+Open data
-Basic information
Entry | Database: PDB / ID: 5j8e | ||||||
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Title | Crystal structure of human Hook3's conserved Hook domain | ||||||
Components | Protein Hook homolog 3 | ||||||
Keywords | PROTEIN TRANSPORT / calponin homology Hook cargo adaptor | ||||||
Function / homology | Function and homology information FHF complex / interkinetic nuclear migration / protein localization to perinuclear region of cytoplasm / Golgi localization / dynein light chain binding / microtubule anchoring at centrosome / cytoskeleton-dependent intracellular transport / endosome organization / neuronal stem cell population maintenance / early endosome to late endosome transport ...FHF complex / interkinetic nuclear migration / protein localization to perinuclear region of cytoplasm / Golgi localization / dynein light chain binding / microtubule anchoring at centrosome / cytoskeleton-dependent intracellular transport / endosome organization / neuronal stem cell population maintenance / early endosome to late endosome transport / cis-Golgi network / dynein light intermediate chain binding / protein localization to centrosome / dynein intermediate chain binding / lysosome organization / endosome to lysosome transport / pericentriolar material / dynactin binding / centriolar satellite / cytoplasmic microtubule organization / negative regulation of neurogenesis / protein transport / microtubule binding / microtubule / centrosome / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Schroeder, C.M. / Ekiert, D.C. / Vale, R.D. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Cell Biol. / Year: 2016 Title: Assembly and activation of dynein-dynactin by the cargo adaptor protein Hook3. Authors: Schroeder, C.M. / Vale, R.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j8e.cif.gz | 138.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j8e.ent.gz | 108.2 KB | Display | PDB format |
PDBx/mmJSON format | 5j8e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j8/5j8e ftp://data.pdbj.org/pub/pdb/validation_reports/j8/5j8e | HTTPS FTP |
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-Related structure data
Related structure data | 1wixS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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3 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 18714.488 Da / Num. of mol.: 2 / Fragment: UNP residues 1-160 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HOOK3 / Plasmid: pGEX-6P-1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86VS8 #2: 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: 1.92 Å3/Da / Density % sol: 36.03 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 2 M sodium formate, 0.1 M sodium acetate pH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.12 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 21, 2014 |
Radiation | Monochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.12 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→45.019 Å / Num. obs: 32558 / % possible obs: 99.7 % / Redundancy: 7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.076 / Net I/σ(I): 15.36 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.952 / Mean I/σ(I) obs: 1.1 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1WIX Resolution: 1.7→45.019 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.95
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.7→45.019 Å
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Refine LS restraints |
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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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