+Open data
-Basic information
Entry | Database: PDB / ID: 6gvm | ||||||
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Title | Tubulin:F3II DARPin complex | ||||||
Components |
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Keywords | CELL 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 / condensed chromosome / regulation of synapse organization / startle response / locomotory exploration behavior / microtubule polymerization / response to tumor necrosis factor / response to mechanical stimulus / homeostasis of number of cells within a tissue / cellular response to calcium ion / adult locomotory behavior / intracellular protein transport / synapse organization / neuron migration / visual learning / neuromuscular junction / recycling endosome / structural constituent of cytoskeleton / memory / cerebral cortex development / microtubule cytoskeleton organization / cytoplasmic ribonucleoprotein granule / mitotic cell cycle / 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Ovis aries (sheep) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å | ||||||
Authors | Gigant, B. / Campanacci, V. / Cantos Fernandes, S. | ||||||
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 | 6gvm.cif.gz | 443.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gvm.ent.gz | 359 KB | Display | PDB format |
PDBx/mmJSON format | 6gvm.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6gvm_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6gvm_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6gvm_validation.xml.gz | 37.8 KB | Display | |
Data in CIF | 6gvm_validation.cif.gz | 51.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gv/6gvm ftp://data.pdbj.org/pub/pdb/validation_reports/gv/6gvm | HTTPS FTP |
-Related structure data
Related structure data | 6gvnC 6gx7C 4f6rS 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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Unit cell |
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-Components
-Protein , 4 types, 4 molecules ABCD
#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: 10117.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
#4: Protein | Mass: 18251.457 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
-Non-polymers , 3 types, 3 molecules
#5: Chemical | ChemComp-GTP / |
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#6: Chemical | ChemComp-MG / |
#7: Chemical | ChemComp-GDP / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 47.68 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: PEG5000MME, Mes pH 6.0, 150 mM AMMONIUM SULFATE, 50 mM KCl |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 4, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 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 shell | Resolution: 3.5→3.73 Å |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 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
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Displacement parameters | Biso mean: 57.48 Å2
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Refine analyze | Luzzati coordinate error obs: 0.65 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 3.5→49.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.5→3.91 Å / Total num. of bins used: 5
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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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