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- PDB-2fcw: Structure of a Complex Between the Pair of the LDL Receptor Ligan... -
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Basic information
Entry | Database: PDB / ID: 2fcw | ||||||
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Title | Structure of a Complex Between the Pair of the LDL Receptor Ligand-Binding Modules 3-4 and the Receptor Associated Protein (RAP). | ||||||
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![]() | LIPID TRANSPORT/ENDOCYTOSIS/CHAPERONE / protein-protein complex / RAP / LDLR / escort protein / calcium-binding / LIPID TRANSPORT-ENDOCYTOSIS-CHAPERONE COMPLEX | ||||||
Function / homology | ![]() extracellular negative regulation of signal transduction / lipase binding / negative regulation of very-low-density lipoprotein particle clearance / regulation of receptor-mediated endocytosis / regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / positive regulation of lysosomal protein catabolic process / very-low-density lipoprotein particle receptor activity / rough endoplasmic reticulum lumen / negative regulation of astrocyte activation ...extracellular negative regulation of signal transduction / lipase binding / negative regulation of very-low-density lipoprotein particle clearance / regulation of receptor-mediated endocytosis / regulation of phosphatidylcholine catabolic process / plasma lipoprotein particle clearance / positive regulation of lysosomal protein catabolic process / very-low-density lipoprotein particle receptor activity / rough endoplasmic reticulum lumen / negative regulation of astrocyte activation / receptor-mediated endocytosis involved in cholesterol transport / negative regulation of microglial cell activation / PCSK9-LDLR complex / cholesterol import / receptor antagonist activity / negative regulation of receptor recycling / low-density lipoprotein particle clearance / clathrin heavy chain binding / amyloid-beta clearance by transcytosis / low-density lipoprotein particle receptor activity / negative regulation of amyloid-beta clearance / 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 / very-low-density lipoprotein particle receptor binding / phospholipid transport / positive regulation of amyloid-beta clearance / low-density lipoprotein particle / cholesterol transport / cis-Golgi network / negative regulation of receptor internalization / 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 / low-density lipoprotein particle receptor binding / amyloid-beta clearance / sorting endosome / lipoprotein particle binding / cellular response to low-density lipoprotein particle stimulus / endoplasmic reticulum-Golgi intermediate compartment / endomembrane system / long-term memory / phagocytosis / Retinoid metabolism and transport / clathrin-coated pit / somatodendritic compartment / cholesterol metabolic process / receptor-mediated endocytosis / negative regulation of protein binding / endosome lumen / cholesterol homeostasis / clathrin-coated endocytic vesicle membrane / lipid metabolic process / Golgi lumen / positive regulation of inflammatory response / endocytosis / late endosome / Cargo recognition for clathrin-mediated endocytosis / apical part of cell / Clathrin-mediated endocytosis / virus receptor activity / heparin binding / amyloid-beta binding / basolateral plasma membrane / protease binding / molecular adaptor activity / receptor ligand activity / lysosome / early endosome / receptor complex / endosome membrane / endosome / external side of plasma membrane / negative regulation of gene expression / signaling receptor binding / calcium ion binding / positive regulation of gene expression / Golgi apparatus / cell surface / endoplasmic reticulum / signal transduction / extracellular region / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Beglova, N. / Fisher, C. / Blacklow, S.C. | ||||||
![]() | ![]() Title: Structure of an LDLR-RAP Complex Reveals a General Mode for Ligand Recognition by Lipoprotein Receptors Authors: Fisher, C. / Beglova, N. / Blacklow, S.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 99.4 KB | Display | ![]() |
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PDB format | ![]() | 74.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.1 KB | Display | ![]() |
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Full document | ![]() | 450.2 KB | Display | |
Data in XML | ![]() | 11.9 KB | Display | |
Data in CIF | ![]() | 16.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
-Protein , 2 types, 2 molecules AB
#1: Protein | Mass: 12791.311 Da / Num. of mol.: 1 / Fragment: Domain Three / Mutation: E215G Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein | Mass: 8809.619 Da / Num. of mol.: 1 / Fragment: A Pair of Ligand-Binding Modules 3 and 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
-Non-polymers , 4 types, 190 molecules ![](data/chem/img/NA.gif)
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#3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-MPD / ( #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.38 Å3/Da / Density % sol: 48.27 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 40% MPD, 100 mM HEPES, 75 mM NaCl, 1.25 mM CaCl2, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 12, 2005 / Details: mirrors |
Radiation | Monochromator: Cryogenically cooled double crystal monochromator Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 1.26→50 Å / Num. obs: 46566 / % possible obs: 80 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2.4 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 22.5 |
Reflection shell | Resolution: 1.26→1.31 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.324 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3151 / % possible all: 57.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: built by ARP/WARP Resolution: 1.26→50 Å / Num. parameters: 15302 / Num. restraintsaints: 18660 / Isotropic thermal model: anisotropic / Cross valid method: FREE R / σ(F): 4 / Stereochemistry target values: ENGH AND HUBER
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Displacement parameters | Biso mean: 18.3 Å2 | |||||||||||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 6 / Occupancy sum hydrogen: 1315 / Occupancy sum non hydrogen: 1690.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.26→50 Å
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Refine LS restraints |
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