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Yorodumi- PDB-3tq7: EB1c/EB3c heterodimer in complex with the CAP-Gly domain of P150glued -
+Open data
-Basic information
Entry | Database: PDB / ID: 3tq7 | ||||||
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Title | EB1c/EB3c heterodimer in complex with the CAP-Gly domain of P150glued | ||||||
Components |
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Keywords | PROTEIN BINDING / CAP-Gly domain / protein-protein interaction / microtubule binding / cytoskeleton | ||||||
Function / homology | Function and homology information centriolar subdistal appendage / positive regulation of neuromuscular junction development / centriole-centriole cohesion / cell cortex region / protein localization to astral microtubule / cortical microtubule cytoskeleton / microtubule anchoring at centrosome / ventral spinal cord development / mitotic spindle astral microtubule end / maintenance of synapse structure ...centriolar subdistal appendage / positive regulation of neuromuscular junction development / centriole-centriole cohesion / cell cortex region / protein localization to astral microtubule / cortical microtubule cytoskeleton / microtubule anchoring at centrosome / ventral spinal cord development / mitotic spindle astral microtubule end / maintenance of synapse structure / melanosome transport / protein localization to microtubule / nuclear membrane disassembly / microtubule plus-end / positive regulation of microtubule nucleation / cell projection membrane / XBP1(S) activates chaperone genes / dynein complex / attachment of mitotic spindle microtubules to kinetochore / COPI-independent Golgi-to-ER retrograde traffic / microtubule plus-end binding / non-motile cilium assembly / microtubule bundle formation / retrograde transport, endosome to Golgi / nuclear migration / protein localization to centrosome / motor behavior / microtubule organizing center / microtubule associated complex / neuromuscular process / negative regulation of microtubule polymerization / neuromuscular junction development / intercellular bridge / mitotic spindle pole / cytoplasmic microtubule / cell leading edge / regulation of microtubule polymerization / establishment of mitotic spindle orientation / microtubule polymerization / positive regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of protein kinase activity / regulation of microtubule polymerization or depolymerization / spindle assembly / spindle midzone / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / regulation of mitotic spindle organization / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / positive regulation of microtubule polymerization / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / Resolution of Sister Chromatid Cohesion / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / neuron projection maintenance / MHC class II antigen presentation / centriole / tubulin binding / AURKA Activation by TPX2 / ciliary basal body / RHO GTPases Activate Formins / tau protein binding / mitotic spindle / kinetochore / spindle pole / spindle / neuron cellular homeostasis / 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 / protein localization / Signaling by ALK fusions and activated point mutants / cell migration / nuclear envelope / mitotic cell cycle / nervous system development / cell cortex / midbody / microtubule binding / microtubule / neuron projection / cadherin binding / cell division / axon / focal adhesion / centrosome / neuronal cell body / protein kinase binding / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / Golgi apparatus / RNA binding / identical protein binding / membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | De Groot, C.O. / Scharer, M.A. / Capitani, G. / Steinmetz, M.O. | ||||||
Citation | Journal: J.Struct.Biol. / Year: 2012 Title: Interaction of mammalian end binding proteins with CAP-Gly domains of CLIP-170 and p150(glued). Authors: Bjelic, S. / De Groot, C.O. / Scharer, M.A. / Jaussi, R. / Bargsten, K. / Salzmann, M. / Frey, D. / Capitani, G. / Kammerer, R.A. / Steinmetz, M.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3tq7.cif.gz | 119.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3tq7.ent.gz | 92.2 KB | Display | PDB format |
PDBx/mmJSON format | 3tq7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tq/3tq7 ftp://data.pdbj.org/pub/pdb/validation_reports/tq/3tq7 | HTTPS FTP |
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-Related structure data
Related structure data | 1wu9S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 9067.903 Da / Num. of mol.: 1 / Fragment: EB1 c-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAPRE1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q15691 | ||
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#2: Protein | Mass: 9517.311 Da / Num. of mol.: 1 / Fragment: EB3 c-terminal domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: MAPRE3 / Plasmid: pDEST17 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q9UPY8 | ||
#3: Protein | Mass: 7781.931 Da / Num. of mol.: 2 / Fragment: CAP-Gly domain of P150glued / Mutation: A49M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DCTN1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q14203 #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.29 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 15% PEG 4000, 0.1M Tris-HCl, 0.2M Magnesium chloride hexahydrate, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 29, 2009 / Details: dynamically bendable mirror | |||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: LN2 cooled fixed-exit Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→44.095 Å / Num. obs: 15694 / % possible obs: 95.2 % / Observed criterion σ(I): -3 / Redundancy: 13.4 % / Biso Wilson estimate: 59.999 Å2 / Net I/σ(I): 27.64 | |||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1wu9 Resolution: 2.3→44.09 Å / SU ML: 0.39 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 1.99 / Phase error: 34.65 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.17 Å / VDW probe radii: 1.4 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.324 Å2 / ksol: 0.305 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.585 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→44.09 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell |
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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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