+Open data
-Basic information
Entry | Database: PDB / ID: 6iyb | ||||||
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Title | Structure of human ORP1 ANK - Rab7 complex | ||||||
Components |
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Keywords | TRANSPORT PROTEIN / oxysterol-binding protein / ORP1 / membrane contact site / Rab7 / Ankyrin repeat / cholesterol / RILP / Late endosome | ||||||
Function / homology | Function and homology information lipophagy / epidermal growth factor catabolic process / positive regulation of viral process / phagosome acidification / protein to membrane docking / organelle membrane contact site / negative regulation of intralumenal vesicle formation / alveolar lamellar body / negative regulation of exosomal secretion / phagosome-lysosome fusion ...lipophagy / epidermal growth factor catabolic process / positive regulation of viral process / phagosome acidification / protein to membrane docking / organelle membrane contact site / negative regulation of intralumenal vesicle formation / alveolar lamellar body / negative regulation of exosomal secretion / phagosome-lysosome fusion / Suppression of autophagy / phagosome maturation / : / establishment of vesicle localization / retromer complex binding / endosome to plasma membrane protein transport / bile acid biosynthetic process / perinuclear endoplasmic reticulum / 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 / RHOF GTPase cycle / RHOD GTPase cycle / retrograde transport, endosome to Golgi / TBC/RABGAPs / cholesterol binding / endosome to lysosome transport / RHOJ GTPase cycle / RHOQ GTPase cycle / autophagosome membrane / RHOH GTPase cycle / autophagosome assembly / CDC42 GTPase cycle / intracellular transport / RHOG GTPase cycle / viral release from host cell / Synthesis of bile acids and bile salts / RAC3 GTPase cycle / RAC2 GTPase cycle / lipid catabolic process / phagocytic vesicle / bone resorption / vesicle-mediated transport / Prevention of phagosomal-lysosomal fusion / cholesterol metabolic process / RAC1 GTPase cycle / MHC class II antigen presentation / lipid droplet / small monomeric GTPase / G protein activity / secretory granule membrane / mitochondrial membrane / response to bacterium / phospholipid binding / synaptic vesicle membrane / small GTPase binding / endocytosis / positive regulation of protein catabolic process / GDP binding / phagocytic vesicle membrane / protein transport / late endosome / late endosome membrane / lysosome / endosome membrane / endosome / lysosomal membrane / intracellular membrane-bounded organelle / GTPase activity / Neutrophil degranulation / GTP binding / Golgi apparatus / mitochondrion / extracellular exosome / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.091 Å | ||||||
Authors | Tong, J. / Im, Y.J. | ||||||
Funding support | Korea, Republic Of, 1items
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Citation | Journal: PLoS ONE / Year: 2019 Title: Structural basis of human ORP1-Rab7 interaction for the late-endosome and lysosome targeting. Authors: Tong, J. / Tan, L. / Chun, C. / Im, Y.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6iyb.cif.gz | 146.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6iyb.ent.gz | 110.4 KB | Display | PDB format |
PDBx/mmJSON format | 6iyb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/iy/6iyb ftp://data.pdbj.org/pub/pdb/validation_reports/iy/6iyb | HTTPS FTP |
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-Related structure data
Related structure data | 1t91S 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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Unit cell |
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-Components
#1: Protein | Mass: 22536.592 Da / Num. of mol.: 2 / Fragment: UNP residues 2-195 / Mutation: Q67L, Leu73 deletion Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RAB7A / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P51149 #2: Protein | Mass: 17011.248 Da / Num. of mol.: 2 / Fragment: UNP residues 5-152 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: OSBPL1A / Plasmid: pHIS2-Thr / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9BXW6 #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: 2.81 Å3/Da / Density % sol: 56.18 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 0.1 M Na3Citrate-HCl, 1 M LiCl, 20% PEG 1000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97949 Å |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Mar 14, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.09→50 Å / Num. obs: 50042 / % possible obs: 99.1 % / Redundancy: 5.7 % / Biso Wilson estimate: 29.7 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 39.3 |
Reflection shell | Resolution: 2.09→2.14 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 7.3 / Num. unique obs: 2496 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1T91 Resolution: 2.091→26.286 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.37
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.3 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.091→26.286 Å
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Refine LS restraints |
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LS refinement shell |
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