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- PDB-6gvm: Tubulin:F3II DARPin complex -

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Basic information

Entry
Database: PDB / ID: 6gvm
TitleTubulin:F3II DARPin complex
Components
  • F3II DARPIN
  • STATHMIN-LIKE DOMAIN R1
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsCELL CYCLE / microtubule / DARPIN / STATHmin-like protein
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 / response to L-glutamate / smoothened signaling pathway / regulation of synapse organization / locomotory exploration behavior / startle response / microtubule polymerization / 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 / 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 / gene expression / neuron apoptotic process / microtubule / hydrolase activity / protein heterodimerization activity / GTPase activity / protein-containing complex binding / GTP binding / identical protein binding / metal ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Ankyrin repeat-containing domain / 60s Ribosomal Protein L30; Chain: A; / Tubulin-beta mRNA autoregulation signal. / Alpha tubulin / Beta tubulin, autoregulation binding site / Beta tubulin / Tubulin ...Helix hairpin bin / Tubulin/FtsZ, C-terminal domain / Tubulin/FtsZ, GTPase domain / Ankyrin repeat-containing domain / 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 / Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat / Alpha Horseshoe / 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 / Tubulin beta chain / Tubulin alpha chain
Similarity search - Component
Biological speciesOvis aries (sheep)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsGigant, B. / Campanacci, V. / Cantos Fernandes, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Insight into microtubule nucleation from tubulin-capping proteins.
Authors: Campanacci, V. / Urvoas, A. / Cantos-Fernandes, S. / Aumont-Nicaise, M. / Arteni, A.A. / Velours, C. / Valerio-Lepiniec, M. / Dreier, B. / Pluckthun, A. / Pilon, A. / Pous, C. / Minard, P. / Gigant, B.
History
DepositionJun 21, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2019Provider: repository / Type: Initial release
Revision 1.1May 1, 2019Group: Data collection / Database references / Category: citation / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.year
Revision 1.2May 8, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3May 22, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.4Jan 17, 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 chain
B: Tubulin beta chain
C: STATHMIN-LIKE DOMAIN R1
D: F3II DARPIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,5647
Polymers128,5734
Non-polymers9913
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10120 Å2
ΔGint-60 kcal/mol
Surface area39130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)189.267, 51.721, 144.137
Angle α, β, γ (deg.)90.00, 121.03, 90.00
Int Tables number5
Space group name H-MC121

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Components

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Protein , 4 types, 4 molecules ABCD

#1: Protein Tubulin alpha chain


Mass: 50204.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: D0VWZ0
#2: Protein Tubulin beta chain


Mass: 49999.887 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: D0VWY9
#3: Protein STATHMIN-LIKE DOMAIN R1


Mass: 10117.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Protein F3II DARPIN


Mass: 18251.457 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 3 molecules

#5: Chemical ChemComp-GTP / GUANOSINE-5'-TRIPHOSPHATE / Guanosine triphosphate


Mass: 523.180 Da / Num. of mol.: 1 / 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.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Chemical ChemComp-GDP / GUANOSINE-5'-DIPHOSPHATE / Guanosine diphosphate


Type: RNA linking / Mass: 443.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O11P2 / Comment: GDP, energy-carrying molecule*YM

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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: 2.35 Å3/Da / Density % sol: 47.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: PEG5000MME, Mes pH 6.0, 150 mM AMMONIUM SULFATE, 50 mM KCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 3.5→49.3 Å / Num. obs: 15398 / % possible obs: 90 % / Redundancy: 3.4 % / Biso Wilson estimate: 46.67 Å2 / Net I/σ(I): 5.8
Reflection shellResolution: 3.5→3.73 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EYP, 4F6R

5eyp

4f6r


Resolution: 3.5→49.28 Å / Cor.coef. Fo:Fc: 0.745 / Cor.coef. Fo:Fc free: 0.716 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 1.204
RfactorNum. reflection% reflectionSelection details
Rfree0.27 738 9.51 %RANDOM
Rwork0.245 ---
obs0.248 7763 50 %-
Displacement parametersBiso mean: 57.48 Å2
Baniso -1Baniso -2Baniso -3
1-7.4087 Å20 Å21.6235 Å2
2---14.5218 Å20 Å2
3---7.113 Å2
Refine analyzeLuzzati coordinate error obs: 0.65 Å
Refinement stepCycle: 1 / Resolution: 3.5→49.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8335 0 61 0 8396
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0098570HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.0711637HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2944SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes231HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1272HARMONIC5
X-RAY DIFFRACTIONt_it8570HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion2.77
X-RAY DIFFRACTIONt_other_torsion19.4
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1129SEMIHARMONIC5
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_contact9605SEMIHARMONIC4
LS refinement shellResolution: 3.5→3.91 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2843 -9.47 %
Rwork0.2439 698 -
all0.2476 771 -
obs--17.72 %
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)
11.8564-1.42860.80883.46090.61270.94140.06130.0245-0.12560.49720.15420.5179-0.3028-0.4269-0.21550.2137-0.03130.5081-0.32610.0772-0.0082-9.5936-27.724548.6187
23.1928-1.08960.05912.80280.59073.64810.211-0.05370.0921-0.25220.0828-0.1162-0.33640.2767-0.29380.1268-0.11990.4613-0.68390.0517-0.089722.8632-32.964322.7274
31.77325.9651-1.71178.5380.52247.322-0.0324-0.3322-0.3236-0.4793-0.03950.10550.3006-0.90720.0719-0.0087-0.2278-0.2766-0.4335-0.2461-0.297337.0287-38.6272-12.7517
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* C|6 - C|62 }
2X-RAY DIFFRACTION2{ B|* C|63 - C|85 }
3X-RAY DIFFRACTION3{ D|* }

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