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Yorodumi- PDB-6gzj: Complex between the dynein light chain DYNLL1/DLC8 and the specif... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6gzj | ||||||
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Title | Complex between the dynein light chain DYNLL1/DLC8 and the specific domain of large myelin-associated glycoprotein L-MAG | ||||||
Components |
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Keywords | PROTEIN BINDING / complex / heterotetramer / cell adhesion / cytoplasmic domain | ||||||
Function / homology | Function and homology information mesaxon / Axonal growth inhibition (RHOA activation) / compact myelin / positive regulation of non-motile cilium assembly / intraciliary retrograde transport / mitocytosis / ganglioside GT1b binding / motile cilium assembly / central nervous system myelination / Activation of BIM and translocation to mitochondria ...mesaxon / Axonal growth inhibition (RHOA activation) / compact myelin / positive regulation of non-motile cilium assembly / intraciliary retrograde transport / mitocytosis / ganglioside GT1b binding / motile cilium assembly / central nervous system myelination / Activation of BIM and translocation to mitochondria / sialic acid binding / ciliary tip / positive regulation of myelination / myelin sheath adaxonal region / central nervous system myelin formation / negative regulation of axon extension / Intraflagellar transport / cell-cell adhesion via plasma-membrane adhesion molecules / paranode region of axon / Schmidt-Lanterman incisure / negative regulation of nitric oxide biosynthetic process / positive regulation of astrocyte differentiation / dynein complex / negative regulation of phosphorylation / COPI-independent Golgi-to-ER retrograde traffic / cytoplasmic dynein complex / enzyme inhibitor activity / axon regeneration / dynein intermediate chain binding / Macroautophagy / transmission of nerve impulse / spermatid development / positive regulation of insulin secretion involved in cellular response to glucose stimulus / tertiary granule membrane / ficolin-1-rich granule membrane / negative regulation of neuron differentiation / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / COPI-mediated anterograde transport / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / axon cytoplasm / 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 / substantia nigra development / myelination / MHC class II antigen presentation / nitric-oxide synthase regulator activity / AURKA Activation by TPX2 / regulation of mitochondrial membrane potential / RHO GTPases Activate Formins / cilium / kinetochore / mitotic spindle / Aggrephagy / HCMV Early Events / cellular response to mechanical stimulus / Separation of Sister Chromatids / Regulation of PLK1 Activity at G2/M Transition / negative regulation of neuron projection development / myelin sheath / scaffold protein binding / carbohydrate binding / microtubule / negative regulation of neuron apoptotic process / cytoskeleton / cell adhesion / membrane raft / protein domain specific binding / signaling receptor binding / centrosome / apoptotic process / Neutrophil degranulation / protein-containing complex binding / protein kinase binding / enzyme binding / protein homodimerization activity / mitochondrion / membrane / identical protein binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.977 Å | ||||||
Authors | Myllykoski, M. / Kursula, P. | ||||||
Citation | Journal: J. Neurochem. / Year: 2018 Title: High-affinity heterotetramer formation between the large myelin-associated glycoprotein and the dynein light chain DYNLL1. Authors: Myllykoski, M. / Eichel, M.A. / Jung, R.B. / Kelm, S. / Werner, H.B. / Kursula, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6gzj.cif.gz | 56.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6gzj.ent.gz | 39.7 KB | Display | PDB format |
PDBx/mmJSON format | 6gzj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gz/6gzj ftp://data.pdbj.org/pub/pdb/validation_reports/gz/6gzj | HTTPS FTP |
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-Related structure data
Related structure data | 6gzlC 3zkeS S: Starting model for refinement C: citing same article (ref.) |
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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: 10468.978 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: DYNLL1, DLC1, DNCL1, DNCLC1, HDLC1 / Plasmid: pJExpress401 / Production host: Escherichia coli (E. coli) / References: UniProt: P63167 |
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#2: Protein | Mass: 6191.895 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Mus musculus (house mouse) / References: UniProt: P20917 |
#3: Chemical | ChemComp-CL / |
#4: 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: 28.43 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.1 M Bis-Tris pH 6.5, 0.2 M lithium sulfate, and 25% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.07175 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.07175 Å / Relative weight: 1 |
Reflection | Resolution: 1.977→50 Å / Num. obs: 7535 / % possible obs: 82.8 % / Redundancy: 17.6 % / Biso Wilson estimate: 44.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.107 / Rrim(I) all: 0.11 / Net I/σ(I): 17 |
Reflection shell | Resolution: 1.977→2.03 Å / Redundancy: 10.9 % / Rmerge(I) obs: 0.813 / Mean I/σ(I) obs: 3.9 / Num. unique obs: 62 / CC1/2: 0.902 / Rrim(I) all: 0.854 / % possible all: 9.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ZKE Resolution: 1.977→38.148 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.19 Details: Refinement was carried out with a set of data that has been anisotropically truncated, due to the strong anisotropy of the crystals. Hydrogen atoms were added to their riding positions.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.977→38.148 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9774→2.4912 Å
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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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