+Open data
-Basic information
Entry | Database: PDB / ID: 1ijq | ||||||
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Title | Crystal Structure of the LDL Receptor YWTD-EGF Domain Pair | ||||||
Components | LOW-DENSITY LIPOPROTEIN RECEPTORLDL receptor | ||||||
Keywords | LIPID TRANSPORT / beta-propeller | ||||||
Function / homology | Function and homology information regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / positive regulation of lysosomal protein catabolic process / very-low-density lipoprotein particle receptor activity / negative regulation of astrocyte activation / receptor-mediated endocytosis involved in cholesterol transport / response to caloric restriction / negative regulation of microglial cell activation / Chylomicron clearance / PCSK9-LDLR complex ...regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / positive regulation of lysosomal protein catabolic process / very-low-density lipoprotein particle receptor activity / negative regulation of astrocyte activation / receptor-mediated endocytosis involved in cholesterol transport / response to caloric restriction / negative regulation of microglial cell activation / Chylomicron clearance / PCSK9-LDLR complex / cholesterol import / negative regulation of receptor recycling / low-density lipoprotein particle clearance / clathrin heavy chain binding / low-density lipoprotein particle receptor activity / high-density lipoprotein particle clearance / lipoprotein catabolic process / intestinal cholesterol absorption / positive regulation of triglyceride biosynthetic process / negative regulation of low-density lipoprotein particle clearance / regulation of protein metabolic process / low-density lipoprotein particle / low-density lipoprotein particle binding / amyloid-beta clearance by cellular catabolic process / LDL clearance / negative regulation of amyloid fibril formation / phospholipid transport / cholesterol transport / endolysosome membrane / negative regulation of protein metabolic process / artery morphogenesis / regulation of cholesterol metabolic process / cellular response to fatty acid / lipoprotein particle binding / amyloid-beta clearance / sorting endosome / cellular response to low-density lipoprotein particle stimulus / long-term memory / Retinoid metabolism and transport / phagocytosis / clathrin-coated pit / somatodendritic compartment / cholesterol metabolic process / receptor-mediated endocytosis / cholesterol homeostasis / clathrin-coated endocytic vesicle membrane / lipid metabolic process / positive regulation of inflammatory response / endocytosis / late endosome / Cargo recognition for clathrin-mediated endocytosis / virus receptor activity / apical part of cell / Clathrin-mediated endocytosis / amyloid-beta binding / basolateral plasma membrane / protease binding / lysosome / molecular adaptor activity / receptor complex / early endosome / endosome membrane / external side of plasma membrane / negative regulation of gene expression / calcium ion binding / positive regulation of gene expression / Golgi apparatus / cell surface / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.5 Å | ||||||
Authors | Jeon, H. / Meng, W. / Takagi, J. / Eck, M.J. / Springer, T.A. / Blacklow, S.C. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 2001 Title: Implications for familial hypercholesterolemia from the structure of the LDL receptor YWTD-EGF domain pair. Authors: Jeon, H. / Meng, W. / Takagi, J. / Eck, M.J. / Springer, T.A. / Blacklow, S.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ijq.cif.gz | 155.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ijq.ent.gz | 126.4 KB | Display | PDB format |
PDBx/mmJSON format | 1ijq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ij/1ijq ftp://data.pdbj.org/pub/pdb/validation_reports/ij/1ijq | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 35593.398 Da / Num. of mol.: 2 / Fragment: YWTD-E3 DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LDLR / Plasmid: PEF1-V5-HIS / Cell (production host): CHO / Organ (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHOlec / References: UniProt: P01130 #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 4 |
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-Sample preparation
Crystal | Density Matthews: 2.6 Å3/Da / Density % sol: 52 % | ||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: PEG4000,2-propanol,HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction |
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Diffraction source |
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Detector |
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Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.5→20 Å / Num. all: 543455 / Num. obs: 127540 / % possible obs: 88.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 22.4 Å2 / Rmerge(I) obs: 0.069 / Net I/σ(I): 22.7 | ||||||||||||||||||
Reflection shell | Resolution: 1.5→1.56 Å / Redundancy: 4 % / Rmerge(I) obs: 0.1 / % possible all: 55.8 | ||||||||||||||||||
Reflection | *PLUS Num. measured all: 543455 | ||||||||||||||||||
Reflection shell | *PLUS % possible obs: 55.8 % / Mean I/σ(I) obs: 2.02 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.5→20 Å / Rfactor Rfree error: 0.003 / Cross valid method: THROUGHOUT / σ(F): 1 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: CNS / Bsol: 53.1313 Å2 / ksol: 0.48116 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.07 Å2
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Refine analyze | Luzzati coordinate error obs: 0.22 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: -0.03 Å | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.57 Å / Rfactor Rfree error: 0.013 / Total num. of bins used: 8
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Software | *PLUS Name: CNS,ARP/WARP / Classification: refinement | |||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 1.5 Å / Lowest resolution: 20 Å / σ(F): 1 / % reflection Rfree: 5 % / Rfactor Rfree: 0.25 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 1.5 Å / Rfactor Rfree: 0.277 / % reflection Rfree: 2.7 % / Rfactor Rwork: 0.277 |