+Open data
-Basic information
Entry | Database: PDB / ID: 8zq3 | ||||||
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Title | Structure of ORP1L-RAB7A in the presence of GDP | ||||||
Components |
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Keywords | ENDOCYTOSIS / Oxysterol binding protein (OSBP) The human OSBP-related gene/protein (ORP) family | ||||||
Function / homology | Function and homology information lipophagy / positive regulation of viral process / phagosome acidification / protein to membrane docking / epidermal growth factor catabolic process / negative regulation of intralumenal vesicle formation / alveolar lamellar body / negative regulation of exosomal secretion / phagosome-lysosome fusion / Suppression of autophagy ...lipophagy / positive regulation of viral process / phagosome acidification / protein to membrane docking / epidermal growth factor catabolic process / negative regulation of intralumenal vesicle formation / alveolar lamellar body / negative regulation of exosomal secretion / phagosome-lysosome fusion / Suppression of autophagy / organelle membrane contact site / establishment of vesicle localization / phagosome maturation / retromer complex binding / bile acid biosynthetic process / perinuclear endoplasmic reticulum / endosome to plasma membrane protein transport / protein targeting to lysosome / RAB geranylgeranylation / phagophore assembly site membrane / early endosome to late endosome transport / melanosome membrane / positive regulation of exosomal secretion / intracellular transport / RAB GEFs exchange GTP for GDP on RABs / RHOF GTPase cycle / RHOD GTPase cycle / TBC/RABGAPs / retrograde transport, endosome to Golgi / lipid transport / cholesterol binding / endosome to lysosome transport / RHOJ GTPase cycle / RHOQ GTPase cycle / viral release from host cell / autophagosome membrane / CDC42 GTPase cycle / RHOH GTPase cycle / autophagosome assembly / RHOG GTPase cycle / Synthesis of bile acids and bile salts / RAC2 GTPase cycle / RAC3 GTPase cycle / bone resorption / phagocytic vesicle / lipid catabolic process / vesicle-mediated transport / Prevention of phagosomal-lysosomal fusion / MHC class II antigen presentation / RAC1 GTPase cycle / cholesterol metabolic process / lipid droplet / small monomeric GTPase / secretory granule membrane / G protein activity / mitochondrial membrane / response to bacterium / phospholipid binding / small GTPase binding / synaptic vesicle membrane / endocytosis / positive regulation of protein catabolic process / phagocytic vesicle membrane / GDP binding / late endosome / protein transport / late endosome membrane / lysosome / endosome membrane / endosome / lysosomal membrane / 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: 2.43 Å | ||||||
Authors | Lu, Q. / Zhang, J. / Xu, C. | ||||||
Funding support | China, 1items
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Citation | Journal: Biochem.Biophys.Res.Commun. / Year: 2024 Title: Structure of GDP-bound Rab7 Q67L in complex with ORP1L. Authors: Lu, Q. / Zhu, Z. / Zhang, J. / Xu, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8zq3.cif.gz | 145 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8zq3.ent.gz | 112.4 KB | Display | PDB format |
PDBx/mmJSON format | 8zq3.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8zq3_validation.pdf.gz | 777.3 KB | Display | wwPDB validaton report |
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Full document | 8zq3_full_validation.pdf.gz | 782.3 KB | Display | |
Data in XML | 8zq3_validation.xml.gz | 13.9 KB | Display | |
Data in CIF | 8zq3_validation.cif.gz | 18.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zq/8zq3 ftp://data.pdbj.org/pub/pdb/validation_reports/zq/8zq3 | HTTPS FTP |
-Related structure data
Related structure data | 1t91S S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-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: RAB7A, RAB7 / Production host: Escherichia coli (E. coli) / References: UniProt: P51149, small monomeric GTPase |
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#2: Protein | Mass: 22756.861 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: OSBPL1A, ORP1, OSBP8, OSBPL1, OSBPL1B / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BXW6 |
#3: Chemical | ChemComp-GDP / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.54 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop Details: 0.2M diammonium tartrate, 20% PEG3350, 0.1 M Ethylenediaminetetraacetic acid disodium salt dihydrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.9791 Å |
Detector | Type: STFC Large Pixel Detector / Detector: PIXEL / Date: Nov 24, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.43→44.72 Å / Num. obs: 17217 / % possible obs: 99.8 % / Redundancy: 25.6 % / CC1/2: 0.999 / Net I/σ(I): 17.8 |
Reflection shell | Resolution: 2.43→2.5 Å / Num. unique obs: 17217 / CC1/2: 0.824 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1T91 Resolution: 2.43→40.21 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 26.54 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.43→40.21 Å
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Refine LS restraints |
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LS refinement shell |
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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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