2DM4 | pdb_00002dm4

Solution structure of the second fn3 domain of human sorLA/LR11

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d2dm4a1	All beta proteins	Immunoglobulin-like beta-sandwich	Fibronectin type III	automated matches	automated matches	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2dm4a3	Artifacts	Tags	Tags	Tags	C-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d2dm4a2	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Fibronectin type III	8079752	4007555	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Fibronectin type III	8079753	3002063	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	fn3	e2dm4A1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: fn3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00041	Fibronectin type III domain (fn3)	Fibronectin type III domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Sortilin-related receptor	small GTPase binding protein binding binding enzyme binding GTPase binding amide binding amyloid-beta binding peptide binding neuropeptide binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity lipoprotein particle receptor activity low-density lipoprotein particle receptor activity small GTPase binding protein binding binding enzyme binding GTPase binding amide binding amyloid-beta binding peptide binding neuropeptide binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity lipoprotein particle receptor activity low-density lipoprotein particle receptor activity cargo receptor activity lipoprotein particle binding protein-containing complex binding protein-lipid complex binding low-density lipoprotein particle binding protein transporter activity transporter activity enzyme regulator activity molecular function inhibitor activity peptidase regulator activity molecular function regulator activity enzyme inhibitor activity aspartic-type endopeptidase inhibitor activity peptidase inhibitor activity endopeptidase regulator activity endopeptidase inhibitor activity	multicellular organismal process response to nutrient levels response to stimulus homeostatic process adaptive thermogenesis multicellular organismal-level homeostasis response to dietary excess diet induced thermogenesis metabolic process cellular process energy homeostasis localization post-Golgi vesicle-mediated transport transport multicellular organismal process response to nutrient levels response to stimulus homeostatic process adaptive thermogenesis multicellular organismal-level homeostasis response to dietary excess diet induced thermogenesis metabolic process cellular process energy homeostasis localization post-Golgi vesicle-mediated transport transport establishment of localization Golgi vesicle transport vesicle-mediated transport regulation of biological process regulation of cellular process regulation of cellular component organization negative regulation of cellular component organization protein-containing complex organization biological regulation negative regulation of biological process regulation of cellular component biogenesis negative regulation of protein-containing complex assembly cellular component organization cellular component biogenesis regulation of protein-containing complex assembly cellular component assembly protein-containing complex assembly negative regulation of cellular process cellular component organization or biogenesis regulation of localization cellular localization positive regulation of biological process endocytic recycling establishment of localization in cell positive regulation of intracellular transport regulation of endocytic recycling positive regulation of cellular process regulation of intracellular transport regulation of transport positive regulation of endocytic recycling intracellular transport localization within membrane regulation of vesicle-mediated transport endosomal transport vesicle-mediated transport to the plasma membrane positive regulation of transport regulation of cellular localization 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 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 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 positive regulation of early endosome to recycling endosome transport regulation of early endosome to recycling endosome transport vesicle-mediated transport between endosomal compartments early endosome to recycling endosome transport cell migration cell motility neutral lipid metabolic process negative regulation of triglyceride metabolic process catabolic process regulation of triglyceride metabolic process regulation of lipid metabolic process glycerolipid catabolic process regulation of primary metabolic process triglyceride catabolic process triglyceride metabolic process negative regulation of lipid catabolic process negative regulation of catabolic process lipid catabolic process neutral lipid catabolic process negative regulation of metabolic process negative regulation of triglyceride catabolic process primary metabolic process acylglycerol catabolic process regulation of catabolic process regulation of lipid catabolic process glycerolipid metabolic process acylglycerol metabolic process regulation of metabolic process regulation of triglyceride catabolic process negative regulation of lipid metabolic process lipid metabolic process regulation of cell motility regulation of smooth muscle cell migration smooth muscle cell migration muscle cell migration regulation of locomotion regulation of cell migration locomotion cellular response to nitrogen compound positive regulation of cell communication positive regulation of signal transduction response to peptide hormone insulin receptor signaling pathway regulation of cellular response to insulin stimulus cell surface receptor protein tyrosine kinase signaling pathway positive regulation of response to stimulus response to hormone cellular response to hormone stimulus positive regulation of cellular response to insulin stimulus regulation of insulin receptor signaling pathway positive regulation of insulin receptor signaling pathway response to oxygen-containing compound cellular response to peptide hormone stimulus response to nitrogen compound cellular response to oxygen-containing compound cellular response to chemical stimulus response to chemical response to insulin cellular response to insulin stimulus positive regulation of signaling positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of biosynthetic process cytokine production regulation of cytokine production regulation of multicellular organismal process positive regulation of macromolecule metabolic process regulation of biosynthetic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression biosynthetic process regulation of glial cell-derived neurotrophic factor production positive regulation of gene expression glial cell-derived neurotrophic factor production positive regulation of multicellular organismal process regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of cytokine production positive regulation of glial cell-derived neurotrophic factor production amyloid precursor protein catabolic process regulation of amide metabolic process regulation of amyloid-beta formation regulation of amyloid precursor protein catabolic process negative regulation of amyloid precursor protein catabolic process amyloid-beta metabolic process protein metabolic process amide metabolic process amyloid precursor protein metabolic process negative regulation of protein metabolic process amyloid-beta formation negative regulation of macromolecule metabolic process negative regulation of amyloid-beta formation negative regulation of amide metabolic process regulation of protein metabolic process establishment of protein localization protein targeting regulation of inclusion body assembly inclusion body assembly neurofibrillary tangle assembly regulation of neurofibrillary tangle assembly negative regulation of neurofibrillary tangle assembly negative regulation of inclusion body assembly cytosolic transport retrograde transport, endosome to Golgi regulation of developmental process cellular developmental process cell development regulation of cell differentiation regulation of neurogenesis regulation of cell development regulation of nervous system development negative regulation of neurogenesis multicellular organism development neurogenesis cell differentiation anatomical structure development negative regulation of nervous system development negative regulation of cell differentiation system development developmental process regulation of multicellular organismal development negative regulation of developmental process nervous system development negative regulation of cell development negative regulation of multicellular organismal process nitrogen compound transport establishment of protein localization to plasma membrane intracellular protein localization protein localization to cell periphery establishment of protein localization to membrane protein localization to plasma membrane protein localization to membrane endosome to plasma membrane protein transport protein transport macromolecule localization intracellular protein transport maintenance of protein location protein localization to Golgi apparatus maintenance of location maintenance of location in cell maintenance of protein location in cell protein localization to organelle protein retention in Golgi apparatus import into cell receptor-mediated endocytosis endocytosis G protein-coupled receptor signaling pathway neuropeptide signaling pathway positive regulation of ER to Golgi vesicle-mediated transport regulation of ER to Golgi vesicle-mediated transport endoplasmic reticulum to Golgi vesicle-mediated transport connective tissue development adipose tissue development positive regulation of adipose tissue development animal organ development tissue development positive regulation of developmental process regulation of adipose tissue development receptor metabolic process receptor recycling insulin receptor recycling positive regulation of protein metabolic process macromolecule catabolic process protein catabolic process positive regulation of protein catabolic process positive regulation of catabolic process regulation of protein catabolic process regulation of protein exit from endoplasmic reticulum protein exit from endoplasmic reticulum regulation of protein localization positive regulation of establishment of protein localization positive regulation of protein transport regulation of establishment of protein localization regulation of protein transport positive regulation of protein exit from endoplasmic reticulum positive regulation of protein localization regulation of intracellular protein transport positive regulation of intracellular protein transport positive regulation of protein localization to early endosome protein localization to endosome protein localization to early endosome regulation of protein localization to endosome positive regulation of protein localization to endosome regulation of protein localization to early endosome establishment of protein localization to vacuole lysosomal transport protein targeting to lysosome protein targeting to vacuole protein localization to vacuole protein localization to lysosome establishment of protein localization to organelle vacuolar transport	cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle intracellular anatomical structure cytoplasm cytosol perinucleolar compartment nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle organelle lumen nuclear lumen endomembrane system organelle envelope lumen organelle envelope nuclear envelope lumen nuclear envelope Golgi apparatus subcompartment Golgi apparatus organelle subcompartment trans-Golgi network Golgi membrane bounding membrane of organelle organelle membrane endosome intracellular vesicle recycling endosome cytoplasmic vesicle endosome membrane cytoplasmic vesicle membrane vesicle membrane somatodendritic compartment cell body neuronal cell body Golgi cisterna Golgi stack transport vesicle transport vesicle membrane multivesicular body membrane late endosome membrane late endosome multivesicular body cell surface cell periphery plasma membrane endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane early endosome recycling endosome membrane early endosome membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR031777	Sortilin, C-terminal	Domain
A	IPR050310	VPS10-related sortilin family receptors	Family
A	IPR036055	LDL receptor-like superfamily	Homologous Superfamily
A	IPR000033	LDLR class B repeat	Repeat
A	IPR006581	VPS10	Domain
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A	IPR023415	Low-density lipoprotein (LDL) receptor class A, conserved site	Conserved Site
A	IPR031778	Sortilin, N-terminal	Domain
A	IPR011042	Six-bladed beta-propeller, TolB-like	Homologous Superfamily
A	IPR002172	Low-density lipoprotein (LDL) receptor class A repeat	Repeat
A	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A	IPR003961	Fibronectin type III	Domain
A	IPR036116	Fibronectin type III superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q92673	Alzheimer disease amyloidosis cholestasis Neoplasm Invasiveness dementia glioblastoma interstitial cystitis lung cancer acquired metabolic disease malignant ependymoma malignant pancreatic neoplasm neurodegenerative disease attention deficit hyperactivity disorder, inattentive type ovarian cancer breast cancer Alzheimer disease amyloidosis cholestasis Neoplasm Invasiveness dementia glioblastoma interstitial cystitis lung cancer acquired metabolic disease malignant ependymoma malignant pancreatic neoplasm neurodegenerative disease attention deficit hyperactivity disorder, inattentive type ovarian cancer breast cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia primitive neuroectodermal tumor dermatomyositis drug-induced liver injury invasive ductal breast carcinoma lung carcinoma malignant mesothelioma medulloblastoma astrocytic tumor oligodendroglioma atypical teratoid rhabdoid tumor pancreatic ductal adenocarcinoma colorectal cancer psoriasis large cell medulloblastoma lymphoplasmacytic lymphoma atrial fibrillation osteosarcoma B-cell chronic lymphocytic leukemia pancreatic intraductal papillary-mucinous carcinoma

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.