+Open data
-Basic information
Entry | Database: PDB / ID: 6gvn | ||||||
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Title | Tubulin:TM-3 DARPin complex | ||||||
Components |
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Keywords | CELL 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 | ||||||
Biological species | synthetic construct (others) Ovis aries (sheep) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å | ||||||
Authors | Gigant, B. / Cantos Fernandes, S. / Campanacci, V. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gvn.cif.gz | 406.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gvn.ent.gz | 327.2 KB | Display | PDB format |
PDBx/mmJSON format | 6gvn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/6gvn ftp://data.pdbj.org/pub/pdb/validation_reports/gv/6gvn | HTTPS FTP |
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-Related structure data
Related structure data | 6gvmC 6gx7C 5eypS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 3 types, 3 molecules ABF
#1: Protein | Mass: 50204.445 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: D0VWZ0 |
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#2: Protein | 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 | 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) |
-Non-polymers , 6 types, 123 molecules
#4: Chemical | #5: Chemical | #6: Chemical | ChemComp-SO4 / | #7: Chemical | ChemComp-MES / | #8: Chemical | #9: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.67 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: PEG5000 MME, 0.1 M Mes pH 6.0, 150 mM AMMONIUM SULFATE |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.966 Å |
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: May 4, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.966 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 2.692→2.789 Å |
-Processing
Software |
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Refinement | Method 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
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Displacement parameters | Biso mean: 51.6 Å2
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Refine analyze | Luzzati coordinate error obs: 0.39 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.69→43.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.69→2.79 Å / Total num. of bins used: 14
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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