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Yorodumi- PDB-6b9h: Complex of Hook Domain with a Dynein Light Intermediate Chain Peptide -
+Open data
-Basic information
Entry | Database: PDB / ID: 6b9h | ||||||
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Title | Complex of Hook Domain with a Dynein Light Intermediate Chain Peptide | ||||||
Components |
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Keywords | PROTEIN TRANSPORT/Motor protein / Dynein / Dynactin / Effector / Hook / Light Intermediate Chain (LIC) / PROTEIN TRANSPORT-Motor protein complex | ||||||
Function / homology | Function and homology information FHF complex / interkinetic nuclear migration / protein localization to perinuclear region of cytoplasm / Golgi localization / microtubule anchoring at centrosome / positive regulation of mitotic cell cycle spindle assembly checkpoint / dynein light chain binding / dynein heavy chain binding / cytoskeleton-dependent intracellular transport / regulation of vesicle-mediated transport ...FHF complex / interkinetic nuclear migration / protein localization to perinuclear region of cytoplasm / Golgi localization / microtubule anchoring at centrosome / positive regulation of mitotic cell cycle spindle assembly checkpoint / dynein light chain binding / dynein heavy chain binding / cytoskeleton-dependent intracellular transport / regulation of vesicle-mediated transport / neuronal stem cell population maintenance / endosome organization / early endosome to late endosome transport / COPI-independent Golgi-to-ER retrograde traffic / cis-Golgi network / cytoplasmic dynein complex / dynein light intermediate chain binding / protein localization to centrosome / dynein intermediate chain binding / lysosome organization / endosome to lysosome transport / microtubule-based movement / pericentriolar material / dynactin binding / ficolin-1-rich granule membrane / centriolar satellite / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / cytoplasmic microtubule organization / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Resolution of Sister Chromatid Cohesion / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / MHC class II antigen presentation / secretory granule membrane / RHO GTPases Activate Formins / kinetochore / microtubule cytoskeleton organization / Aggrephagy / negative regulation of neurogenesis / spindle pole / HCMV Early Events / recycling endosome membrane / Separation of Sister Chromatids / endocytic vesicle membrane / GDP binding / protein transport / microtubule binding / microtubule / molecular adaptor activity / cell cycle / cell division / centrosome / Neutrophil degranulation / RNA binding / ATP binding / membrane / identical protein binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Lee, I.G. / Dominguez, R. | ||||||
Funding support | United States, 1items
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Citation | Journal: Nat Commun / Year: 2018 Title: A conserved interaction of the dynein light intermediate chain with dynein-dynactin effectors necessary for processivity. Authors: Lee, I.G. / Olenick, M.A. / Boczkowska, M. / Franzini-Armstrong, C. / Holzbaur, E.L.F. / Dominguez, R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6b9h.cif.gz | 78.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6b9h.ent.gz | 58.5 KB | Display | PDB format |
PDBx/mmJSON format | 6b9h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b9/6b9h ftp://data.pdbj.org/pub/pdb/validation_reports/b9/6b9h | HTTPS FTP |
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-Related structure data
Related structure data | 5j8eS S: Starting model for refinement |
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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
#1: Protein | Mass: 18390.109 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HOOK3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86VS8 |
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#2: Protein/peptide | Mass: 2676.032 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q9Y6G9 |
#3: 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: 1.72 Å3/Da / Density % sol: 28.69 % / Description: Needles |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.25 / Details: 1.44 M Ammonium Citrate Tribasic |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.9775 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 29, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9775 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. obs: 23303 / % possible obs: 98.7 % / Redundancy: 11.2 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 50.7 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 3.8 / Num. unique obs: 2089 / % possible all: 90.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5j8e Resolution: 1.5→20.54 Å / SU ML: 0.12 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.71 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→20.54 Å
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Refine LS restraints |
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LS refinement shell |
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