9QAW | pdb_00009qaw

CryoEM structure of the human LRP2 receptor ectodomain in complex with LRPAP1

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
L [auth K]	SCOP2B Superfamily	RAP domain-like	8040777	3001254	SCOP2B (2022-06-29)
A [auth L]	SCOP2B Superfamily	RAP domain-like	8040777	3001254	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth A], C [auth B]	PF24468	LRP2-like, EGF-like domain (EGF_LRP2)	LRP2-like, EGF-like domain	This EGF-like domain is found in human Low-density lipoprotein receptor-related protein 2 (LRP2) and similar animal proteins. LRP2 is a multiligand endocytic receptor.	Domain
B [auth A], C [auth B]	PF12662	Complement Clr-like EGF-like (cEGF)	Complement Clr-like EGF-like	cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL recepto ...	cEGF, or complement Clr-like EGF, domains have six conserved cysteine residues disulfide-bonded into the characteristic pattern 'ababcc'. They are found in blood coagulation proteins such as fibrillin, Clr and Cls, thrombomodulin, and the LDL receptor. The core fold of the EGF domain consists of two small beta-hairpins packed against each other. Two major structural variants have been identified based on the structural context of the C-terminal cysteine residue of disulfide 'c' in the C-terminal hairpin: hEGFs and cEGFs. In cEGFs the C-terminal thiol resides on the C-terminal beta-sheet, resulting in long loop-lengths between the cysteine residues of disulfide 'c', typically C[10+]XC. These longer loop-lengths may have arisen by selective cysteine loss from a four-disulfide EGF template such as laminin or integrin. Tandem cEGF domains have five linking residues between terminal cysteines of adjacent domains. cEGF domains may or may not bind calcium in the linker region. cEGF domains with the consensus motif CXN4X[F,Y]XCXC are hydroxylated exclusively on the asparagine residue.	Domain
B [auth A], C [auth B]	PF14670	Coagulation Factor Xa inhibitory site (FXa_inhibition)	Coagulation Factor Xa inhibitory site	This short domain on coagulation enzyme factor Xa is found to be the target for a potent inhibitor of coagulation, TAK-442 [1].	Domain
B [auth A], C [auth B]	PF07645	Calcium-binding EGF domain (EGF_CA)	Calcium-binding EGF domain		Domain
B [auth A], C [auth B]	PF00057	Low-density lipoprotein receptor domain class A (Ldl_recept_a)	Low-density lipoprotein receptor domain class A	-	Repeat
B [auth A], C [auth B]	PF00058	Low-density lipoprotein receptor repeat class B (Ldl_recept_b)	Low-density lipoprotein receptor repeat class B	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
J [auth G]	Unidentified peptide 5	-	-	-
I	Unidentified peptide 4	-	-	-
H	Unidentified peptide 3	-	-	-
E [auth C], F, K [auth J]	Unidentified peptide 2	-	-	-
D, G [auth E]	Unidentified peptide 1	-	-	-
B [auth A], C [auth B]	Low-density lipoprotein receptor-related protein 2	protein binding binding protein-folding chaperone binding SH3 domain binding protein domain specific binding hormone binding cation binding ion binding calcium ion binding metal ion binding small molecule binding cargo receptor activity insulin-like growth factor binding insulin-like growth factor I binding protein binding binding protein-folding chaperone binding SH3 domain binding protein domain specific binding hormone binding cation binding ion binding calcium ion binding metal ion binding small molecule binding cargo receptor activity insulin-like growth factor binding insulin-like growth factor I binding growth factor binding lipoprotein particle receptor activity low-density lipoprotein particle receptor activity protein transporter activity transporter activity	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 import into cell 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 folic acid transport dicarboxylic acid transport cellular process modified amino acid transport vitamin transmembrane transport heart development heart formation heart morphogenesis specification of animal organ identity pattern specification process regionalization circulatory system development 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 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 response to 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 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 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 circulatory system process vascular process in circulatory system vascular transport transport across blood-brain barrier response to hormone response to chemical response to leptin kidney development renal system development diterpenoid metabolic process retinoid metabolic process primary metabolic process terpenoid metabolic process isoprenoid metabolic process lipid metabolic process receptor-mediated endocytosis endocytosis vesicle-mediated transport 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 establishment of protein localization protein transport macromolecule localization intracellular protein localization amyloid-beta clearance coronary vasculature development coronary artery morphogenesis coronary vasculature morphogenesis head development forebrain development brain development central nervous system development biosynthetic process macromolecule metabolic process gene expression macromolecule biosynthetic process cobalamin transport transcytosis monoatomic ion transport monoatomic cation transport metal ion transport regulation of protein catabolic process in the vacuole catabolic process positive regulation of protein metabolic process lysosomal protein catabolic process macromolecule catabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of macromolecule metabolic process positive regulation of lysosomal protein catabolic process protein metabolic process regulation of protein metabolic process protein catabolic process in the vacuole regulation of macromolecule metabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of lysosomal protein catabolic process positive regulation of protein catabolic process in the vacuole regulation of metabolic process regulation of protein catabolic process cell projection organization plasma membrane bounded cell projection morphogenesis neuron projection development cell morphogenesis cellular component organization cell projection morphogenesis neuron differentiation neuron projection morphogenesis cellular component organization or biogenesis plasma membrane bounded cell projection organization generation of neurons neuron projection arborization neuron development steroid metabolic process vitamin D 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	cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane clathrin-coated pit endomembrane system membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle bounding membrane of organelle cell periphery cellular anatomical structure cell surface membrane plasma membrane external side of plasma membrane side of membrane clathrin-coated pit endomembrane system membrane-bounded organelle intracellular anatomical structure intracellular vesicle intracellular organelle bounding membrane of organelle cytoplasmic vesicle vesicle membrane clathrin-coated vesicle endocytic vesicle membrane coated vesicle vesicle endocytic vesicle clathrin-coated vesicle membrane clathrin-coated endocytic vesicle membrane intracellular membrane-bounded organelle clathrin-coated endocytic vesicle cytoplasmic vesicle membrane coated vesicle membrane organelle cytoplasm organelle membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular membrane-bounded organelle somatodendritic compartment cell projection dendrite dendritic tree neuron projection plasma membrane bounded cell projection protein-containing complex signaling receptor complex vacuolar membrane lytic vacuole vacuole lytic vacuole membrane lysosomal membrane lysosome Golgi apparatus axon apical part of cell plasma membrane region apical plasma membrane brush border membrane cluster of actin-based cell projections brush border cell projection membrane endosome membrane-enclosed lumen intracellular organelle lumen organelle lumen endosome lumen endoplasmic reticulum
A [auth L], L [auth K]	Alpha-2-macroglobulin receptor-associated protein	protein binding binding signaling receptor binding amyloid-beta binding peptide binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity molecular function inhibitor activity signaling receptor inhibitor activity receptor antagonist activity enzyme binding protein binding binding signaling receptor binding amyloid-beta binding peptide binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity molecular function inhibitor activity signaling receptor inhibitor activity receptor antagonist activity enzyme binding lipase binding low-density lipoprotein particle receptor binding lipoprotein particle receptor binding very-low-density lipoprotein particle receptor binding heparin binding glycosaminoglycan binding carbohydrate derivative binding sulfur compound binding	multicellular organismal process regulation of biological process biological regulation positive regulation of biological process positive regulation of amyloid-beta clearance positive regulation of multicellular organismal process regulation of multicellular organismal process amyloid-beta clearance regulation of amyloid-beta clearance regulation of localization import into cell regulation of cellular process regulation of cellular component organization receptor internalization multicellular organismal process regulation of biological process biological regulation positive regulation of biological process positive regulation of amyloid-beta clearance positive regulation of multicellular organismal process regulation of multicellular organismal process amyloid-beta clearance regulation of amyloid-beta clearance regulation of localization import into cell regulation of cellular process regulation of cellular component organization receptor internalization transport negative regulation of biological process negative regulation of transport negative regulation of endocytosis regulation of receptor internalization vesicle-mediated transport cellular component organization localization negative regulation of cellular process cellular component organization or biogenesis regulation of endocytosis negative regulation of cellular component organization regulation of transport negative regulation of receptor-mediated endocytosis regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport establishment of localization cellular process endocytosis receptor-mediated endocytosis negative regulation of receptor internalization cellular response to stimulus response to stimulus signaling signal transduction cell communication regulation of signaling negative regulation of signaling negative regulation of response to stimulus regulation of signal transduction negative regulation of signal transduction negative regulation of cell communication extracellular negative regulation of signal transduction regulation of response to stimulus regulation of cell communication extracellular regulation of signal transduction very-low-density lipoprotein particle clearance regulation of plasma lipoprotein particle levels plasma lipoprotein particle clearance negative regulation of very-low-density lipoprotein particle clearance negative regulation of lipoprotein particle clearance regulation of lipoprotein particle clearance regulation of very-low-density lipoprotein particle clearance negative regulation of multicellular organismal process amyloid-beta clearance by transcytosis transcytosis negative regulation of amyloid-beta clearance	cellular anatomical structure endomembrane system membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus cis-Golgi network organelle intracellular membrane-bounded organelle cytoplasm cell surface cell periphery plasma membrane membrane cellular anatomical structure endomembrane system membrane-bounded organelle intracellular organelle intracellular anatomical structure Golgi apparatus cis-Golgi network organelle intracellular membrane-bounded organelle cytoplasm cell surface cell periphery plasma membrane membrane membrane-enclosed lumen intracellular organelle lumen endoplasmic reticulum lumen rough endoplasmic reticulum rough endoplasmic reticulum lumen organelle lumen endoplasmic reticulum Golgi lumen endosome intracellular vesicle cytoplasmic vesicle vesicle extracellular region endoplasmic reticulum-Golgi intermediate compartment endosome lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth A], C [auth B]	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
B [auth A], C [auth B]	IPR026823	Complement Clr-like EGF domain	Domain
B [auth A], C [auth B]	IPR036055	LDL receptor-like superfamily	Homologous Superfamily
B [auth A], C [auth B]	IPR000033	LDLR class B repeat	Repeat
B [auth A], C [auth B]	IPR001881	EGF-like calcium-binding domain	Domain
B [auth A], C [auth B]	IPR023415	Low-density lipoprotein (LDL) receptor class A, conserved site	Conserved Site
B [auth A], C [auth B]	IPR011042	Six-bladed beta-propeller, TolB-like	Homologous Superfamily
B [auth A], C [auth B]	IPR049883	NOTCH1, EGF-like calcium-binding domain	Domain
B [auth A], C [auth B]	IPR002172	Low-density lipoprotein (LDL) receptor class A repeat	Repeat
B [auth A], C [auth B]	IPR019825	Legume lectin, beta chain, Mn/Ca-binding site	Binding Site
B [auth A], C [auth B]	IPR000742	EGF-like domain	Domain
B [auth A], C [auth B]	IPR051221	Low-density lipoprotein receptor-related	Family
B [auth A], C [auth B]	IPR056588	LRP2, EGF-like domain	Domain
B [auth A], C [auth B]	IPR009030	Growth factor receptor cysteine-rich domain superfamily	Homologous Superfamily
B [auth A], C [auth B]	IPR000152	EGF-type aspartate/asparagine hydroxylation site	PTM
A [auth L], L [auth K]	IPR036744	RAP domain superfamily	Homologous Superfamily
A [auth L], L [auth K]	IPR038003	Alpha-2-macroglobulin receptor-associated protein	Family
A [auth L], L [auth K]	IPR010483	Alpha-2-macroglobulin RAP, C-terminal	Domain
A [auth L], L [auth K]	IPR037999	Alpha-2-macroglobulin RAP, domain 3	Domain
A [auth L], L [auth K]	IPR009066	Alpha-2-macroglobulin receptor-associated protein, domain 1	Domain
A [auth L], L [auth K]	IPR038001	Alpha-2-macroglobulin RAP, domain 2	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B [auth A], C [auth B]	: P98164	Donnai-Barrow syndrome prostate cancer kidney disease Craniofacial Abnormalities congenital diaphragmatic hernia progressive supranuclear palsy acute kidney failure psoriasis atypical teratoid rhabdoid tumor X-linked mixed deafness with perilymphatic gusher colorectal cancer intellectual disability lung adenocarcinoma nephrosclerosis ovarian cancer Donnai-Barrow syndrome prostate cancer kidney disease Craniofacial Abnormalities congenital diaphragmatic hernia progressive supranuclear palsy acute kidney failure psoriasis atypical teratoid rhabdoid tumor X-linked mixed deafness with perilymphatic gusher colorectal cancer intellectual disability lung adenocarcinoma nephrosclerosis ovarian cancer schizophrenia subependymal giant cell astrocytoma lung cancer non-small cell lung carcinoma Pick disease breast cancer coloboma developmental disability
A [auth L], L [auth K]	: P30533	myopia myopia 23, autosomal recessive atypical teratoid rhabdoid tumor heart disease medulloblastoma ovarian cancer plasma cell myeloma dermatomyositis large cell medulloblastoma Pick disease primitive neuroectodermal tumor glioblastoma malignant glioma pilocytic astrocytoma psoriasis

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.