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Yorodumi- PDB-7c1m: Complex structure of tyrosinated alpha-tubulin carboxy-terminal p... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7c1m | ||||||
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Title | Complex structure of tyrosinated alpha-tubulin carboxy-terminal peptide and A1aY1 binder | ||||||
Components |
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Keywords | PROTEIN BINDING / Tyrosinated / Microtubule / Binder / SSO7d / yeast display | ||||||
Function / homology | Function and homology information Post-chaperonin tubulin folding pathway / axonemal microtubule / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / organelle transport along microtubule / glial cell differentiation / cytoskeleton-dependent intracellular transport / forebrain morphogenesis / Intraflagellar transport ...Post-chaperonin tubulin folding pathway / axonemal microtubule / Carboxyterminal post-translational modifications of tubulin / Microtubule-dependent trafficking of connexons from Golgi to the plasma membrane / Cilium Assembly / organelle transport along microtubule / glial cell differentiation / cytoskeleton-dependent intracellular transport / forebrain morphogenesis / Intraflagellar transport / Sealing of the nuclear envelope (NE) by ESCRT-III / neuron projection arborization / Gap junction assembly / Formation of tubulin folding intermediates by CCT/TriC / cerebellar cortex morphogenesis / dentate gyrus development / COPI-independent Golgi-to-ER retrograde traffic / pyramidal neuron differentiation / Prefoldin mediated transfer of substrate to CCT/TriC / Kinesins / Assembly and cell surface presentation of NMDA receptors / centrosome cycle / COPI-dependent Golgi-to-ER retrograde traffic / motor behavior / response to L-glutamate / smoothened signaling pathway / regulation of synapse organization / locomotory exploration behavior / startle response / microtubule polymerization / Recycling pathway of L1 / RHO GTPases activate IQGAPs / Hedgehog 'off' state / response to tumor necrosis factor / microtubule-based process / COPI-mediated anterograde transport / Activation of AMPK downstream of NMDARs / response to mechanical stimulus / Mitotic Prometaphase / homeostasis of number of cells within a tissue / EML4 and NUDC in mitotic spindle formation / condensed chromosome / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / Resolution of Sister Chromatid Cohesion / Recruitment of NuMA to mitotic centrosomes / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / Anchoring of the basal body to the plasma membrane / MHC class II antigen presentation / cellular response to calcium ion / adult locomotory behavior / AURKA Activation by TPX2 / RHO GTPases Activate Formins / Translocation of SLC2A4 (GLUT4) to the plasma membrane / synapse organization / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / intracellular protein transport / neuron migration / neuromuscular junction / visual learning / PKR-mediated signaling / structural constituent of cytoskeleton / cytoplasmic ribonucleoprotein granule / cerebral cortex development / memory / microtubule cytoskeleton organization / recycling endosome / Aggrephagy / HCMV Early Events / Separation of Sister Chromatids / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / mitotic cell cycle / gene expression / neuron apoptotic process / microtubule / hydrolase activity / protein heterodimerization activity / cell division / protein-containing complex binding / GTP binding / structural molecule activity / extracellular exosome / identical protein binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Saccharolobus solfataricus 98/2 (archaea) Homo sapiens (human) | ||||||
Method | SOLUTION NMR / torsion angle dynamics | ||||||
Authors | Kesarwani, S. / Reddy, P.P. / Sirajuddin, M. / Das, R. | ||||||
Funding support | India, 1items
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Citation | Journal: J.Cell Biol. / Year: 2020 Title: Genetically encoded live-cell sensor for tyrosinated microtubules. Authors: Kesarwani, S. / Lama, P. / Chandra, A. / Reddy, P.P. / Jijumon, A.S. / Bodakuntla, S. / Rao, B.M. / Janke, C. / Das, R. / Sirajuddin, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7c1m.cif.gz | 463.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7c1m.ent.gz | 391.2 KB | Display | PDB format |
PDBx/mmJSON format | 7c1m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/7c1m ftp://data.pdbj.org/pub/pdb/validation_reports/c1/7c1m | HTTPS FTP |
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-Related structure data
Similar structure data | |
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Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Antibody | Mass: 7486.859 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharolobus solfataricus 98/2 (archaea) Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria) |
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#2: Protein/peptide | Mass: 1355.272 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q71U36*PLUS |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 50 mM unlabeled sodium phosphate, 200 mM unlabeled sodium chloride, 90% H2O/10% D2O Label: 13C_15N_sample / Solvent system: 90% H2O/10% D2O | ||||||||||||
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Sample |
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Sample conditions | Ionic strength: 200 mM / Label: conditions_1 / pH: 6.5 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 6 | |||||||||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 200 / Conformers submitted total number: 20 |