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Yorodumi- PDB-2hl3: Crystal structure of the A49M mutant CAP-Gly domain of human Dyna... -
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-Basic information
Entry | Database: PDB / ID: 2hl3 | ||||||
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Title | Crystal structure of the A49M mutant CAP-Gly domain of human Dynactin-1 (p150-Glued) in complex with human EB1 C-terminal hexapeptide | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / microtubule binding / dynactin / cytoskeleton associated protein / p150Glued / EB1 / +TIP protein Complex structure / EEY/F-COO- sequence motif / CLIP-170 / alpha-tubulin | ||||||
Function / homology | Function and homology information positive regulation of neuromuscular junction development / centriolar subdistal appendage / protein localization to astral microtubule / cortical microtubule cytoskeleton / centriole-centriole cohesion / cell cortex region / mitotic spindle astral microtubule end / ventral spinal cord development / microtubule anchoring at centrosome / maintenance of synapse structure ...positive regulation of neuromuscular junction development / centriolar subdistal appendage / protein localization to astral microtubule / cortical microtubule cytoskeleton / centriole-centriole cohesion / cell cortex region / mitotic spindle astral microtubule end / ventral spinal cord development / microtubule anchoring at centrosome / 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 / attachment of mitotic spindle microtubules to kinetochore / dynein complex / 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 / microtubule associated complex / motor behavior / microtubule organizing center / neuromuscular process / negative regulation of microtubule polymerization / neuromuscular junction development / intercellular bridge / mitotic spindle pole / microtubule polymerization / cell leading edge / establishment of mitotic spindle orientation / Signaling by ALK fusions and activated point mutants / spindle assembly / regulation of microtubule polymerization or depolymerization / spindle midzone / cytoplasmic microtubule / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / Mitotic Prometaphase / regulation of mitotic spindle organization / EML4 and NUDC in mitotic spindle formation / positive regulation of microtubule polymerization / 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 / neuron projection maintenance / centriole / tubulin binding / AURKA Activation by TPX2 / ciliary basal body / RHO GTPases Activate Formins / tau protein binding / protein localization / spindle / mitotic spindle / kinetochore / spindle pole / 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 / cell migration / mitotic cell cycle / nuclear envelope / nervous system development / cell cortex / microtubule binding / microtubule / molecular adaptor activity / neuron projection / cadherin binding / cell division / axon / focal adhesion / centrosome / neuronal cell body / protein kinase binding / Golgi apparatus / RNA binding / membrane / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.03 Å | ||||||
Authors | Honnappa, S. / Winkler, F.K. / Steinmetz, M.O. | ||||||
Citation | Journal: Mol.Cell / Year: 2006 Title: Key interaction modes of dynamic +TIP networks. Authors: Honnappa, S. / Okhrimenko, O. / Jaussi, R. / Jawhari, H. / Jelesarov, I. / Winkler, F.K. / Steinmetz, M.O. | ||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 3 CHAIN(S). IN THE CRYSTAL STRUCTURE, THE BIOLOGICAL UNIT IS COMPRISED OF CHAINS A, B AND C. HOWEVER, THE ACTIVE BIOLOGICAL UNIT IS A COMPLEX OF CHAINS A AND C. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hl3.cif.gz | 43.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hl3.ent.gz | 30.2 KB | Display | PDB format |
PDBx/mmJSON format | 2hl3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hl/2hl3 ftp://data.pdbj.org/pub/pdb/validation_reports/hl/2hl3 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10369.531 Da / Num. of mol.: 2 / Fragment: CAP-Gly domain / Mutation: A49M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DCTN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q14203 #2: Protein/peptide | | Mass: 825.773 Da / Num. of mol.: 1 / Fragment: C-terminal hexapeptide / Source method: obtained synthetically Details: The peptide was chemically synthesized. The sequence of the peptide is naturally found in Homo sapiens (human). References: UniProt: Q15691 #3: 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: 1.82 Å3/Da / Density % sol: 32.42 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 25% PEG 3350, 0.05M Sodium Citrate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 8, 2005 / Details: Osmic mirrors |
Radiation | Monochromator: Osmic mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→42.33 Å / Num. all: 10303 / Num. obs: 10303 / % possible obs: 98 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.03→2.085 Å / % possible all: 92.17 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.03→42.33 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.683 / SU ML: 0.104 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.197 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.088 Å2
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Refinement step | Cycle: LAST / Resolution: 2.03→42.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.03→2.085 Å / Total num. of bins used: 20
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