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- PDB-2fyj: NMR Solution structure of calcium-loaded LRP double module -

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Basic information

Entry
Database: PDB / ID: 2fyj
TitleNMR Solution structure of calcium-loaded LRP double module
ComponentsLow-density lipoprotein receptor-related protein 1
KeywordsPROTEIN BINDING / DOUBLE MODULE / COMPLEMENT TYPE REPEAT / CALCIUM / BETA-2 HAIRPIN / LOOP-STRUCTURES
Function / homology
Function and homology information


alpha-2 macroglobulin receptor activity / apolipoprotein receptor activity / : / positive regulation of lipid transport / positive regulation of transcytosis / lipoprotein particle receptor binding / negative regulation of metallopeptidase activity / negative regulation of platelet-derived growth factor receptor-beta signaling pathway / positive regulation of lysosomal protein catabolic process / regulation of cholesterol transport ...alpha-2 macroglobulin receptor activity / apolipoprotein receptor activity / : / positive regulation of lipid transport / positive regulation of transcytosis / lipoprotein particle receptor binding / negative regulation of metallopeptidase activity / negative regulation of platelet-derived growth factor receptor-beta signaling pathway / positive regulation of lysosomal protein catabolic process / regulation of cholesterol transport / aorta morphogenesis / amyloid-beta clearance by transcytosis / regulation of extracellular matrix disassembly / clathrin heavy chain binding / negative regulation of smooth muscle cell migration / low-density lipoprotein particle receptor activity / amyloid-beta clearance by cellular catabolic process / positive regulation of amyloid-beta clearance / transcytosis / plasma membrane protein complex / heparan sulfate proteoglycan binding / astrocyte activation involved in immune response / apoptotic cell clearance / cargo receptor activity / lipoprotein transport / scavenger receptor activity / lysosomal transport / enzyme-linked receptor protein signaling pathway / negative regulation of SMAD protein signal transduction / negative regulation of Wnt signaling pathway / positive regulation of endocytosis / microtubule organizing center / amyloid-beta clearance / apolipoprotein binding / positive regulation of cholesterol efflux / phagocytosis / Scavenging of heme from plasma / transport across blood-brain barrier / retinoid metabolic process / Retinoid metabolism and transport / clathrin-coated pit / receptor-mediated endocytosis / positive regulation of protein localization to plasma membrane / regulation of actin cytoskeleton organization / receptor internalization / lipid metabolic process / cellular response to amyloid-beta / endocytic vesicle membrane / signaling receptor activity / amyloid-beta binding / basolateral plasma membrane / early endosome / receptor complex / lysosomal membrane / negative regulation of gene expression / focal adhesion / calcium ion binding / protein-containing complex binding / nucleolus / Golgi apparatus / RNA binding / membrane / plasma membrane / cytosol
Similarity search - Function
Domain of unknown function DUF5050 / Domain of unknown function (DUF5050) / Complement Clr-like EGF domain / Complement Clr-like EGF-like / : / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Low-density lipoprotein receptor domain class A ...Domain of unknown function DUF5050 / Domain of unknown function (DUF5050) / Complement Clr-like EGF domain / Complement Clr-like EGF-like / : / Low-density lipoprotein receptor repeat class B / LDL-receptor class B (LDLRB) repeat profile. / LDLR class B repeat / Low-density lipoprotein-receptor YWTD domain / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / : / Calcium-binding EGF domain / LDL-receptor class A (LDLRA) domain profile. / Low-density lipoprotein receptor domain class A / Low-density lipoprotein (LDL) receptor class A repeat / LDL receptor-like superfamily / Six-bladed beta-propeller, TolB-like / Coagulation Factor Xa inhibitory site / EGF-type aspartate/asparagine hydroxylation site / EGF-like calcium-binding, conserved site / Calcium-binding EGF-like domain signature. / Aspartic acid and asparagine hydroxylation site. / EGF-like calcium-binding domain / Calcium-binding EGF-like domain / Epidermal growth factor-like domain. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 1. / EGF-like domain signature 2. / EGF-like domain
Similarity search - Domain/homology
Prolow-density lipoprotein receptor-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / SIMMULATED ANNEALING USING XPLOR-NIH, REFINEMENT IN EXPLICIT WATER LAYER USING CNS
AuthorsJensen, G.A. / Andersen, O.M. / Bonvin, A.M. / Bjerrum-Bohr, I. / Etzerodt, M. / O'shea, C. / Poulsen, F.M. / Kragelund, B.B.
Citation
Journal: J.Mol.Biol. / Year: 2006
Title: Binding Site Structure of One LRP-RAP Complex:Implications for a Common Ligand-Receptor Binding Motif.
Authors: Jensen, G.A. / Andersen, O.M. / Bonvin, A.M. / Bjerrum-Bohr, I. / Etzerodt, M. / O'shea, C. / Poulsen, F.M. / Kragelund, B.B.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1997
Title: The solution structure of the N-terminal domain of alpha2-macroglobulin receptor-associated protein.
Authors: Nielsen, P.R. / Ellgaard, L. / Etzerodt, M. / Thogersen, H.C. / Poulsen, F.M.
#2: Journal: J.Biol.Chem. / Year: 2000
Title: Identification of the minimal functional unit in the low density lipoprotein receptor-related protein for binding the receptor-associated protein (RAP). A conserved acidic residue in the ...Title: Identification of the minimal functional unit in the low density lipoprotein receptor-related protein for binding the receptor-associated protein (RAP). A conserved acidic residue in the complement-type repeats is important for recognition of RAP
Authors: Andersen, O.M. / Christensen, L.L. / Chrsitensen, P.A. / Sorensen, E.S. / Jakobsen, C. / Moestrup, S.K. / Etzerodt, M. / Thogersen, H.C.
History
DepositionFeb 8, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 9, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Nov 20, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
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Assembly

Deposited unit
A: Low-density lipoprotein receptor-related protein 1


Theoretical massNumber of molelcules
Total (without water)8,9451
Polymers8,9451
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)15 / 200lowest energy, fewest violations
RepresentativeModel #1lowest energy

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Components

#1: Protein Low-density lipoprotein receptor-related protein 1 / LRP / Alpha-2-macroglobulin receptor


Mass: 8944.620 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRP1 / Plasmid: pT7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q07954
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
2122D NOESY
2222D TOCSY
1313D 15N-separated NOESY
141DQF-COSY
2523D-15N-separated TOCSY
16115N,1H-HSQC

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Sample preparation

Details
Solution-IDContentsSolvent system
10.5mM [U-99% 15N]-CR56298 K, pH 7.0, no salt
20.5mM CR56298 K, pH 7.0, no salt
Sample conditions
Conditions-IDpHPressure (kPa)Temperature (K)
17ambient 298 K
27ambient 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA8002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipeDelaglioprocessing
X-PLORNIHClorestructure solution
CNSstructure solution
Pronto3D20020517Kjaer et aldata analysis
CNSrefinement
RefinementMethod: SIMMULATED ANNEALING USING XPLOR-NIH, REFINEMENT IN EXPLICIT WATER LAYER USING CNS
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: lowest energy, fewest violations
Conformers calculated total number: 200 / Conformers submitted total number: 15

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