+Open data
-Basic information
Entry | Database: PDB / ID: 2e9s | ||||||
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Title | human neuronal Rab6B in three intermediate forms | ||||||
Components | Ras-related protein Rab-6B | ||||||
Keywords | PROTEIN TRANSPORT / human neuron / Rab6B / GDP MG NO3 complex / GDP MG complex / GDP complex | ||||||
Function / homology | Function and homology information protein localization to Golgi membrane / Retrograde transport at the Trans-Golgi-Network / intra-Golgi vesicle-mediated transport / RAB geranylgeranylation / myosin V binding / COPI-independent Golgi-to-ER retrograde traffic / RAB GEFs exchange GTP for GDP on RABs / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / retrograde transport, endosome to Golgi / TBC/RABGAPs ...protein localization to Golgi membrane / Retrograde transport at the Trans-Golgi-Network / intra-Golgi vesicle-mediated transport / RAB geranylgeranylation / myosin V binding / COPI-independent Golgi-to-ER retrograde traffic / RAB GEFs exchange GTP for GDP on RABs / retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum / retrograde transport, endosome to Golgi / TBC/RABGAPs / Golgi organization / endoplasmic reticulum-Golgi intermediate compartment / endomembrane system / small monomeric GTPase / intracellular protein transport / neuron projection development / presynapse / cytoplasmic vesicle / Golgi membrane / GTPase activity / GTP binding / Golgi apparatus / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 Å | ||||||
Authors | Vellieux, F.M. / Tcherniuk, S. / Garcia-Saez, I. / Kozielski, F. | ||||||
Citation | Journal: To be Published Title: 3D structure of human neuronal Rab6B in three intermediate forms Authors: Vellieux, F.M. / Tcherniuk, S. / Garcia-Saez, I. / Kozielski, F. #1: Journal: ACTA CRYSTALLOGR.,SECT.D / Year: 2006 Title: The structure of human neuronal Rab6B in the active and inactive form Authors: Garcia-Saez, I. / Tcherniuk, S. / Kozielski, F. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2e9s.cif.gz | 117.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2e9s.ent.gz | 89.5 KB | Display | PDB format |
PDBx/mmJSON format | 2e9s.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e9/2e9s ftp://data.pdbj.org/pub/pdb/validation_reports/e9/2e9s | HTTPS FTP |
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-Related structure data
Related structure data | 2fe4S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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-Components
#1: Protein | Mass: 19793.441 Da / Num. of mol.: 3 / Fragment: residues in database 13-174 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAB6B / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9NRW1 #2: Chemical | ChemComp-NO3 / | #3: Chemical | #4: Chemical | #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: 1.81 Å3/Da / Density % sol: 32.17 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.3 Details: 0.2M ammonium nitrate, 20% PEG 3350, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.934 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 12, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 1.78→19.74 Å / Num. obs: 42010 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Biso Wilson estimate: 12.2 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 24.7 |
Reflection shell | Resolution: 1.78→1.9 Å / Rmerge(I) obs: 0.157 / Mean I/σ(I) obs: 9.8 / Num. unique all: 7141 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ID 2FE4 Resolution: 1.78→19.74 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 2088564.3 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 43.2543 Å2 / ksol: 0.39709 e/Å3 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.78→19.74 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.78→1.89 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
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Xplor file |
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