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- PDB-3fm7: Quaternary Structure of Drosophila melanogaster IC/Tctex-1/LC8; A... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3fm7 | ||||||
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Title | Quaternary Structure of Drosophila melanogaster IC/Tctex-1/LC8; Allosteric Interactions of Dynein Light Chains with Dynein Intermediate Chain | ||||||
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![]() | CONTRACTILE PROTEIN / Cytoplasmic Dynein / Light Chain Tctex-1 / Tctex / Light Chain 8 / LC8 / Intermediate Chain / IC / Dynein Cargo Attachment Complex / Dynein Light Chain / Quaternary Structure / Dynein / Microtubule / Motor protein / Lysosome / Membrane / Nucleus / WD repeat | ||||||
Function / homology | ![]() cellularization / spermatid nucleus elongation / eye photoreceptor cell differentiation / chaeta morphogenesis / positive regulation of neuron remodeling / Macroautophagy / Aggrephagy / wing disc development / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-mediated anterograde transport ...cellularization / spermatid nucleus elongation / eye photoreceptor cell differentiation / chaeta morphogenesis / positive regulation of neuron remodeling / Macroautophagy / Aggrephagy / wing disc development / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / COPI-mediated anterograde transport / COPI-independent Golgi-to-ER retrograde traffic / microtubule anchoring at centrosome / transport along microtubule / chaeta development / sperm individualization / imaginal disc-derived wing morphogenesis / dynein light chain binding / dynein heavy chain binding / Neutrophil degranulation / dynein complex / dynein light intermediate chain binding / cytoplasmic dynein complex / protein localization to kinetochore / axo-dendritic transport / retrograde axonal transport / centrosome localization / spindle organization / dynein intermediate chain binding / oogenesis / microtubule-based movement / establishment of mitotic spindle orientation / dynactin binding / actin filament bundle assembly / spermatid development / axon cytoplasm / centriole / determination of adult lifespan / microtubule cytoskeleton organization / disordered domain specific binding / mitotic cell cycle / spermatogenesis / nuclear membrane / microtubule / molecular adaptor activity / neuron projection / lysosomal membrane / protein homodimerization activity / protein-containing complex / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hall, J.D. / Karplus, P.A. / Barbar, E.J. | ||||||
![]() | ![]() Title: Multivalency in the assembly of intrinsically disordered Dynein intermediate chain. Authors: Hall, J. / Karplus, P.A. / Barbar, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 98.5 KB | Display | ![]() |
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PDB format | ![]() | 77.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 464.6 KB | Display | ![]() |
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Full document | ![]() | 494.8 KB | Display | |
Data in XML | ![]() | 20.5 KB | Display | |
Data in CIF | ![]() | 26.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3glwC ![]() 2pg1S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 12491.021 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 3054.404 Da / Num. of mol.: 2 / Fragment: IC, Residues 109-135 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #3: Protein | Mass: 10388.849 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.36 Å3/Da / Density % sol: 63.44 % |
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Crystal grow | Temperature: 277.15 K / Method: hanging drop / pH: 6.5 Details: 16% PEG 8K, 100 mM sodium cacodylate, 200 mM calcium acetate, pH 6.5, Hanging Drop, temperature 277.15K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 20, 2008 |
Radiation | Monochromator: KOHZU: Double Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 3.5→100 Å / Num. all: 8756 / Num. obs: 8745 / % possible obs: 98.84 % / Observed criterion σ(F): 8.2 / Observed criterion σ(I): 6.6 / Redundancy: 7.1 % / Rmerge(I) obs: 0.088 / Rsym value: 0.06 / Net I/σ(I): 15.9 |
Reflection shell | Resolution: 3.5→3.64 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.358 / Mean I/σ(I) obs: 6.2 / Rsym value: 0.53 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: chains A and F in pdb structure 2PG1 Resolution: 3.5→100 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.877 / SU B: 63.772 / SU ML: 0.446 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.659 / 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: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 94.445 Å2
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Refinement step | Cycle: LAST / Resolution: 3.5→100 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.501→3.592 Å / Total num. of bins used: 20
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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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