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- PDB-2i1p: Solution structure of the twelfth cysteine-rich ligand-binding re... -

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Basic information

Entry
Database: PDB / ID: 2i1p
TitleSolution structure of the twelfth cysteine-rich ligand-binding repeat in rat megalin
ComponentsLow-density lipoprotein receptor-related protein 2
KeywordsLIGAND BINDING PROTEIN / low density lipoprotein receptor / cysteine-rich repeat / ligand binding domain / calcium cage
Function / homology
Function and homology information


Transport of RCbl within the body / endocytic hemoglobin import into cell / Retinoid metabolism and transport / chemoattraction of axon / diol metabolic process / positive regulation of oligodendrocyte progenitor proliferation / pulmonary artery morphogenesis / secondary heart field specification / positive regulation of lysosomal protein catabolic process / folate import across plasma membrane ...Transport of RCbl within the body / endocytic hemoglobin import into cell / Retinoid metabolism and transport / chemoattraction of axon / diol metabolic process / positive regulation of oligodendrocyte progenitor proliferation / pulmonary artery morphogenesis / secondary heart field specification / positive regulation of lysosomal protein catabolic process / folate import across plasma membrane / Vitamin D (calciferol) metabolism / metanephric proximal tubule development / ventricular compact myocardium morphogenesis / response to leptin / protein transporter activity / metal ion transport / transcytosis / Cargo recognition for clathrin-mediated endocytosis / Clathrin-mediated endocytosis / vitamin D metabolic process / cranial skeletal system development / neuron projection arborization / coronary artery morphogenesis / insulin-like growth factor I binding / protein import / outflow tract septum morphogenesis / coronary vasculature development / response to vitamin D / cargo receptor activity / positive regulation of neurogenesis / endosomal transport / ventricular septum development / aorta development / low-density lipoprotein particle receptor binding / hemoglobin binding / negative regulation of thrombin-activated receptor signaling pathway / positive regulation of lipoprotein transport / forebrain development / vagina development / amyloid-beta clearance / outflow tract morphogenesis / hormone binding / brush border / animal organ regeneration / positive regulation of endocytosis / endocytic vesicle / negative regulation of BMP signaling pathway / response to X-ray / response to retinoic acid / axonal growth cone / clathrin-coated pit / receptor-mediated endocytosis / endosome lumen / nuclear receptor binding / PDZ domain binding / phosphatidylinositol 3-kinase/protein kinase B signal transduction / neural tube closure / kidney development / brush border membrane / sensory perception of sound / SH3 domain binding / cellular response to growth factor stimulus / male gonad development / endocytosis / apical part of cell / protein transport / protein-folding chaperone binding / heart development / gene expression / cell population proliferation / receptor complex / apical plasma membrane / endosome / response to xenobiotic stimulus / axon / external side of plasma membrane / calcium ion binding / dendrite / negative regulation of apoptotic process / protein-containing complex binding / cell surface / endoplasmic reticulum / Golgi apparatus / protein-containing complex / extracellular space / membrane / 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 / 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 / : / Calcium-binding EGF domain / Low-density lipoprotein (LDL) receptor class A, conserved site / LDL-receptor class A (LDLRA) domain signature. / 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 speciesRattus norvegicus (Norway rat)
MethodSOLUTION NMR / simulated annealing
AuthorsWolf, C.A. / Dancea, F. / Shi, M. / Bade-Noskova, V. / Rueterjans, H. / Kerjaschki, D. / Luecke, C.
CitationJournal: J.Biomol.Nmr / Year: 2007
Title: Solution structure of the twelfth cysteine-rich ligand-binding repeat in rat megalin.
Authors: Wolf, C.A. / Dancea, F. / Shi, M. / Bade-Noskova, V. / Rueterjans, H. / Kerjaschki, D. / Luecke, C.
History
DepositionAug 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 13, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 19, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list / struct_ref_seq_dif
Item: _pdbx_database_status.status_code_cs / _pdbx_nmr_software.name / _struct_ref_seq_dif.details
Revision 1.4Jun 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_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
Revision 1.5Nov 13, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)5,1382
Polymers5,0981
Non-polymers401
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)20 / 200structures with the lowest energy
RepresentativeModel #1lowest energy

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Components

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


Mass: 5097.622 Da / Num. of mol.: 1 / Fragment: Meg-A12
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pKM263 / Production host: Escherichia coli (E. coli) / References: UniProt: P98158
#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 TOCSY
1212D NOESY

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Sample preparation

DetailsContents: 1.5mM Meg-A12, 10mM CaCl2, 90% H20, 10% D20 / Solvent system: 90% H20, 10% D20
Sample conditionsIonic strength: 10mM CaCl2 / pH: 5.5 / Pressure: ambient / Temperature: 298 K

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NMR measurement

RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M
Radiation wavelengthRelative weight: 1
NMR spectrometerType: Bruker DMX / Manufacturer: Bruker / Model: DMX / Field strength: 600 MHz

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Processing

NMR software
NameVersionDeveloperClassification
XwinNMR2.6BRUKERcollection
AURELIA2.5.9BRUKERdata analysis
ARIA1.2Linge et al.structure solution
ARIA1.2Linge et al.refinement
RefinementMethod: simulated annealing / Software ordinal: 1
Details: structures are based on 606 non-redundant NOE restraints
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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