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- PDB-6tiy: DROSOPHILA GMPCPP-TUBULIN -

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Basic information

Entry
Database: PDB / ID: 6tiy
TitleDROSOPHILA GMPCPP-TUBULIN
Components
  • Stathmin-4
  • Tubulin alpha-1 chain
  • Tubulin beta-1 chain
KeywordsCELL CYCLE / MICROTUBULE / MICROTUBULE DYNAMICS / MICROTULE NUCLEATION
Function / homology
Function and homology information


HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-mediated anterograde transport / COPI-independent Golgi-to-ER retrograde traffic / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / astral microtubule / Neutrophil degranulation / lysosome localization / microtubule depolymerization / regulation of microtubule polymerization or depolymerization ...HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-mediated anterograde transport / COPI-independent Golgi-to-ER retrograde traffic / COPI-dependent Golgi-to-ER retrograde traffic / Kinesins / astral microtubule / Neutrophil degranulation / lysosome localization / microtubule depolymerization / regulation of microtubule polymerization or depolymerization / tubulin binding / structural constituent of cytoskeleton / microtubule cytoskeleton organization / spindle / neuron projection development / mitotic cell cycle / growth cone / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / microtubule / hydrolase activity / neuron projection / GTPase activity / centrosome / GTP binding / perinuclear region of cytoplasm / Golgi apparatus / nucleus / metal ion binding / cytoplasm
Similarity search - Function
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 ...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 GUANYLATE ESTER / GUANOSINE-5'-TRIPHOSPHATE / Tubulin alpha-1 chain / Stathmin-4 / Tubulin beta-1 chain
Similarity search - Component
Biological speciesDrosophila melanogaster (fruit fly)
Rattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.293 Å
AuthorsGigant, B.
CitationJournal: J.Cell Biol. / Year: 2021
Title: GTP-dependent formation of straight tubulin oligomers leads to microtubule nucleation.
Authors: Ayukawa, R. / Iwata, S. / Imai, H. / Kamimura, S. / Hayashi, M. / Ngo, K.X. / Minoura, I. / Uchimura, S. / Makino, T. / Shirouzu, M. / Shigematsu, H. / Sekimoto, K. / Gigant, B. / Muto, E.
History
DepositionNov 22, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 17, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)220,55325
Polymers217,2185
Non-polymers3,33520
Water7,746430
1


  • Idetical with deposited unit
  • defined by software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22400 Å2
ΔGint-271 kcal/mol
Surface area64890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.669, 126.564, 251.012
Angle α, β, γ (deg.)90, 90, 90
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-1 chain


Mass: 49989.266 Da / Num. of mol.: 2 / Mutation: K40R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: alphaTub84B, tubA84B, CG1913 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P06603
#2: Protein Tubulin beta-1 chain / Beta-1-tubulin


Mass: 50194.137 Da / Num. of mol.: 2 / Mutation: Y222F
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: betaTub56D, CG9277 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: Q24560
#3: Protein Stathmin-4 / Stathmin-like protein B3 / RB3


Mass: 16851.133 Da / Num. of mol.: 1 / Mutation: S4A, C14A, F20W
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

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Non-polymers , 6 types, 450 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.: 4 / Source method: obtained synthetically / Formula: Mg
#6: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#8: Chemical ChemComp-G2P / PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER


Mass: 521.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H18N5O13P3 / Comment: GMP-CPP, energy-carrying molecule analogue*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN

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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: 49.84 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: PEG1500, LISO4, PIPES BUFFER, PH 6.8

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 27, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.29→48.21 Å / Num. obs: 95769 / % possible obs: 99.4 % / Redundancy: 7.4 % / CC1/2: 0.999 / Net I/σ(I): 13.71
Reflection shellResolution: 2.29→2.35 Å / Mean I/σ(I) obs: 1.23 / Num. unique obs: 6535 / CC1/2: 0.63

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Processing

Software
NameVersionClassification
BUSTER2.10.3 (3-OCT-2019)refinement
XDSdata reduction
Aimlessdata scaling
BUSTERphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3RYC

3ryc


Resolution: 2.293→33 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.906 / SU R Cruickshank DPI: 0.305 / Cross valid method: THROUGHOUT / SU R Blow DPI: 0.308 / SU Rfree Blow DPI: 0.204 / SU Rfree Cruickshank DPI: 0.205
RfactorNum. reflection% reflectionSelection details
Rfree0.2171 4565 -RANDOM
Rwork0.1872 ---
obs0.1887 91616 95.3 %-
Displacement parametersBiso mean: 64.18 Å2
Baniso -1Baniso -2Baniso -3
1--31.395 Å20 Å20 Å2
2--18.9784 Å20 Å2
3---12.4165 Å2
Refine analyzeLuzzati coordinate error obs: 0.32 Å
Refinement stepCycle: LAST / Resolution: 2.293→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms14560 0 193 430 15183
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00815085HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.9820467HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d5239SINUSOIDAL2
X-RAY DIFFRACTIONt_gen_planes2640HARMONIC5
X-RAY DIFFRACTIONt_it15085HARMONIC10
X-RAY DIFFRACTIONt_chiral_improper_torsion1959SEMIHARMONIC5
X-RAY DIFFRACTIONt_ideal_dist_contact11356SEMIHARMONIC4
X-RAY DIFFRACTIONt_omega_torsion3.04
X-RAY DIFFRACTIONt_other_torsion18.83
LS refinement shellResolution: 2.293→2.316 Å
RfactorNum. reflection% reflection
Rfree0.2082 92 -
Rwork0.2397 --
obs--65.2 %
Refinement TLS params.

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)
10.7955-0.44-0.27071.45160.24291.41570.0026-0.01070.063-0.0107-0.07710.07050.0630.07050.0745-0.08210.0167-0.0025-0.249-0.027-0.289910.129632.547574.9136
21.0907-0.7828-0.07252.78120.07630.9470.0107-0.0746-0.0016-0.0746-0.01680.1431-0.00160.14310.0061-0.12110.01790.0262-0.283-0.0225-0.28441.655570.18491.5286
30.8868-0.8745-0.15042.13760.27070.9316-0.07880.0613-0.00980.06130.06280.1072-0.00980.10720.016-0.09450.018-0.0454-0.3084-0.0628-0.2369-13.6311108.702102.992
41.0921-0.34730.10671.48370.13471.36460.08930.0061-0.01480.0061-0.08270.1239-0.01480.1239-0.0066-0.12090.02620.0049-0.2607-0.0425-0.274-34.2299142.531116.769
50.6071-1.3425-0.3512.61640.73850.26090.028-0.07920.0011-0.0792-0.2076-0.14170.0011-0.14170.17950.00390.1035-0.051-0.2027-0.1652-0.0964-26.488278.008286.6014
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ C|* }
4X-RAY DIFFRACTION4{ D|* }
5X-RAY DIFFRACTION5{ E|* }

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