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- PDB-2m0p: Solution structure of the tenth complement type repeat of human m... -

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Basic information

Entry
Database: PDB / ID: 2m0p
TitleSolution structure of the tenth complement type repeat of human megalin
ComponentsLow-density lipoprotein receptor-related protein 2
KeywordsLIPID BINDING PROTEIN / Complement type repeat / receptor / megalin / ldl receptor family / lrp2
Function / homology
Function and homology information


diol metabolic process / positive regulation of oligodendrocyte progenitor proliferation / pulmonary artery morphogenesis / Transport of RCbl within the body / secondary heart field specification / folate import across plasma membrane / positive regulation of lysosomal protein catabolic process / cobalamin transport / ventricular compact myocardium morphogenesis / response to leptin ...diol metabolic process / positive regulation of oligodendrocyte progenitor proliferation / pulmonary artery morphogenesis / Transport of RCbl within the body / secondary heart field specification / folate import across plasma membrane / positive regulation of lysosomal protein catabolic process / cobalamin transport / ventricular compact myocardium morphogenesis / response to leptin / protein transporter activity / metal ion transport / Vitamin D (calciferol) metabolism / low-density lipoprotein particle receptor activity / hormone binding / vitamin D metabolic process / cranial skeletal system development / neuron projection arborization / coronary artery morphogenesis / transcytosis / insulin-like growth factor I binding / outflow tract septum morphogenesis / cargo receptor activity / aorta development / ventricular septum development / positive regulation of neurogenesis / vagina development / amyloid-beta clearance / negative regulation of BMP signaling pathway / transport across blood-brain barrier / retinoid metabolic process / Retinoid metabolism and transport / forebrain development / clathrin-coated pit / receptor-mediated endocytosis / endosome lumen / kidney development / phosphatidylinositol 3-kinase/protein kinase B signal transduction / neural tube closure / sensory perception of sound / clathrin-coated endocytic vesicle membrane / brush border membrane / cellular response to growth factor stimulus / SH3 domain binding / lipid metabolic process / endocytosis / male gonad development / protein transport / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / protein-folding chaperone binding / gene expression / lysosome / cell population proliferation / receptor complex / apical plasma membrane / axon / external side of plasma membrane / lysosomal membrane / dendrite / calcium ion binding / negative regulation of apoptotic process / endoplasmic reticulum / Golgi apparatus / extracellular exosome / plasma membrane
Similarity search - Function
Low-density Lipoprotein Receptor / Low-density Lipoprotein Receptor / LRP2-like, EGF-like 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 / Low-density Lipoprotein Receptor / LRP2-like, EGF-like 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 / Legume lectin, beta chain, Mn/Ca-binding site / 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 / Few Secondary Structures / Irregular
Similarity search - Domain/homology
Low-density lipoprotein receptor-related protein 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / simulated annealing
AuthorsDagil, R. / Kragelund, B.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Gentamicin binds to the megalin receptor as a competitive inhibitor using the common ligand binding motif of complement type repeats: insight from the nmr structure of the 10th complement type ...Title: Gentamicin binds to the megalin receptor as a competitive inhibitor using the common ligand binding motif of complement type repeats: insight from the nmr structure of the 10th complement type repeat domain alone and in complex with gentamicin.
Authors: Dagil, R. / O'Shea, C. / Nykjar, A. / Bonvin, A.M. / Kragelund, B.B.
History
DepositionNov 1, 2012Deposition site: BMRB / Processing site: RCSB
Revision 1.0Jan 9, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Jun 14, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_spectrometer / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / 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_nmr_spectrometer.model / _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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Low-density lipoprotein receptor-related protein 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,9142
Polymers5,8741
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

#1: Protein Low-density lipoprotein receptor-related protein 2 / LRP-2 / Glycoprotein 330 / gp330 / Megalin


Mass: 5874.158 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LRP2 / Plasmid: pPICaC / Production host: Komagataella pastoris (fungus) / References: UniProt: P98164
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
Has protein modificationY

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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
1312D 1H-1H TOCSY aromatic
1413D HNCO
1513D HNCA
1613D HN(CA)CB
1713D C(CO)NH
1813D CBCA(CO)NH
1923D (H)CCH-TOCSY
11013D HN(CO)CA
11123D 1H-13C NOESY aliphatic
11222D 1H-13C NOESY aromatic
11313D H(CCO)NH
11413D 1H-15N NOESY
11513D 1H-15N TOCSY

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Sample preparation

Details
Solution-IDContentsSolvent system
10.6 mM [U-100% 13C; U-100% 15N] CR10, 100 mM sodium chloride, 50 mM calcium chloride, 50 mM TRIS, 0.1 mM DSS, 0.1 % sodium azide, 90% H2O/10% D2O90% H2O/10% D2O
20.6 mM [U-100% 13C; U-100% 15N] CR10, 50 mM calcium chloride, 100 mM sodium chloride, 50 mM TRIS, 0.1 mM DSS, 0.1 % sodium azide, 100% D2O100% D2O
Sample
Conc. (mg/ml)ComponentIsotopic labelingSolution-ID
0.6 mMCR10-1[U-100% 13C; U-100% 15N]1
100 mMsodium chloride-21
50 mMcalcium chloride-31
50 mMTRIS-41
0.1 mMDSS-51
0.1 %sodium azide-61
0.6 mMCR10-7[U-100% 13C; U-100% 15N]2
50 mMcalcium chloride-82
100 mMsodium chloride-92
50 mMTRIS-102
0.1 mMDSS-112
0.1 %sodium azide-122
Sample conditionsIonic strength: 0.2 / pH: 6.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Varian INOVAVarianINOVA7501
Varian INOVAVarianINOVA8002
Bruker AvanceBrukerAVANCE8003

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Processing

NMR software
NameVersionDeveloperClassification
Analysis2.2CCPNchemical shift assignment
Analysis2.2CCPNpeak picking
ARIALinge, O'Donoghue and Nilgesstructure solution
ARIALinge, O'Donoghue and Nilgesrefinement
NMRDrawDelaglio, Grzesiek, Vuister, Zhu, Pfeifer and Baxprocessing
RefinementMethod: simulated annealing / Software ordinal: 1
NMR constraintsNOE constraints total: 555 / NOE intraresidue total count: 273 / NOE long range total count: 101 / NOE medium range total count: 87 / NOE sequential total count: 94 / Disulfide bond constraints total count: 3 / Hydrogen bond constraints total count: 15 / Protein phi angle constraints total count: 21 / Protein psi angle constraints total count: 17
NMR representativeSelection criteria: lowest energy
NMR ensembleConformer selection criteria: structures with the lowest energy
Conformers calculated total number: 200 / Conformers submitted total number: 20

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