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Open data
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Basic information
Entry | Database: PDB / ID: 1n7d | |||||||||
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Title | Extracellular domain of the LDL receptor | |||||||||
![]() | Low-density lipoprotein receptor | |||||||||
![]() | LIPID TRANSPORT / LDL-Receptor / familial hypercholesterolemia / LDL / cholesterol metabolism | |||||||||
Function / homology | ![]() 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 / lipoprotein particle binding / sorting endosome / 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 / virus receptor activity / Clathrin-mediated endocytosis / 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 / membrane / identical protein binding / plasma membrane Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Rudenko, G. / Henry, L. / Henderson, K. / Ichtchenko, K. / Brown, M.S. / Goldstein, J.L. / Deisenhofer, J. | |||||||||
![]() | ![]() Title: Structure of the LDL receptor extracellular domain at endosomal pH Authors: Rudenko, G. / Henry, L. / Henderson, K. / Ichtchenko, K. / Brown, M.S. / Goldstein, J.L. / Deisenhofer, J. | |||||||||
History |
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Remark 300 | BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). THE AUTHORS BELIEVE THE BIOLOGICAL UNIT IS A MONOMER. | |||||||||
Remark 600 | HETEROGEN THE ATOMS W1 AND W2 OF THE LIGAND KEG 6003 ARE ON A TWO-FOLD AXIS. COORDINATES FOR THE ...HETEROGEN THE ATOMS W1 AND W2 OF THE LIGAND KEG 6003 ARE ON A TWO-FOLD AXIS. COORDINATES FOR THE HALF OF THE CLUSTER KEG 6003 IN THE ASYMMETRIC UNIT ARE INCLUDED IN THIS ENTRY. THE SECOND HALF OF THE CLUSTER CAN BE GENERATED USING SYMMETRY OPERATION Y,X,1-Z. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 129.4 KB | Display | ![]() |
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PDB format | ![]() | 99.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 729.1 KB | Display | ![]() |
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Full document | ![]() | 887 KB | Display | |
Data in XML | ![]() | 37.2 KB | Display | |
Data in CIF | ![]() | 52.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ajjS ![]() 1d2jS ![]() 1fx5S ![]() 1i0uS ![]() 1ijqS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 77703.617 Da / Num. of mol.: 1 / Fragment: extracellular domain, RESIDUES 1-699 / Mutation: N494Q, N636Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||
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#2: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#3: Polysaccharide | alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#4: Chemical | ChemComp-CA / #5: Chemical | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 5.43 Å3/Da / Density % sol: 77.36 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.3 Details: acetate buffer pH 5.3, 1,2-hexanediol, 0.5 mM CaCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 74 % | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||||||||||||||
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: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 3.7→45.3 Å / Num. obs: 17303 / % possible obs: 95.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 74.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.8 | ||||||||||||||||||||
Reflection shell | Resolution: 3.7→3.83 Å / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 2.7 / % possible all: 64.5 | ||||||||||||||||||||
Reflection | *PLUS Lowest resolution: 33.7 Å / Num. measured all: 64801 / Rmerge(I) obs: 0.09 | ||||||||||||||||||||
Reflection shell | *PLUS Highest resolution: 3.7 Å / % possible obs: 64.5 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRIES: 1AJJ, 1D2J, 1I0U, 1IJQ, 1FX5 Resolution: 3.7→45.3 Å / Rfactor Rfree error: 0.011 / Isotropic thermal model: OVERALL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: The sugars have not been refined, just manually placed in the density. The exact identity of the sugars in these N-linked glycosylation sites is not known. At this resolution positional ...Details: The sugars have not been refined, just manually placed in the density. The exact identity of the sugars in these N-linked glycosylation sites is not known. At this resolution positional refinement is of limited use. Harmonic restraints were used on most core residues. No simulated annealing was used. The resolution of the MAD data used in the structure determination is 3.7 Ang and the B-factors were high. This means that the positions of the side chains are not well determined in the model. The authors urge users to exercize caution and restraint interpreting this model. The authors are available for questions. The clusters were included in the positional refinement (regularization of the model). The carbohydrates were not included in the positional refinement (regularization of the model) but fitted manually. The carbohydrates were modelled as the N-linked high mannose type.
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 10 Å2 / ksol: 0.156563 e/Å3 | |||||||||||||||||||||||||
Displacement parameters | Biso mean: 124.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.7→45.3 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.7→3.87 Å / Rfactor Rfree error: 0.062 / Total num. of bins used: 8
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Xplor file |
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Refinement | *PLUS Highest resolution: 3.7 Å / Lowest resolution: 33.1 Å / % reflection Rfree: 7 % / Rfactor Rfree: 0.392 / Rfactor Rwork: 0.388 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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