2I1P

Solution structure of the twelfth cysteine-rich ligand-binding repeat in rat megalin

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Ldl_recept_a	e2i1pA1	A: few secondary structure elements	X: EGF-like	H: LDL receptor-like module (From Topology)	T: LDL receptor-like module	F: Ldl_recept_a	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	4.10.400.10	Few Secondary Structures	Irregular	Low-density Lipoprotein Receptor	Low-density Lipoprotein Receptor	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00057	Low-density lipoprotein receptor domain class A (Ldl_recept_a)	Low-density lipoprotein receptor domain class A	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Low-density lipoprotein receptor-related protein 2	protein binding binding protein-folding chaperone binding SH3 domain binding protein domain specific binding protein-containing complex binding hormone binding cation binding ion binding calcium ion binding metal ion binding small molecule binding hemoglobin binding PDZ domain binding protein binding binding protein-folding chaperone binding SH3 domain binding protein domain specific binding protein-containing complex binding hormone binding cation binding ion binding calcium ion binding metal ion binding small molecule binding hemoglobin binding PDZ domain binding cargo receptor activity insulin-like growth factor binding insulin-like growth factor I binding growth factor binding protein transporter activity transporter activity low-density lipoprotein particle receptor binding signaling receptor binding lipoprotein particle receptor binding transcription factor binding RNA polymerase II-specific DNA-binding transcription factor binding nuclear receptor binding DNA-binding transcription factor binding	developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development developmental process multicellular organismal process gonad development reproductive system development reproductive process sex differentiation animal organ development developmental process involved in reproduction male gonad development male sex differentiation multicellular organism development development of primary male sexual characteristics development of primary sexual characteristics anatomical structure development reproductive structure development system development response to stimulus response to chemical response to xenobiotic stimulus heart development circulatory system development organic acid transmembrane transport import into cell organic anion transport nitrogen compound transport carboxylic acid transport carboxylic acid transmembrane transport transport import across plasma membrane vitamin transport folate transmembrane transport establishment of localization transmembrane transport organic acid transport localization folate import across plasma membrane amide transport folic acid transport dicarboxylic acid transport cellular process modified amino acid transport vitamin transmembrane transport heart formation heart morphogenesis specification of animal organ identity pattern specification process regionalization anatomical structure morphogenesis anatomical structure formation involved in morphogenesis secondary heart field specification animal organ morphogenesis animal organ formation heart field specification positive regulation of nervous system development oligodendrocyte progenitor proliferation regulation of cellular process cellular developmental process regulation of developmental process positive regulation of cell population proliferation positive regulation of biological process cell development regulation of neurogenesis regulation of cell differentiation positive regulation of oligodendrocyte progenitor proliferation regulation of gliogenesis positive regulation of gliogenesis regulation of cell development regulation of nervous system development positive regulation of developmental process neurogenesis gliogenesis positive regulation of cell differentiation cell differentiation regulation of multicellular organismal process positive regulation of neurogenesis positive regulation of cellular process regulation of neural precursor cell proliferation regulation of multicellular organismal development regulation of biological process cell population proliferation biological regulation positive regulation of cell development nervous system development positive regulation of neural precursor cell proliferation regulation of cell population proliferation positive regulation of multicellular organismal process neural precursor cell proliferation regulation of oligodendrocyte progenitor proliferation response to X-ray response to ionizing radiation response to radiation response to abiotic stimulus artery development aorta development vasculature development blood vessel development cellular response to stimulus cell surface receptor protein serine/threonine kinase signaling pathway cellular response to growth factor stimulus signaling negative regulation of signaling regulation of transmembrane receptor protein serine/threonine kinase signaling pathway negative regulation of biological process regulation of signal transduction negative regulation of cellular response to growth factor stimulus negative regulation of BMP signaling pathway negative regulation of cell communication cell communication cellular response to endogenous stimulus negative regulation of cellular process signal transduction BMP signaling pathway enzyme-linked receptor protein signaling pathway cellular response to BMP stimulus regulation of signaling cell surface receptor signaling pathway regulation of BMP signaling pathway negative regulation of response to stimulus response to endogenous stimulus regulation of cellular response to growth factor stimulus negative regulation of signal transduction response to BMP regulation of response to stimulus regulation of cell communication transforming growth factor beta receptor superfamily signaling pathway response to growth factor negative regulation of transmembrane receptor protein serine/threonine kinase signaling pathway cardiac chamber morphogenesis cardiac septum development cardiac septum morphogenesis cardiac chamber development outflow tract septum morphogenesis outflow tract morphogenesis protein localization establishment of protein localization cellular localization vesicle-mediated transport establishment of protein localization to organelle protein transport cellular macromolecule localization macromolecule localization protein localization to organelle receptor-mediated endocytosis endocytosis endocytic hemoglobin import into cell embryonic epithelial tube formation chordate embryonic development tube formation embryo development epithelial tube formation tube morphogenesis primary neural tube formation embryo development ending in birth or egg hatching epithelial tube morphogenesis morphogenesis of embryonic epithelium epithelium development neural tube development tube development embryonic morphogenesis morphogenesis of an epithelium tissue development tissue morphogenesis neural tube closure neural tube formation tube closure establishment of localization in cell intracellular transport endosomal transport polyol metabolic process diol metabolic process alcohol metabolic process small molecule metabolic process metabolic process system process sensory perception nervous system process sensory perception of sound sensory perception of mechanical stimulus blood vessel morphogenesis pulmonary artery morphogenesis artery morphogenesis response to hormone response to leptin kidney development renal system development positive chemotaxis axonogenesis cell projection organization plasma membrane bounded cell projection morphogenesis neuron projection development cell morphogenesis cellular component organization cell projection morphogenesis neuron differentiation taxis neuron projection morphogenesis cellular component organization or biogenesis locomotion chemoattraction of axon chemotaxis plasma membrane bounded cell projection organization axon guidance response to external stimulus axon development cell morphogenesis involved in neuron differentiation generation of neurons cellular response to chemical stimulus neuron projection guidance neuron development ventricular septum development cardiac ventricle development genitalia development female genitalia development female sex differentiation vagina development intracellular signal transduction intracellular signaling cassette phosphatidylinositol 3-kinase/protein kinase B signal transduction cranial skeletal system development negative regulation of programmed cell death regulation of apoptotic process regulation of programmed cell death cell death negative regulation of apoptotic process apoptotic process programmed cell death amyloid-beta clearance kidney epithelium development metanephric proximal tubule development nephron tubule development metanephric epithelium development metanephros development renal tubule development nephron development metanephric nephron epithelium development nephron epithelium development proximal tubule development metanephric nephron tubule development metanephric tubule development response to retinoic acid response to lipid response to oxygen-containing compound regulation of localization regulation of protein localization positive regulation of establishment of protein localization positive regulation of protein transport regulation of lipoprotein transport regulation of transport positive regulation of lipoprotein transport regulation of establishment of protein localization regulation of protein transport lipoprotein transport positive regulation of transport regulation of cellular localization positive regulation of protein localization lipoprotein localization coronary vasculature development coronary artery morphogenesis coronary vasculature morphogenesis protein import head development forebrain development brain development central nervous system development negative regulation of hydrolase activity negative regulation of proteolysis regulation of catalytic activity negative regulation of catalytic activity negative regulation of endopeptidase activity regulation of primary metabolic process negative regulation of peptidase activity regulation of proteolysis proteolysis regulation of endopeptidase activity protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of protein metabolic process negative regulation of metabolic process regulation of peptidase activity negative regulation of molecular function primary metabolic process regulation of macromolecule metabolic process regulation of molecular function regulation of hydrolase activity macromolecule metabolic process regulation of metabolic process biosynthetic process gene expression macromolecule biosynthetic process transcytosis response to nutrient levels response to vitamin D response to nutrient response to vitamin monoatomic ion transport monoatomic cation transport metal ion transport animal organ regeneration regeneration neuron projection arborization fat-soluble vitamin metabolic process steroid metabolic process vitamin D metabolic process vitamin metabolic process lipid metabolic process ventricular cardiac muscle tissue morphogenesis striated muscle tissue development muscle structure development ventricular cardiac muscle tissue development muscle tissue development muscle organ development cardiac muscle tissue development muscle tissue morphogenesis ventricular compact myocardium morphogenesis cardiac ventricle morphogenesis cardiac muscle tissue morphogenesis muscle organ morphogenesis positive regulation of cellular component organization regulation of cellular component organization regulation of vesicle-mediated transport positive regulation of endocytosis regulation of endocytosis	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane clathrin-coated pit endomembrane system apical part of cell cluster of actin-based cell projections brush border somatodendritic compartment cell projection cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane clathrin-coated pit endomembrane system apical part of cell cluster of actin-based cell projections brush border somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle cytoplasm vesicle endocytic vesicle protein-containing complex receptor complex Golgi apparatus axon extracellular region extracellular space growth cone distal axon axonal growth cone site of polarized growth plasma membrane region apical plasma membrane endosome brush border membrane cell projection membrane membrane-enclosed lumen intracellular organelle lumen organelle lumen endosome lumen endoplasmic reticulum

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
A	IPR026823	Complement Clr-like EGF domain	Domain
A	IPR036055	LDL receptor-like superfamily	Homologous Superfamily
A	IPR049883	NOTCH1 EGF-like calcium-binding domain	Domain
A	IPR000033	LDLR class B repeat	Repeat
A	IPR001881	EGF-like calcium-binding domain	Domain
A	IPR023415	Low-density lipoprotein (LDL) receptor class A, conserved site	Conserved Site
A	IPR011042	Six-bladed beta-propeller, TolB-like	Homologous Superfamily
A	IPR002172	Low-density lipoprotein (LDL) receptor class A repeat	Repeat
A	IPR000742	EGF-like domain	Domain
A	IPR051221	Low-density lipoprotein receptor-related	Family
A	IPR009030	Growth factor receptor cysteine-rich domain superfamily	Homologous Superfamily
A	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.