+Open data
-Basic information
Entry | Database: PDB / ID: 1yhn | ||||||
---|---|---|---|---|---|---|---|
Title | Structure basis of RILP recruitment by Rab7 | ||||||
Components |
| ||||||
Keywords | PROTEIN TRANSPORT / RILP / Rab7 | ||||||
Function / homology | Function and homology information lipophagy / epidermal growth factor catabolic process / positive regulation of viral process / phagosome acidification / protein to membrane docking / negative regulation of intralumenal vesicle formation / small GTPase binding => GO:0031267 / regulation of multivesicular body size / alveolar lamellar body / negative regulation of exosomal secretion ...lipophagy / epidermal growth factor catabolic process / positive regulation of viral process / phagosome acidification / protein to membrane docking / negative regulation of intralumenal vesicle formation / small GTPase binding => GO:0031267 / regulation of multivesicular body size / alveolar lamellar body / negative regulation of exosomal secretion / phagosome-lysosome fusion / Suppression of autophagy / phagosome maturation / intralumenal vesicle formation / establishment of vesicle localization / retromer complex binding / endosome to plasma membrane protein transport / endosome transport via multivesicular body sorting pathway / melanosome membrane / phagophore assembly site membrane / protein targeting to lysosome / RAB geranylgeranylation / early endosome to late endosome transport / positive regulation of exosomal secretion / RAB GEFs exchange GTP for GDP on RABs / dynein light intermediate chain binding / RHOF GTPase cycle / RHOD GTPase cycle / retrograde transport, endosome to Golgi / TBC/RABGAPs / endosome to lysosome transport / RHOJ GTPase cycle / RHOQ GTPase cycle / autophagosome membrane / RHOH GTPase cycle / autophagosome assembly / CDC42 GTPase cycle / intracellular transport / cilium assembly / RHOG GTPase cycle / viral release from host cell / RAC3 GTPase cycle / RAC2 GTPase cycle / lipid catabolic process / phagocytic vesicle / bone resorption / Prevention of phagosomal-lysosomal fusion / RAC1 GTPase cycle / MHC class II antigen presentation / lipid droplet / small monomeric GTPase / G protein activity / secretory granule membrane / ciliary basal body / mitochondrial membrane / response to bacterium / negative regulation of protein catabolic process / synaptic vesicle membrane / small GTPase binding / endocytosis / phagocytic vesicle membrane / GDP binding / positive regulation of protein catabolic process / antigen processing and presentation of exogenous peptide antigen via MHC class II / protein transport / late endosome / late endosome membrane / lysosome / protein dimerization activity / endosome membrane / lysosomal membrane / GTPase activity / Neutrophil degranulation / GTP binding / Golgi apparatus / protein-containing complex / mitochondrion / extracellular exosome / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å | ||||||
Authors | Wu, M. / Wang, T. / Hong, W. / Song, H. | ||||||
Citation | Journal: Embo J. / Year: 2005 Title: Structural basis for recruitment of RILP by small GTPase Rab7. Authors: Wu, M. / Wang, T. / Loh, E. / Hong, W. / Song, H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1yhn.cif.gz | 65.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1yhn.ent.gz | 47.5 KB | Display | PDB format |
PDBx/mmJSON format | 1yhn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yh/1yhn ftp://data.pdbj.org/pub/pdb/validation_reports/yh/1yhn | HTTPS FTP |
---|
-Related structure data
Related structure data | 1t91SC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The biological assembly is a dimer generated from the monomer in the asymmetric unit by symmetric operation. |
-Components
#1: Protein | Mass: 23501.748 Da / Num. of mol.: 1 / Mutation: Q67L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: Rab7 / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21* / References: UniProt: P51149 |
---|---|
#2: Protein | Mass: 7786.252 Da / Num. of mol.: 1 / Fragment: RILP effector domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RILP / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL-21* / References: UniProt: Q96NA2 |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-GTP / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 47.87 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: ammonium sulfate, polyvinylpyrrolidone K15, HEPS, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 0.9175 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 29, 2004 / Details: bent mirror |
Radiation | Monochromator: double crystal focusing / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9175 Å / Relative weight: 1 |
Reflection | Resolution: 3→51 Å / Num. all: 7314 / Num. obs: 7272 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1 / Redundancy: 11.3 % / Biso Wilson estimate: 64 Å2 / Rmerge(I) obs: 0.097 / Rsym value: 0.097 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 11.4 % / Rmerge(I) obs: 0.426 / Mean I/σ(I) obs: 1.8 / Num. unique all: 690 / Rsym value: 0.426 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1T91 Resolution: 3→20 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→20 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|