+Open data
-Basic information
Entry | Database: PDB / ID: 4q95 | ||||||
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Title | Crystal structure of HRASLS3/LRAT chimeric protein | ||||||
Components | HRAS-like suppressor 3, Lecithin retinol acyltransferase | ||||||
Keywords | TRANSFERASE / Lecithin:retinol acyltransferase / alpha/beta fold / Acylation / Membrane | ||||||
Function / homology | Function and homology information phosphatidylcholine-retinol O-acyltransferase / 1,2-diacyl-sn-glycero-3-phosphocholine metabolic process / phosphatidylcholine-retinol O-acyltransferase activity / : / The canonical retinoid cycle in rods (twilight vision) / membrane disassembly / ether lipid metabolic process / regulation of adipose tissue development / positive regulation of lipid transport / organelle disassembly ...phosphatidylcholine-retinol O-acyltransferase / 1,2-diacyl-sn-glycero-3-phosphocholine metabolic process / phosphatidylcholine-retinol O-acyltransferase activity / : / The canonical retinoid cycle in rods (twilight vision) / membrane disassembly / ether lipid metabolic process / regulation of adipose tissue development / positive regulation of lipid transport / organelle disassembly / phosphatidylethanolamine acyl-chain remodeling / N-acylphosphatidylethanolamine metabolic process / Retinoid metabolism and transport / phospholipase A1 / O-acyltransferase activity / phosphatidylserine 1-acylhydrolase activity / 1-acyl-2-lysophosphatidylserine acylhydrolase activity / phospholipase A1 activity / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / peroxisome organization / N-acyltransferase activity / vitamin A metabolic process / phospholipid biosynthetic process / phospholipase A2 activity / lens fiber cell differentiation / retinoic acid binding / response to vitamin A / phospholipase A2 / peroxisomal membrane / retinol metabolic process / retinol binding / triglyceride metabolic process / acyltransferase activity / localization / phospholipid metabolic process / lipid catabolic process / response to retinoic acid / rough endoplasmic reticulum / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / visual perception / multivesicular body / cellular response to leukemia inhibitory factor / mitochondrial membrane / response to bacterium / peroxisome / nuclear envelope / membrane => GO:0016020 / lysosome / lysosomal membrane / intracellular membrane-bounded organelle / lipid binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / mitochondrion / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Golczak, M. / Kiser, P.D. / Sears, A.E. / Palczewski, K. | ||||||
Citation | Journal: Nat.Chem.Biol. / Year: 2015 Title: LRAT-specific domain facilitates vitamin A metabolism by domain swapping in HRASLS3. Authors: Golczak, M. / Sears, A.E. / Kiser, P.D. / Palczewski, K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4q95.cif.gz | 124.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4q95.ent.gz | 97.5 KB | Display | PDB format |
PDBx/mmJSON format | 4q95.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4q95_validation.pdf.gz | 444.1 KB | Display | wwPDB validaton report |
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Full document | 4q95_full_validation.pdf.gz | 444.8 KB | Display | |
Data in XML | 4q95_validation.xml.gz | 12.1 KB | Display | |
Data in CIF | 4q95_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q9/4q95 ftp://data.pdbj.org/pub/pdb/validation_reports/q9/4q95 | HTTPS FTP |
-Related structure data
Related structure data | 4dotS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: 7 - 140 / Label seq-ID: 9 - 142
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-Components
#1: Protein | Mass: 16956.447 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Mus musculus (house mouse) Gene: HRASLS3, HREV107, human PLA2G16 and mouse Lrat, Lrat, PLA2G16 Plasmid: pGEX-2T / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE References: UniProt: P53816, UniProt: Q9JI60, phosphatidylcholine-retinol O-acyltransferase #2: Chemical | #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: 2.32 Å3/Da / Density % sol: 46.98 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: 0.1 M Tris/HCl, pH 8.5, 0.2 M NaCl, 20% (w/v) polyethylene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 77 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Jul 30, 2013 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→49.32 Å / Num. all: 16836 / Num. obs: 16797 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4DOT Resolution: 2.2→49.32 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.923 / SU B: 16.84 / SU ML: 0.195 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.264 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.186 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→49.32 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 6511 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.18 Å / Weight position: 0.05
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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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