+Open data
-Basic information
Entry | Database: PDB / ID: 1ajj | ||||||
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Title | LDL RECEPTOR LIGAND-BINDING MODULE 5, CALCIUM-COORDINATING | ||||||
Components | LOW-DENSITY LIPOPROTEIN RECEPTOR | ||||||
Keywords | RECEPTOR / LDL RECEPTOR / CYSTEINE-RICH MODULE / CALCIUM | ||||||
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 / negative regulation of microglial cell activation / PCSK9-LDLR complex / cholesterol import / negative regulation of receptor recycling ...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 / negative regulation of microglial cell activation / 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 / positive regulation of triglyceride biosynthetic process / negative regulation of low-density lipoprotein particle clearance / intestinal cholesterol absorption / low-density lipoprotein particle binding / Chylomicron clearance / response to caloric restriction / amyloid-beta clearance by cellular catabolic process / LDL clearance / regulation of protein metabolic process / high-density lipoprotein particle clearance / lipoprotein catabolic process / phospholipid transport / cholesterol transport / low-density lipoprotein particle / endolysosome membrane / negative regulation of amyloid fibril formation / negative regulation of protein metabolic process / artery morphogenesis / cellular response to fatty acid / regulation of cholesterol metabolic process / amyloid-beta clearance / sorting endosome / lipoprotein particle binding / cellular response to low-density lipoprotein particle stimulus / long-term memory / phagocytosis / Retinoid metabolism and transport / 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 / Cargo recognition for clathrin-mediated endocytosis / late endosome / apical part of cell / Clathrin-mediated endocytosis / virus receptor activity / amyloid-beta binding / basolateral plasma membrane / protease binding / molecular adaptor activity / lysosome / early endosome / receptor complex / endosome membrane / external side of plasma membrane / negative regulation of gene expression / calcium ion binding / positive regulation of gene expression / Golgi apparatus / cell surface / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 1.7 Å | ||||||
Authors | Fass, D. / Blacklow, S.C. / Kim, P.S. / Berger, J.M. | ||||||
Citation | Journal: Nature / Year: 1997 Title: Molecular basis of familial hypercholesterolaemia from structure of LDL receptor module. Authors: Fass, D. / Blacklow, S. / Kim, P.S. / Berger, J.M. #1: Journal: Nat.Struct.Biol. / Year: 1996 Title: Protein Folding and Calcium Binding Defects Arising from Familial Hypercholesterolemia Mutations of the Ldl Receptor Authors: Blacklow, S.C. / Kim, P.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ajj.cif.gz | 16.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ajj.ent.gz | 11.5 KB | Display | PDB format |
PDBx/mmJSON format | 1ajj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ajj_validation.pdf.gz | 371.3 KB | Display | wwPDB validaton report |
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Full document | 1ajj_full_validation.pdf.gz | 371.3 KB | Display | |
Data in XML | 1ajj_validation.xml.gz | 2.3 KB | Display | |
Data in CIF | 1ajj_validation.cif.gz | 3.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/1ajj ftp://data.pdbj.org/pub/pdb/validation_reports/aj/1ajj | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein/peptide | Mass: 4069.431 Da / Num. of mol.: 1 / Fragment: LIGAND-BINDING DOMAIN, FIFTH REPEAT Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Plasmid: PMM-LR5 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P01130 |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-CA / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.81 Å3/Da / Density % sol: 28 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5 Details: PROTEIN WAS CRYSTALLIZED FROM 2.1 M AMMONIUM SULFATE, PH 5.0, 25% SUCROSE | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 15 ℃ / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Nov 1, 1996 / Details: MIRRORS |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→15 Å / Num. obs: 2959 / % possible obs: 94.3 % / Observed criterion σ(I): 1.5 / Redundancy: 4.5 % / Rsym value: 0.054 / Net I/σ(I): 20 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 3 % / Mean I/σ(I) obs: 7 / Rsym value: 0.169 / % possible all: 87.7 |
Reflection | *PLUS Rmerge(I) obs: 0.054 |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 1.7→15 Å / Cross valid method: THROUGHOUT
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Refinement step | Cycle: LAST / Resolution: 1.7→15 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor Rfree: 0.24 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |