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Yorodumi- PDB-2pg1: Structural analysis of a cytoplasmic dynein Light Chain-Intermedi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2pg1 | ||||||
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Title | Structural analysis of a cytoplasmic dynein Light Chain-Intermediate Chain complex | ||||||
Components |
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Keywords | STRUCTURAL PROTEIN / Dynein intermediate chain / dynein light chain / LC8 / PIN / TcTex1 | ||||||
Function / homology | Function and homology information Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Resolution of Sister Chromatid Cohesion / COPI-independent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / RHO GTPases Activate Formins / Aggrephagy / spermatid nucleus elongation / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes ...Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Resolution of Sister Chromatid Cohesion / COPI-independent Golgi-to-ER retrograde traffic / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / RHO GTPases Activate Formins / Aggrephagy / spermatid nucleus elongation / Loss of Nlp from mitotic centrosomes / Recruitment of mitotic centrosome proteins and complexes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of NuMA to mitotic centrosomes / Anchoring of the basal body to the plasma membrane / AURKA Activation by TPX2 / Regulation of PLK1 Activity at G2/M Transition / chaeta morphogenesis / positive regulation of neuron remodeling / Separation of Sister Chromatids / Macroautophagy / Aggrephagy / COPI-mediated anterograde transport / 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 / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / transport along microtubule / : / chaeta development / sperm individualization / dynein light chain binding / microtubule anchoring at centrosome / imaginal disc-derived wing morphogenesis / dynein heavy chain binding / MHC class II antigen presentation / Neutrophil degranulation / dynein complex / cytoplasmic dynein complex / retrograde axonal transport / dynein light intermediate chain binding / dynein intermediate chain binding / oogenesis / microtubule-based movement / spermatid development / establishment of mitotic spindle orientation / actin filament bundle assembly / cytoskeletal motor activity / axon cytoplasm / centriole / cellular response to nerve growth factor stimulus / determination of adult lifespan / brain development / autophagy / disordered domain specific binding / negative regulation of neuron projection development / mitotic cell cycle / spermatogenesis / vesicle / microtubule / centrosome / protein-containing complex binding / protein homodimerization activity / protein-containing complex / identical protein binding / cytoplasm Similarity search - Function | ||||||
Biological species | Drosophila melanogaster (fruit fly) Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.8 Å | ||||||
Authors | Williams, J.C. / Hendrickson, W.A. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.Usa / Year: 2007 Title: Structural and thermodynamic characterization of a cytoplasmic dynein light chain-intermediate chain complex Authors: Williams, J.C. / Roulhac, P.L. / Roy, A.G. / Vallee, R.B. / Fitzgerald, M.C. / Hendrickson, W.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2pg1.cif.gz | 177 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2pg1.ent.gz | 148.4 KB | Display | PDB format |
PDBx/mmJSON format | 2pg1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pg/2pg1 ftp://data.pdbj.org/pub/pdb/validation_reports/pg/2pg1 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 10635.133 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: ctp, Cdlc1, ddlc1 / Plasmid: pET21D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: Q24117 #2: Protein | Mass: 12631.708 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: Dlc90F, Tctex / Plasmid: pET24D / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: Q94524 #3: Protein/peptide | Mass: 3677.293 Da / Num. of mol.: 4 Fragment: LC binding site, sequence database residues 132-164 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Dync1i2, Dnci2, Dncic2 / Plasmid: pET28-SMT3 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Rosetta / References: UniProt: Q62871 #4: Chemical | ChemComp-SO4 / #5: 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: 3.44 Å3/Da / Density % sol: 64.26 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 1.8 M - 2.2 M Ammonium Sulfate, 0 - 20 % glycerol, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9791 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 14, 2001 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Av σ(I) over netI: 13.9 / Number: 411870 / Rmerge(I) obs: 0.085 / Χ2: 1.27 / D res high: 2.8 Å / D res low: 30 Å / Num. obs: 36881 / % possible obs: 99.9 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Diffraction reflection shell |
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Reflection | Resolution: 2.8→30 Å / Num. obs: 36881 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.085 / Rsym value: 0.071 / Net I/σ(I): 31 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Resolution: 2.8→2.9 Å / Mean I/σ(I) obs: 6.7 / Rsym value: 0.362 / % possible all: 100 |
-Phasing
Phasing | Method: SAD | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing MAD set site |
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-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.8→19.98 Å / FOM work R set: 0.831 / σ(F): 0
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Solvent computation | Bsol: 21.882 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 46.024 Å2
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Refinement step | Cycle: LAST / Resolution: 2.8→19.98 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 36
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Xplor file |
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