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- PDB-6gvn: Tubulin:TM-3 DARPin complex -

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Basic information

Entry
Database: PDB / ID: 6gvn
TitleTubulin:TM-3 DARPin complex
Components
  • TM-3 DARPIN
  • Tubulin alpha chain
  • Tubulin beta chain
KeywordsCELL CYCLE / microtubule / DARPIN
Function / homology
Function and homology information


cerebellar cortex morphogenesis / axonemal microtubule / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / neuron projection arborization / dentate gyrus development / pyramidal neuron differentiation / centrosome cycle / motor behavior ...cerebellar cortex morphogenesis / axonemal microtubule / organelle transport along microtubule / glial cell differentiation / forebrain morphogenesis / neuron projection arborization / dentate gyrus development / pyramidal neuron differentiation / centrosome cycle / motor behavior / response to L-glutamate / startle response / smoothened signaling pathway / regulation of synapse organization / locomotory exploration behavior / 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 / visual learning / intracellular protein transport / neuron migration / neuromuscular junction / memory / structural constituent of cytoskeleton / cerebral cortex development / recycling endosome / cytoplasmic ribonucleoprotein granule / gene expression / neuron apoptotic process / microtubule / hydrolase activity / protein heterodimerization activity / GTPase activity / protein-containing complex binding / GTP binding / metal ion binding / identical protein 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'-TRIPHOSPHATE / Tubulin beta chain / Tubulin alpha chain
Similarity search - Component
Biological speciessynthetic construct (others)
Ovis aries (sheep)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsGigant, B. / Cantos Fernandes, S. / Campanacci, V.
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 ...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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_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
F: TM-3 DARPIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,82311
Polymers118,2533
Non-polymers1,5708
Water2,072115
1
A: Tubulin alpha chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,8484
Polymers50,2041
Non-polymers6443
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1270 Å2
ΔGint-26 kcal/mol
Surface area17210 Å2
MethodPISA
2
B: Tubulin beta chain
F: TM-3 DARPIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,9757
Polymers68,0482
Non-polymers9275
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2790 Å2
ΔGint-21 kcal/mol
Surface area21970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)73.100, 84.260, 81.980
Angle α, β, γ (deg.)90.00, 99.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 3 types, 3 molecules ABF

#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 TM-3 DARPIN


Mass: 18048.408 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: Escherichia coli (E. coli)

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Non-polymers , 6 types, 123 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.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#8: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#9: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O

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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: 2.11 Å3/Da / Density % sol: 41.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG5000 MME, 0.1 M Mes pH 6.0, 150 mM AMMONIUM SULFATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 4, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.966 Å / Relative weight: 1
ReflectionResolution: 2.69→43.08 Å / Num. obs: 26956 / % possible obs: 98.25 % / Redundancy: 3.4 % / Biso Wilson estimate: 60.6 Å2 / Net I/σ(I): 6.22
Reflection shellResolution: 2.692→2.789 Å

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Processing

Software
NameVersionClassification
BUSTER2.10.3refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5EYP
Resolution: 2.69→43.08 Å / Cor.coef. Fo:Fc: 0.923 / Cor.coef. Fo:Fc free: 0.895 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.306
RfactorNum. reflection% reflectionSelection details
Rfree0.216 1349 5 %RANDOM
Rwork0.193 ---
obs0.194 26956 98.1 %-
Displacement parametersBiso mean: 51.6 Å2
Baniso -1Baniso -2Baniso -3
1-2.823 Å20 Å2-4.8975 Å2
2---2.0723 Å20 Å2
3----0.7506 Å2
Refine analyzeLuzzati coordinate error obs: 0.39 Å
Refinement stepCycle: 1 / Resolution: 2.69→43.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7680 0 95 115 7890
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017937HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.1510788HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2715SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes205HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1180HARMONIC5
X-RAY DIFFRACTIONt_it7937HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion3.01
X-RAY DIFFRACTIONt_other_torsion18.88
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1042SEMIHARMONIC5
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_contact8978SEMIHARMONIC4
LS refinement shellResolution: 2.69→2.79 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2954 130 5 %
Rwork0.239 2470 -
all0.2418 2600 -
obs--89.88 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
10.96970.0549-0.19760.97420.10.72140.07870.01220.044-0.057-0.01130.0141-0.0376-0.0793-0.0674-0.00280.0110.2551-0.3409-0.00390.0304-2.65776.035632.7041
21.59810.1162-1.03671.2540.10841.9752-0.05910.049-0.0214-0.0462-0.0144-0.00070.1248-0.21250.0735-0.0362-0.01590.276-0.3953-0.05210.010423.6408-7.31993.1773
31.2186-0.0378-0.5761.42360.65871.6959-0.0721-0.1055-0.079-0.0059-0.0168-0.2213-0.15340.00670.0889-0.0124-0.00320.3116-0.35040.00330.046457.4532-3.721-16.7616
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ F|* }

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