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Yorodumi- PDB-1hj7: NMR study of a pair of LDL receptor Ca2+ binding epidermal growth... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1hj7 | ||||||
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Title | NMR study of a pair of LDL receptor Ca2+ binding epidermal growth factor-like domains, 20 structures | ||||||
Components | LDL RECEPTOR | ||||||
Keywords | CELL-SURFACE RECEPTOR / CALCIUM-BINDING / EGF-LIKE DOMAIN / MODULE / APO-E / APO-B / LDL / VLDL | ||||||
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 / 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 / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | SOLUTION NMR / simulated annealing | ||||||
Authors | Saha, S. / Handford, P.A. / Campbell, I.D. / Downing, A.K. | ||||||
Citation | Journal: Structure / Year: 2001 Title: Solution Structure of the Ldl Receptor Egf-Ab Pair: A Paradigm for the Assembly of Tandem Calcium Binding Egf Domains Authors: Saha, S. / Boyd, J. / Werner, J.M. / Knott, V. / Handford, P.A. / Campbell, I.D. / Downing, A.K. #1: Journal: Methods Mol.Biol. / Year: 2002 Title: The Use of Dipolar Couplings for the Structure Refinement of a Pair of Calcium-Binding Egf Domains. Authors: Boyd, J. / Campbell, I.D. / Downing, A.K. #2: Journal: Biochemistry / Year: 2001 Title: The First Epidermal Growth Factor-Like Domain of the Low-Density Lipoprotein Receptor Contains a Noncanonical Calcium Binding Site Authors: Malby, S. / Pickering, R. / Saha, S. / Smallridge, R.S. / Linse, S. / Downing, A.K. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: AUTHOR PROVIDED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1hj7.cif.gz | 456.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1hj7.ent.gz | 393.2 KB | Display | PDB format |
PDBx/mmJSON format | 1hj7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hj/1hj7 ftp://data.pdbj.org/pub/pdb/validation_reports/hj/1hj7 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 8830.804 Da / Num. of mol.: 1 Fragment: CA2+ BINDING EPIDERMAL GROWTH FACTOR-LIKE DOMAIN PAIR, RESIDUES 293-372 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Cellular location: TRANSMEMBRANETransmembrane protein / Gene: LDLR / Plasmid: PQE30 (QIAGEN) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P01130 |
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#2: Chemical |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||
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NMR experiment |
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NMR details | Text: NOE DISTANCE CONSTRAINTS WERE DERIVED FROM CROSS PEAK INTENSITIES MEASURED IN 1H-HOMONUCLEAR AND 1H-15N HETERONUCLEAR NMR SPECTRA. COUPLING CONSTANTS USED TO DERIVE TORSION ANGLE CONSTRAINTS ...Text: NOE DISTANCE CONSTRAINTS WERE DERIVED FROM CROSS PEAK INTENSITIES MEASURED IN 1H-HOMONUCLEAR AND 1H-15N HETERONUCLEAR NMR SPECTRA. COUPLING CONSTANTS USED TO DERIVE TORSION ANGLE CONSTRAINTS WERE MEASURED IN A 1H-15N HMQC-J SPECTRUM. SEE REFERENCE 1 FOR DETAILS OF 1JHN CONSTRAINT IMPLEMENTATION. |
-Sample preparation
Details | Contents: SEE REFERENCES |
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Sample conditions | Ionic strength: SEE REFERENCES / pH: 6.5 / Temperature: 303 K |
Crystal grow | *PLUS Method: other / Details: NMR |
-NMR measurement
NMR spectrometer |
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-Processing
NMR software |
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Refinement | Method: simulated annealing / Software ordinal: 1 / Details: REFINEMENT DETAILS CAN BE FOUND IN REFERENCE 1. | ||||||||||||
NMR ensemble | Conformer selection criteria: NO NOE, 3JHN OR 1JHN CONSTRAINTS VIOLATED BY > 0.5 A, 5 DEGREES OR 2 HERTZ Conformers calculated total number: 280 / Conformers submitted total number: 20 |