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- PDB-2fyl: Haddock model of the complex between double module of LRP, CR56, ... -

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Basic information

Entry
Database: PDB / ID: 2fyl
TitleHaddock model of the complex between double module of LRP, CR56, and first domain of receptor associated protein, RAP-d1.
Components
  • Alpha-2-macroglobulin receptor-associated protein
  • Low-density lipoprotein receptor-related protein 1
KeywordsSURFACE ACTIVE PROTEIN / Complex / shift-mapping / haddock / interface
Function / homology
Function and homology information


alpha-2 macroglobulin receptor activity / apolipoprotein receptor activity / positive regulation of lipid transport / regulation of phospholipase A2 activity / extracellular negative regulation of signal transduction / positive regulation of transcytosis / lipoprotein particle receptor binding / negative regulation of platelet-derived growth factor receptor-beta signaling pathway / negative regulation of metallopeptidase activity / lipase binding ...alpha-2 macroglobulin receptor activity / apolipoprotein receptor activity / positive regulation of lipid transport / regulation of phospholipase A2 activity / extracellular negative regulation of signal transduction / positive regulation of transcytosis / lipoprotein particle receptor binding / negative regulation of platelet-derived growth factor receptor-beta signaling pathway / negative regulation of metallopeptidase activity / lipase binding / negative regulation of very-low-density lipoprotein particle clearance / regulation of receptor-mediated endocytosis / positive regulation of lysosomal protein catabolic process / rough endoplasmic reticulum lumen / aorta morphogenesis / negative regulation of smooth muscle cell migration / regulation of cholesterol transport / receptor antagonist activity / clathrin heavy chain binding / amyloid-beta clearance by transcytosis / low-density lipoprotein particle receptor activity / regulation of extracellular matrix disassembly / negative regulation of amyloid-beta clearance / amyloid-beta clearance by cellular catabolic process / scavenger receptor activity / very-low-density lipoprotein particle receptor binding / plasma membrane protein complex / positive regulation of amyloid-beta clearance / transcytosis / cis-Golgi network / negative regulation of receptor internalization / heparan sulfate proteoglycan binding / astrocyte activation involved in immune response / apoptotic cell clearance / cargo receptor activity / retinoid metabolic process / lysosomal transport / microtubule organizing center / lipoprotein transport / low-density lipoprotein particle receptor binding / enzyme-linked receptor protein signaling pathway / negative regulation of SMAD protein signal transduction / negative regulation of Wnt signaling pathway / amyloid-beta clearance / positive regulation of endocytosis / apolipoprotein binding / transport across blood-brain barrier / endoplasmic reticulum-Golgi intermediate compartment / positive regulation of cholesterol efflux / endomembrane system / Scavenging of heme from plasma / phagocytosis / Retinoid metabolism and transport / clathrin-coated pit / receptor-mediated endocytosis / negative regulation of protein binding / endosome lumen / regulation of actin cytoskeleton organization / positive regulation of protein localization to plasma membrane / lipid metabolic process / receptor internalization / Golgi lumen / cellular response to amyloid-beta / endocytic vesicle membrane / positive regulation of protein binding / signaling receptor activity / heparin binding / amyloid-beta binding / basolateral plasma membrane / receptor ligand activity / early endosome / receptor complex / endosome / lysosomal membrane / negative regulation of gene expression / focal adhesion / signaling receptor binding / calcium ion binding / protein-containing complex binding / Golgi apparatus / cell surface / endoplasmic reticulum / signal transduction / RNA binding / extracellular region / membrane / nucleus / plasma membrane
Similarity search - Function
Domain of unknown function DUF5050 / Domain of unknown function (DUF5050) / RAP domain / Receptor-associated Protein / Alpha-2-macroglobulin receptor-associated protein, domain 1 / Alpha-2-macroglobulin RAP, C-terminal / RAP domain superfamily / Alpha-2-macroglobulin RAP, domain 3 / Alpha-2-macroglobulin RAP, domain 2 / Alpha-2-macroglobulin receptor-associated protein ...Domain of unknown function DUF5050 / Domain of unknown function (DUF5050) / RAP domain / Receptor-associated Protein / Alpha-2-macroglobulin receptor-associated protein, domain 1 / Alpha-2-macroglobulin RAP, C-terminal / RAP domain superfamily / Alpha-2-macroglobulin RAP, domain 3 / Alpha-2-macroglobulin RAP, domain 2 / Alpha-2-macroglobulin receptor-associated protein / Alpha-2-macroglobulin RAP, N-terminal domain / Alpha-2-macroglobulin RAP, C-terminal domain / 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 / Endoplasmic reticulum targeting sequence. / : / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / LDL-receptor class A (LDLRA) domain profile. / Calcium-binding EGF domain / 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 2. / EGF-like domain signature 1. / EGF-like domain / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Alpha-2-macroglobulin receptor-associated protein / Prolow-density lipoprotein receptor-related protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / HADDOCK modelling from chemical shift perturbation data on both complex partners
AuthorsJensen, G.A. / Andersen, O.M. / Bonvin, A.M. / Bjerrum-Bohr, I. / Etzerodt, M. / O'shea, C. / Poulsen, F.M. / Kragelund, B.B.
CitationJournal: 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.
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: Database references / Derived calculations
Category: database_2 / pdbx_struct_assembly ...database_2 / pdbx_struct_assembly / pdbx_struct_conn_angle / pdbx_struct_oper_list / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-2-macroglobulin receptor-associated protein
B: Low-density lipoprotein receptor-related protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,5614
Polymers18,4812
Non-polymers802
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)1 / 200Best averaged HADDOCK score
RepresentativeModel #5lowest energy

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Components

#1: Protein Alpha-2-macroglobulin receptor-associated protein / Alpha-2- MRAP / Low density lipoprotein receptor-related protein-associated protein 1 / RAP


Mass: 9536.008 Da / Num. of mol.: 1 / Fragment: Rapd1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRPAP1, A2MRAP / Production host: Escherichia coli (E. coli) / References: UniProt: P30533
#2: Protein Low-density lipoprotein receptor-related protein 1 / LRP / Alpha-2-macroglobulin receptor


Mass: 8944.620 Da / Num. of mol.: 1 / Fragment: CR56
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRP1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07954
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
111Exchange 15N,1H-HSQC
222Exchange 15N,1H,-HSQC
13115N,1H-HSQC
24215N,1H-HSQC
353HNCA
363HN(CA)CB, HN(CO)CACB

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Sample preparation

Details
Solution-IDContentsSolvent system
10.1mM [U-99% 15N]-CR56; 0.1mM RAPd1; H2O/D2O (90:10)H2O/D2O (90:10)
20.5mM [U-99% 15N]-RAPd1; 0.5mM CR56; H2O/D2O (90:10)H2O/D2O (90:10)
30.08 mM [U-99% 15N, U-99% 13C]-CR56; 0.08 mM [U-99% 15N, U-99% 13C]-RAPd1; H2O/D2O (90:10)H2O/D2O (90:10)
Sample conditionspH: 7.0 / Pressure: ambient / Temperature: 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
Pronto3D20020517Kjaer et aldata analysis
HADDOCKBonvin et alstructure solution
HADDOCKBonvin et alrefinement
RefinementMethod: HADDOCK modelling from chemical shift perturbation data on both complex partners
Software ordinal: 1
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: Best averaged HADDOCK score / Conformers calculated total number: 200 / Conformers submitted total number: 1

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