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- PDB-2m7p: RXFP1 utilises hydrophobic moieties on a signalling surface of th... -

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Basic information

Entry
Database: PDB / ID: 2m7p
TitleRXFP1 utilises hydrophobic moieties on a signalling surface of the LDLa module to mediate receptor activation
ComponentsLow-density lipoprotein receptor, Relaxin receptor 1LDL receptor
KeywordsPROTEIN BINDING / RXFP1 / Relaxin / LDLA
Function / homology
Function and homology information


lung connective tissue development / nipple morphogenesis / Relaxin receptors / 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 / parturition / receptor-mediated endocytosis involved in cholesterol transport ...lung connective tissue development / nipple morphogenesis / Relaxin receptors / 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 / parturition / receptor-mediated endocytosis involved in cholesterol transport / myofibroblast differentiation / 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 / intestinal cholesterol absorption / positive regulation of triglyceride biosynthetic process / negative regulation of low-density lipoprotein particle clearance / hormone binding / low-density lipoprotein particle binding / response to caloric restriction / Chylomicron clearance / amyloid-beta clearance by cellular catabolic process / LDL clearance / regulation of protein metabolic process / high-density lipoprotein particle clearance / lipoprotein catabolic process / phospholipid transport / low-density lipoprotein particle / cholesterol transport / G protein-coupled peptide receptor activity / 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 / clathrin-coated pit / Retinoid metabolism and transport / somatodendritic compartment / cholesterol metabolic process / hormone-mediated signaling pathway / extracellular matrix organization / receptor-mediated endocytosis / cholesterol homeostasis / G protein-coupled receptor activity / clathrin-coated endocytic vesicle membrane / lipid metabolic process / adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of inflammatory response / endocytosis / Cargo recognition for clathrin-mediated endocytosis / late endosome / virus receptor activity / apical part of cell / Clathrin-mediated endocytosis / amyloid-beta binding / G alpha (s) signalling events / 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 / metal ion binding / plasma membrane
Similarity search - Function
Relaxin receptor / Low-density Lipoprotein Receptor / Low-density Lipoprotein Receptor / 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. ...Relaxin receptor / Low-density Lipoprotein Receptor / Low-density Lipoprotein Receptor / 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. / 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 / Leucine-rich repeat, SDS22-like subfamily / 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 / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Epidermal growth factor-like domain. / Leucine-rich repeat profile. / EGF-like domain profile. / Growth factor receptor cysteine-rich domain superfamily / EGF-like domain signature 2. / Leucine-rich repeat / EGF-like domain / Leucine-rich repeat domain superfamily / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Low-density lipoprotein receptor / Relaxin receptor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / torsion angle dynamics
Model detailsclosest to the average, model1
AuthorsKong, R.CK. / Petrie, E.J. / Mohanty, B. / Ling, J. / Lee, J.C.Y. / Gooley, P.R. / Bathgate, R.A.D.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: The relaxin receptor (RXFP1) utilizes hydrophobic moieties on a signaling surface of its N-terminal low density lipoprotein class A module to mediate receptor activation.
Authors: Kong, R.C.K. / Petrie, E.J. / Mohanty, B. / Ling, J. / Lee, J.C. / Gooley, P.R. / Bathgate, R.A.D.
History
DepositionApr 29, 2013Deposition site: BMRB / Processing site: PDBJ
Revision 1.0Aug 14, 2013Provider: repository / Type: Initial release
Revision 1.1Dec 18, 2019Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_nmr_software / pdbx_nmr_spectrometer / struct_ref_seq_dif
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_nmr_software.name / _pdbx_nmr_spectrometer.model / _struct_ref_seq_dif.details
Revision 1.2Jun 14, 2023Group: Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_nmr_data / _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_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_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: Low-density lipoprotein receptor, Relaxin receptor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)4,5902
Polymers4,5501
Non-polymers401
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 40target function
RepresentativeModel #1closest to the average

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Components

#1: Protein/peptide Low-density lipoprotein receptor, Relaxin receptor 1 / LDL receptor / LDL receptor / Leucine-rich repeat-containing G-protein coupled receptor 7 / Relaxin family peptide receptor 1


Mass: 4549.967 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: chimera protein of the Low Density Liproprotein receptor (LDLR_Human, UNP P01130) and Relaxin receptor 1(RXFP1_HUMAN, UNP Q9HBX9).
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01130, UniProt: Q9HBX9
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
Sequence detailsBACKBONE OF THE PROTEIN IS THE SECOND LIGAND BINDING DOMAIN OF HUMAN LDLR (LDLR_HUMAN, UNP RESIDUES ...BACKBONE OF THE PROTEIN IS THE SECOND LIGAND BINDING DOMAIN OF HUMAN LDLR (LDLR_HUMAN, UNP RESIDUES 66-104 FROM P01130), REPLACED RESIDUES 69-81 WITH PEPTIDE FROM RELAXIN RECEPTOR 1 (RXFP1_HUMAN, UNP RESIDUES 28-39 FROM Q9HBX9)

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experiment
Conditions-IDExperiment-IDSolution-IDType
1112D 1H-15N HSQC
1212D 1H-13C HSQC
1315D APSY-CBCA(CO)NH
1415D APSY-(HA)CA(CO)NH
1514D APSY-HACANH
1613D [1H,1H]-NOESY-15N-HSQC
1713D [1H,1H]-NOESY-13C(ali)-HSQC
1813D [1H,1H]-NOESY-13C(aro)-HSQC

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Sample preparation

DetailsContents: 1 mM [U-98% 13C; U-98% 15N] LDLA-1, 50 mM Immidazole-2, 10 mM CaCl2-3, 90% H2O/10% D2O
Solvent system: 90% H2O/10% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
1 mMLDLA-1[U-98% 13C; U-98% 15N]1
50 mMImmidazole-21
10 mMCaCl2-31
Sample conditionsIonic strength: 0.01 / pH: 6.0 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker AvanceBrukerAVANCE5001
Bruker Avance IIBrukerAVANCE II8002

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Processing

NMR software
NameVersionDeveloperClassification
CYANA3G ntert P.refinement
CARAKeller and Wuthrichchemical shift assignment
UNIO2.0.2Dr. Torsten Herrmannchemical shift assignment
UNIO2.0.2Dr. Torsten Herrmannpeak picking
UNIO2.0.2Dr. Torsten Herrmannstructure solution
TopSpin3BRUKERcollection
TopSpin3BRUKERprocessing
RefinementMethod: torsion angle dynamics / Software ordinal: 1
NMR constraintsNOE constraints total: 665 / NOE intraresidue total count: 135 / NOE long range total count: 181 / NOE medium range total count: 159 / NOE sequential total count: 190
NMR representativeSelection criteria: closest to the average
NMR ensembleConformer selection criteria: target function / Conformers calculated total number: 40 / Conformers submitted total number: 20 / Representative conformer: 1

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