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- PDB-3hke: Tubulin-T138067: RB3 stathmin-like domain complex -

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Basic information

Entry
Database: PDB / ID: 3hke
TitleTubulin-T138067: RB3 stathmin-like domain complex
Components
  • Stathmin-4
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsCELL CYCLE / ALPHA-TUBULIN / BETA-TUBULIN / COLCHICINE DOMAIN / COVALENT BINDING / GTPASE / MICROTUBULE / STATHMIN / TUBULIN
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 / locomotory exploration behavior / startle response / microtubule polymerization / regulation of microtubule polymerization or depolymerization / response to tumor necrosis factor / microtubule-based process / response to mechanical stimulus / homeostasis of number of cells within a tissue / condensed chromosome / cellular response to calcium ion / tubulin binding / adult locomotory behavior / synapse organization / intracellular protein transport / neuron migration / neuromuscular junction / visual learning / structural constituent of cytoskeleton / cytoplasmic ribonucleoprotein granule / cerebral cortex development / memory / recycling endosome / neuron projection development / 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; / 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 / 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-T13 / 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: 3.6 Å
AuthorsDorleans, A. / Gigant, B. / Ravelli, R.B.G. / Mailliet, P. / Mikol, V. / Knossow, M.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Variations in the colchicine-binding domain provide insight into the structural switch of tubulin
Authors: Dorleans, A. / Gigant, B. / Ravelli, R.B.G. / Mailliet, P. / Mikol, V. / Knossow, M.
History
DepositionMay 23, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 1, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / 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_conn / struct_ref_seq / 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_conn.pdbx_leaving_atom_flag / _struct_ref_seq.db_align_end / _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 chain
B: Tubulin beta chain
C: Tubulin alpha chain
D: Tubulin beta chain
E: Stathmin-4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)220,52016
Polymers217,0295
Non-polymers3,49111
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17360 Å2
ΔGint-120 kcal/mol
Surface area65520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)326.710, 326.710, 54.120
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

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Protein , 3 types, 5 molecules ACBDE

#1: Protein Tubulin alpha chain


Mass: 50188.441 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: brain / References: UniProt: D0VWZ0*PLUS
#2: Protein Tubulin beta chain


Mass: 49969.797 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / Organ: brain / References: UniProt: D0VWY9*PLUS
#3: Protein Stathmin-4 / / Stathmin-like protein B3 / RB3


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

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Non-polymers , 4 types, 11 molecules

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


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-T13 / 2,3,4,5,6-pentafluoro-N-(3-fluoro-4-methoxyphenyl)benzenesulfonamide


Mass: 371.255 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C13H7F6NO3S
#7: 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

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Details

Nonpolymer detailsTHE FAE ATOM OF T13 IS MISSING IN RESIDUE B1241 AND D1241 CAUSED BY COVALENT BINDING OF T13 TO CYS 241
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. AS THE SEQUENCE OF OVIS ARIES(SHEEP) TUBULIN IS NOT AVAILABLE, THE BOS TAURUS TUBULIN SEQUENCES (ALPHA: ISOTYPE 1A, GI:194666935, BETA: ISOTYPE 2, GI:51491829) WERE USED AS A REFERENCE BUT FOR THE ILE TO VAL SUBSTITUTION AT POSITION 318 ON BETA TUBULIN. THIS IS BASED ON DIFFERENCES BETWEEN TUBULIN ISOTYPES AND ON THE RELATIVE EXPRESSION ON THESE ISOTYPES IN MAMMALIAN BRAIN.

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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: 3.84 Å3/Da / Density % sol: 68 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG, PIPES BUFFER, pH 7.00, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.978 / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 20, 2006
RadiationMonochromator: CHANNEL CUT ESRF MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 38708 / % possible obs: 98.6 % / Redundancy: 4.88 % / Rsym value: 0.073 / Net I/σ(I): 14.2
Reflection shellResolution: 3.6→3.7 Å / Redundancy: 4.5 % / Mean I/σ(I) obs: 2.29 / Rsym value: 0.639 / % possible all: 88.5

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Processing

Software
NameVersionClassification
AMoREphasing
REFMAC5.1.24refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SA0

1sa0


Resolution: 3.6→20 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.924 / SU B: 41.846 / SU ML: 0.569 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.578 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25254 1940 5 %RANDOM
Rwork0.20701 ---
obs0.20934 36545 99.62 %-
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: 65.605 Å2
Baniso -1Baniso -2Baniso -3
1--0.78 Å2-0.39 Å20 Å2
2---0.78 Å20 Å2
3---1.17 Å2
Refinement stepCycle: LAST / Resolution: 3.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14027 0 217 0 14244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02114539
X-RAY DIFFRACTIONr_angle_refined_deg1.6261.95619792
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.23351816
X-RAY DIFFRACTIONr_chiral_restr0.1170.22179
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0211187
X-RAY DIFFRACTIONr_nbd_refined0.2720.27322
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.180.2512
X-RAY DIFFRACTIONr_metal_ion_refined0.130.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3340.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2130.25
X-RAY DIFFRACTIONr_mcbond_it0.1961.59075
X-RAY DIFFRACTIONr_mcangle_it0.389214539
X-RAY DIFFRACTIONr_scbond_it0.66135464
X-RAY DIFFRACTIONr_scangle_it1.0774.55253
LS refinement shellResolution: 3.6→3.69 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.43 114
Rwork0.403 2272
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)
18.25461.13980.00622.741-0.01222.91680.0962-0.40780.80060.0817-0.13510.0789-0.25090.01990.03890.5726-0.15410.12860.5771-0.01640.6341134.997104.96717.396
28.56052.3953-0.14074.1834-0.50563.55590.10390.0484-0.5359-0.2521-0.0652-0.34290.3196-0.2135-0.03870.6664-0.29420.0131.03230.0940.5446101.40481.0675.337
38.6482.54360.18033.8253-0.47153.86920.10820.534-0.6052-0.35480.2191-0.51360.13260.5175-0.32730.7227-0.3026-0.33031.45550.2520.865863.53961.33-3.017
47.91871.5418-0.21014.4463-0.12946.45960.05830.6358-0.0392-0.2729-0.31530.54870.2289-0.29830.2570.5114-0.1025-0.55561.3750.12540.895624.17948.013-5.791
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 437
2X-RAY DIFFRACTION1E4 - 64
3X-RAY DIFFRACTION2B2 - 439
4X-RAY DIFFRACTION2E65 - 89
5X-RAY DIFFRACTION3C2 - 438
6X-RAY DIFFRACTION3E90 - 115
7X-RAY DIFFRACTION4D2 - 438
8X-RAY DIFFRACTION4E116 - 141

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