da / Density % sol: 49.79 %
Crystal growTemperature: 293 K / pH: 6.8
Details: PEG, LISO4, PIPES BUFFER, PH 6.80, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 10, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.73→43.02 Å / Num. obs: 56466 / % possible obs: 97.3 % / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 72.47 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 14.8
Reflection shellResolution: 2.73→2.87 Å / Redundancy: 3 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 1.7 / % possible all: 81.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
AMoREphasing
BUSTER2.8.0refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.73→38.26 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.925 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.222 2872 5.1 %RANDOM
Rwork0.184 ---
obs0.186 56364 --
Displacement parametersBiso mean: 93.87 Å2
Baniso -1Baniso -2Baniso -3
1--7.7229 Å20 Å20 Å2
2--13.2388 Å20 Å2
3----5.5159 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
Refinement stepCycle: LAST / Resolution: 2.73→38.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14683 0 205 137 15025
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00915303HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1320781HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5313SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes444HARMONIC2
X-RAY DIFFRACTIONt_gen_planes2245HARMONIC5
X-RAY DIFFRACTIONt_it15303HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.69
X-RAY DIFFRACTIONt_other_torsion23.66
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1971SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact17596SEMIHARMONIC4
LS refinement shellResolution: 2.73→2.8 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2701 169 5.01 %
Rwork0.2311 3207 -
all0.233 3376 -
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)
11.7808-0.8549-0.83783.95671.30762.0704-0.18360.0883-0.19840.12440.0951-0.23630.39160.07070.08850.39850.03010.1197-0.3417-0.13-0.42279.317432.722274.7785
21.2512-1.4306-0.47565.70891.42291.13250.08240.20180.16490.0784-0.0453-0.5140.0390.0317-0.03720.33340.06550.0404-0.2771-0.0341-0.43612.787271.743791.763
30.8781-0.9199-0.24363.26610.96781.5126-0.02260.15020.1111-0.33470.0126-0.58480.22570.1660.00990.1880.05540.1606-0.2439-0.0308-0.1422-11.3968110.811105.313
42.0431-0.6751-0.1563.09070.6642.23330.040.21040.4142-0.1319-0.1638-0.0041-0.28580.07720.12380.1224-0.0314-0.0021-0.3038-0.0275-0.1655-32.42144.702118.363
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|1 - A|440 A|501 - A|504 A|601 - A|625 B|601 - B|601 E|4 - E|64 }A1 - 440
2X-RAY DIFFRACTION1{ A|1 - A|440 A|501 - A|504 A|601 - A|625 B|601 - B|601 E|4 - E|64 }A501 - 504
3X-RAY DIFFRACTION1{ A|1 - A|440 A|501 - A|504 A|601 - A|625 B|601 - B|601 E|4 - E|64 }A601 - 625
4X-RAY DIFFRACTION1{ A|1 - A|440 A|501 - A|504 A|601 - A|625 B|601 - B|601 E|4 - E|64 }B601
5X-RAY DIFFRACTION1{ A|1 - A|440 A|501 - A|504 A|601 - A|625 B|601 - B|601 E|4 - E|64 }E4 - 64
6X-RAY DIFFRACTION2{ A|626 - A|627 C|701 - C|701 B|1 - B|442 B|501 - B|503 B|602 - B|628 E|65 - E|89 F|1 - F|4 }A626 - 627
7X-RAY DIFFRACTION2{ A|626 - A|627 C|701 - C|701 B|1 - B|442 B|501 - B|503 B|602 - B|628 E|65 - E|89 F|1 - F|4 }C701
8X-RAY DIFFRACTION2{ A|626 - A|627 C|701 - C|701 B|1 - B|442 B|501 - B|503 B|602 - B|628 E|65 - E|89 F|1 - F|4 }B1 - 442
9X-RAY DIFFRACTION2{ A|626 - A|627 C|701 - C|701 B|1 - B|442 B|501 - B|503 B|602 - B|628 E|65 - E|89 F|1 - F|4 }B501 - 503
10X-RAY DIFFRACTION2{ A|626 - A|627 C|701 - C|701 B|1 - B|442 B|501 - B|503 B|602 - B|628 E|65 - E|89 F|1 - F|4 }B602 - 628
11X-RAY DIFFRACTION2{ A|626 - A|627 C|701 - C|701 B|1 - B|442 B|501 - B|503 B|602 - B|628 E|65 - E|89 F|1 - F|4 }E65 - 89
12X-RAY DIFFRACTION2{ A|626 - A|627 C|701 - C|701 B|1 - B|442 B|501 - B|503 B|602 - B|628 E|65 - E|89 F|1 - F|4 }F1 - 4
13X-RAY DIFFRACTION3{ C|1 - C|440 C|600 - C|601 C|702 - C|743 E|90 - E|115 D|601 - D|601 }C1 - 440
14X-RAY DIFFRACTION3{ C|1 - C|440 C|600 - C|601 C|702 - C|743 E|90 - E|115 D|601 - D|601 }C600 - 601
15X-RAY DIFFRACTION3{ C|1 - C|440 C|600 - C|601 C|702 - C|743 E|90 - E|115 D|601 - D|601 }C702 - 743
16X-RAY DIFFRACTION3{ C|1 - C|440 C|600 - C|601 C|702 - C|743 E|90 - E|115 D|601 - D|601 }E90 - 115
17X-RAY DIFFRACTION3{ C|1 - C|440 C|600 - C|601 C|702 - C|743 E|90 - E|115 D|601 - D|601 }D601
18X-RAY DIFFRACTION4{ E|116 - E|141 D|1 - D|442 D|501 - D|504 D|602 - D|636 }E116 - 141
19X-RAY DIFFRACTION4{ E|116 - E|141 D|1 - D|442 D|501 - D|504 D|602 - D|636 }D1 - 442
20X-RAY DIFFRACTION4{ E|116 - E|141 D|1 - D|442 D|501 - D|504 D|602 - D|636 }D501 - 504
21X-RAY DIFFRACTION4{ E|116 - E|141 D|1 - D|442 D|501 - D|504 D|602 - D|636 }D602 - 636

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