+Open data
-Basic information
Entry | Database: PDB / ID: 6stf | ||||||
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Title | Human Rab8a phosphorylated at Ser111 in complex with GDP | ||||||
Components | Ras-related protein Rab-8A | ||||||
Keywords | SIGNALING PROTEIN / Parkinson Disease / Phosphorylation / Small G-Protein / SF3 Motif | ||||||
Function / homology | Function and homology information neurotransmitter receptor transport to postsynaptic membrane / Golgi vesicle fusion to target membrane / vesicle-mediated transport in synapse / regulation of protein transport / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / RAB geranylgeranylation / myosin V binding / vesicle docking involved in exocytosis / trans-Golgi network transport vesicle ...neurotransmitter receptor transport to postsynaptic membrane / Golgi vesicle fusion to target membrane / vesicle-mediated transport in synapse / regulation of protein transport / VxPx cargo-targeting to cilium / neurotransmitter receptor transport, endosome to postsynaptic membrane / RAB geranylgeranylation / myosin V binding / vesicle docking involved in exocytosis / trans-Golgi network transport vesicle / regulation of exocytosis / protein localization to cilium / RAB GEFs exchange GTP for GDP on RABs / non-motile cilium / endocytic recycling / TBC/RABGAPs / ciliary membrane / ciliary base / Golgi organization / cilium assembly / protein secretion / phagocytic vesicle / protein tyrosine kinase binding / Anchoring of the basal body to the plasma membrane / centriole / axonogenesis / small monomeric GTPase / trans-Golgi network membrane / ciliary basal body / regulation of autophagy / Translocation of SLC2A4 (GLUT4) to the plasma membrane / protein localization to plasma membrane / regulation of long-term neuronal synaptic plasticity / cilium / small GTPase binding / autophagy / cellular response to insulin stimulus / recycling endosome membrane / GDP binding / phagocytic vesicle membrane / Regulation of PLK1 Activity at G2/M Transition / synaptic vesicle / midbody / dendritic spine / postsynaptic density / endosome membrane / endosome / Golgi membrane / GTPase activity / neuronal cell body / centrosome / glutamatergic synapse / GTP binding / extracellular exosome / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Vieweg, S. / Mulholland, K. / Braeuning, B. / Kachariya, N. / Lai, Y. / Toth, R. / Sattler, M. / Groll, M. / Itzen, A. / Muqit, M.M.K. | ||||||
Funding support | Germany, 1items
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Citation | Journal: Biochem.J. / Year: 2020 Title: PINK1-dependent phosphorylation of Serine111 within the SF3 motif of Rab GTPases impairs effector interactions and LRRK2-mediated phosphorylation at Threonine72. Authors: Vieweg, S. / Mulholland, K. / Brauning, B. / Kachariya, N. / Lai, Y.C. / Toth, R. / Singh, P.K. / Volpi, I. / Sattler, M. / Groll, M. / Itzen, A. / Muqit, M.M.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6stf.cif.gz | 350.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6stf.ent.gz | 286.7 KB | Display | PDB format |
PDBx/mmJSON format | 6stf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/st/6stf ftp://data.pdbj.org/pub/pdb/validation_reports/st/6stf | HTTPS FTP |
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-Related structure data
Related structure data | 6stgC 4lhvS 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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Unit cell |
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-Components
#1: Protein | Mass: 20725.699 Da / Num. of mol.: 5 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAB8A, MEL, RAB8 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P61006 #2: Chemical | ChemComp-GDP / #3: Chemical | ChemComp-MG / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.26 Å3/Da / Density % sol: 45.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M Sodium Cacodylate, 0.2 M MgAc2, 20% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 10, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→50 Å / Num. obs: 35267 / % possible obs: 97.2 % / Redundancy: 3 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.4→2.5 Å / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4015 / % possible all: 96.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LHV Resolution: 2.4→30 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.911 / SU B: 23.313 / SU ML: 0.233 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.306 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 127.09 Å2 / Biso mean: 48.379 Å2 / Biso min: 25.07 Å2
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Refinement step | Cycle: final / Resolution: 2.4→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / 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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