+Open data
-Basic information
Entry | Database: PDB / ID: 6f6p | |||||||||
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Title | Crystal structure of tetrameric human Rabin8 GEF domain | |||||||||
Components | (Rab-3A-interacting protein) x 2 | |||||||||
Keywords | HYDROLASE / Rabin8 / GEF / guanine nucleotide exchange factor / tetramer / RAB3I | |||||||||
Function / homology | Function and homology information Golgi to plasma membrane transport vesicle / ciliary basal body-plasma membrane docking / protein localization to organelle / negative regulation of filopodium assembly / proximal dendrite / VxPx cargo-targeting to cilium / BBSome-mediated cargo-targeting to cilium / Golgi to plasma membrane transport / RAB GEFs exchange GTP for GDP on RABs / protein targeting to membrane ...Golgi to plasma membrane transport vesicle / ciliary basal body-plasma membrane docking / protein localization to organelle / negative regulation of filopodium assembly / proximal dendrite / VxPx cargo-targeting to cilium / BBSome-mediated cargo-targeting to cilium / Golgi to plasma membrane transport / RAB GEFs exchange GTP for GDP on RABs / protein targeting to membrane / exocytosis / cilium assembly / Anchoring of the basal body to the plasma membrane / guanyl-nucleotide exchange factor activity / ciliary basal body / protein transport / GTPase binding / lamellipodium / centrosome / perinuclear region of cytoplasm / identical protein binding / nucleus / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å | |||||||||
Authors | Lorentzen, E. / Vetter, M. | |||||||||
Funding support | Denmark, 1items
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Citation | Journal: Proteins / Year: 2018 Title: Crystal structure of tetrameric human Rabin8 GEF domain. Authors: Vetter, M. / Boegholm, N. / Christensen, A. / Bhogaraju, S. / Andersen, M.B. / Lorentzen, A. / Lorentzen, E. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6f6p.cif.gz | 166 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f6p.ent.gz | 138.8 KB | Display | PDB format |
PDBx/mmJSON format | 6f6p.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f6/6f6p ftp://data.pdbj.org/pub/pdb/validation_reports/f6/6f6p | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 11994.736 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAB3IP, RABIN8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96QF0 #2: Protein | | Mass: 12010.736 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAB3IP, RABIN8 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96QF0 #3: 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: 2.61 Å3/Da / Density % sol: 56 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion / pH: 7.3 / Details: 50 mM Tris pH 7.3 and 40% MPD |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X9A / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 11, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→68.6 Å / Num. obs: 19008 / % possible obs: 99.8 % / Redundancy: 8.7 % / CC1/2: 0.998 / Rmerge(I) obs: 0.094 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.45→2.49 Å / Redundancy: 8.7 % / Rmerge(I) obs: 1.12 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 962 / CC1/2: 0.992 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: SAD / Resolution: 2.45→68.6 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 40.58
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.45→68.6 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 45.4853 Å / Origin y: 38.3367 Å / Origin z: 68.6932 Å
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Refinement TLS group | Selection details: all |