9FJF | pdb_00009fjf

Lysosomal transporting complex of beta-glucocerebrosidase (GCase) and lysosomal integral membrane protein 2 (LIMP-2) with bound Pro-macrobodies (Combined focus map)

External Resource: Annotation

Domain Annotation: SCOP2 Classification
SAbDab Antibody Annotation
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)
B	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8043253	3001528	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8043253	3001528	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	(Trans)glycosidases	8043254	3000313	SCOP2B (2022-06-29)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C	Heavy Chain	IGHV1	-	lysosomal acid glucosylceramidase	SAbDab (2025-12-19)
D	Heavy Chain	IGHV1	-	lysosomal acid glucosylceramidase	SAbDab (2025-12-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01130	CD36 family (CD36)	CD36 family	The CD36 family is thought to be a novel class of scavenger receptors. There is also evidence suggesting a possible role in signal transduction. CD36 is involved in cell adhesion.	Domain
B	PF17189	Glycosyl hydrolase family 30 beta sandwich domain (Glyco_hydro_30C)	Glycosyl hydrolase family 30 beta sandwich domain		Domain
B	PF02055	Glycosyl hydrolase family 30 TIM-barrel domain (Glyco_hydro_30)	Glycosyl hydrolase family 30 TIM-barrel domain		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Lysosome membrane protein 2	protein binding binding virus receptor activity exogenous protein binding sterol binding alcohol binding steroid binding lipid binding cholesterol binding small molecule binding cargo receptor activity scavenger receptor activity protein-folding chaperone binding identical protein binding protein binding binding virus receptor activity exogenous protein binding sterol binding alcohol binding steroid binding lipid binding cholesterol binding small molecule binding cargo receptor activity scavenger receptor activity protein-folding chaperone binding identical protein binding protein homodimerization activity protein dimerization activity cation binding ion binding phosphatidylcholine binding phospholipid binding quaternary ammonium group binding enzyme binding modified amino acid binding anion binding phosphatidylserine binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity	localization nitrogen compound transport transport macromolecule localization phospholipid transport lipid localization aminophospholipid transport lipid transport establishment of localization organophosphate ester transport sphingolipid catabolic process regulation of amide metabolic process catabolic process regulation of cellular process localization nitrogen compound transport transport macromolecule localization phospholipid transport lipid localization aminophospholipid transport lipid transport establishment of localization organophosphate ester transport sphingolipid catabolic process regulation of amide metabolic process catabolic process regulation of cellular process glycolipid metabolic process regulation of lipid metabolic process carbohydrate derivative metabolic process regulation of primary metabolic process regulation of glucosylceramide catabolic process ceramide catabolic process amide metabolic process glycosylceramide metabolic process membrane lipid metabolic process ceramide metabolic process regulation of biological process carbohydrate derivative catabolic process regulation of membrane lipid metabolic process lipid catabolic process glycosphingolipid catabolic process glycosphingolipid metabolic process biological regulation liposaccharide metabolic process primary metabolic process sphingolipid metabolic process glucosylceramide metabolic process regulation of catabolic process regulation of lipid catabolic process membrane lipid catabolic process glycosylceramide catabolic process glycolipid catabolic process metabolic process cellular process glucosylceramide catabolic process regulation of metabolic process lipid metabolic process regulation of cellular component organization vacuole organization lytic vacuole organization regulation of vacuole organization regulation of organelle organization cellular component organization lysosome organization organelle organization regulation of lysosome organization cellular component organization or biogenesis regulation of neuron projection development multicellular organismal process positive regulation of cellular component organization cellular developmental process cell projection organization positive regulation of biological process cell development neuron projection development neurogenesis multicellular organism development neuron differentiation positive regulation of neuron projection development cell differentiation anatomical structure development positive regulation of cell projection organization positive regulation of cellular process system development developmental process plasma membrane bounded cell projection organization regulation of cell projection organization nervous system development generation of neurons neuron development regulation of plasma membrane bounded cell projection organization regulation of carbohydrate catabolic process carbohydrate metabolic process carbohydrate catabolic process regulation of carbohydrate metabolic process system process sensory perception nervous system process sensory perception of sound sensory perception of mechanical stimulus regulation of endosome organization vesicle organization endosome organization endomembrane system organization cellular localization establishment of protein localization protein targeting establishment of protein localization to vacuole lysosomal transport protein targeting to lysosome establishment of localization in cell intracellular protein localization protein targeting to vacuole intracellular transport protein localization to vacuole protein localization to lysosome establishment of protein localization to organelle protein transport protein localization to organelle vacuolar transport intracellular protein transport establishment of protein localization to plasma membrane vesicle-mediated transport endocytic recycling protein localization to cell periphery establishment of protein localization to membrane protein localization to plasma membrane localization within membrane protein localization to membrane endosomal transport vesicle-mediated transport to the plasma membrane endosome to plasma membrane protein transport import into cell receptor-mediated endocytosis endocytosis	cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction membrane membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen lytic vacuole vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction membrane membrane-bounded organelle intracellular anatomical structure membrane-enclosed lumen lytic vacuole vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle organelle lumen organelle cytoplasm lysosome intracellular vesicle 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 clathrin-coated endocytic vesicle cytoplasmic vesicle membrane coated vesicle membrane organelle membrane extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cell periphery plasma membrane endosome membrane endosome late endosome membrane endomembrane system late endosome organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane vacuolar membrane lytic vacuole membrane lysosomal membrane Golgi membrane Golgi apparatus
B	Lysosomal acid glucosylceramidase	glycosyltransferase activity transferase activity glucosyltransferase activity hexosyltransferase activity catalytic activity glucosylceramidase activity hydrolase activity, acting on glycosyl bonds glycosylceramidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity protein binding binding signaling receptor binding scavenger receptor binding glycosyltransferase activity transferase activity glucosyltransferase activity hexosyltransferase activity catalytic activity glucosylceramidase activity hydrolase activity, acting on glycosyl bonds glycosylceramidase activity hydrolase activity, hydrolyzing O-glycosyl compounds hydrolase activity protein binding binding signaling receptor binding scavenger receptor binding glucosidase activity steryl-beta-glucosidase activity beta-glucosidase activity galactosylceramidase activity	developmental process stem cell proliferation cell population proliferation cellular developmental process hemopoiesis cell differentiation anatomical structure development hematopoietic stem cell proliferation cell development cellular process regulation of biological process catabolic process regulation of cellular process macroautophagy developmental process stem cell proliferation cell population proliferation cellular developmental process hemopoiesis cell differentiation anatomical structure development hematopoietic stem cell proliferation cell development cellular process regulation of biological process catabolic process regulation of cellular process macroautophagy autophagy biological regulation regulation of catabolic process regulation of autophagy regulation of macroautophagy metabolic process process utilizing autophagic mechanism regulation of metabolic process interleukin-6 production multicellular organismal process negative regulation of biological process regulation of interleukin-6 production regulation of cytokine production cytokine production negative regulation of cellular process regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of metabolic process negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of interleukin-6 production negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process macromolecule metabolic process negative regulation of multicellular organismal process cerebellar cortex morphogenesis hindbrain morphogenesis cerebellar Purkinje cell layer formation multicellular organism development cerebellar Purkinje cell layer development metencephalon development cerebellar Purkinje cell layer morphogenesis cerebellar cortex formation system development cerebellum morphogenesis head development animal organ development brain development nervous system development cerebellar cortex development anatomical structure morphogenesis cerebellum development central nervous system development anatomical structure formation involved in morphogenesis hindbrain development establishment of skin barrier epithelium development skin development skin epidermis development epidermis development tissue development response to ketone response to lipid response to stimulus response to chemical response to oxygen-containing compound response to testosterone regulation of type 2 mitophagy positive regulation of type 2 mitophagy positive regulation of biological process positive regulation of autophagy of mitochondrion positive regulation of metabolic process mitophagy regulation of autophagy of mitochondrion positive regulation of macroautophagy positive regulation of cellular process positive regulation of autophagy positive regulation of mitophagy regulation of mitophagy positive regulation of catabolic process type 2 mitophagy autophagy of mitochondrion positive regulation of proteasomal protein catabolic process positive regulation of protein metabolic process proteolysis involved in protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of ubiquitin-dependent protein catabolic process regulation of primary metabolic process positive regulation of ubiquitin-dependent protein catabolic process regulation of proteolysis regulation of proteolysis involved in protein catabolic process modification-dependent macromolecule catabolic process proteolysis positive regulation of macromolecule metabolic process protein metabolic process regulation of protein metabolic process primary metabolic process proteasomal protein catabolic process protein catabolic process positive regulation of protein catabolic process positive regulation of proteolysis involved in protein catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process positive regulation of proteolysis regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process regulation of protein catabolic process regulation of cellular component organization negative regulation of cellular component organization protein-containing complex organization 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 cellular component organization or biogenesis system process nervous system process neuromuscular process cell activation mononuclear cell differentiation lymphocyte activation lymphocyte differentiation leukocyte activation T cell differentiation in thymus T cell activation immune system process T cell differentiation leukocyte differentiation cellular response to stimulus cellular response to nutrient levels response to nutrient levels cellular response to stress response to stress response to starvation cellular response to starvation negative regulation of protein metabolic process response to endogenous stimulus response to glucocorticoid response to corticosteroid response to hormone response to steroid hormone response to dexamethasone regulation of protein catabolic process in the vacuole protein catabolic process in the vacuole lysosomal protein catabolic process regulation of lysosomal protein catabolic process sphingolipid catabolic process glycolipid metabolic process carbohydrate derivative metabolic process ceramide catabolic process amide metabolic process glycosylceramide metabolic process membrane lipid metabolic process ceramide metabolic process carbohydrate derivative catabolic process glycosphingolipid catabolic process lipid catabolic process glycosphingolipid metabolic process liposaccharide metabolic process sphingolipid metabolic process glucosylceramide metabolic process membrane lipid catabolic process glycosylceramide catabolic process glycolipid catabolic process glucosylceramide catabolic process lipid metabolic process positive regulation of cell communication regulation of system process positive regulation of transmission of nerve impulse cell communication neuronal action potential regulation of transmission of nerve impulse positive regulation of nervous system process regulation of biological quality regulation of neuronal action potential regulation of action potential action potential transmission of nerve impulse regulation of nervous system process positive regulation of action potential regulation of cell communication positive regulation of multicellular organismal process positive regulation of neuronal action potential regulation of membrane potential response to estrogen multicellular organismal-level homeostasis homeostatic process homeostasis of number of cells polyol metabolic process sphingoid biosynthetic process sphingolipid biosynthetic process small molecule biosynthetic process lipid biosynthetic process alcohol metabolic process diol biosynthetic process sphingosine metabolic process sphingoid metabolic process sphingosine biosynthetic process diol metabolic process polyol biosynthetic process alcohol biosynthetic process small molecule metabolic process membrane lipid biosynthetic process glycoside catabolic process glycoside metabolic process glycosyl compound catabolic process beta-glucoside catabolic process amide biosynthetic process ceramide biosynthetic process brain morphogenesis animal organ morphogenesis leukocyte migration mononuclear cell migration lymphocyte migration cell migration cell motility regulation of defense response regulation of response to external stimulus negative regulation of inflammatory response defense response negative regulation of response to stimulus response to external stimulus regulation of inflammatory response regulation of response to stimulus negative regulation of response to external stimulus regulation of response to stress negative regulation of defense response inflammatory response regulation of signaling negative regulation of signaling signaling termination of signal transduction regulation of signal transduction negative regulation of signal transduction negative regulation of cell communication signal transduction secondary alcohol metabolic process sterol metabolic process steroid metabolic process cholesterol metabolic process neuron apoptotic process negative regulation of neuron apoptotic process 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 regulation of neuron apoptotic process lysosome organization organelle organization vacuole organization lytic vacuole organization myeloid leukocyte differentiation macrophage differentiation neurogenesis gliogenesis glial cell differentiation myeloid cell differentiation microglia differentiation anatomical structure maturation cell maturation developmental maturation response to peptide cellular response to tumor necrosis factor response to cytokine cellular response to cytokine stimulus response to tumor necrosis factor response to pH response to abiotic stimulus negative regulation of intracellular signal transduction intracellular signal transduction regulation of intracellular signal transduction intracellular signaling cassette regulation of MAPK cascade MAPK cascade negative regulation of MAPK cascade determination of adult lifespan response to thyroid hormone lipid storage nutrient storage generation of neurons central nervous system neuron differentiation neuron differentiation pyramidal neuron differentiation microglial cell proliferation leukocyte proliferation macrophage proliferation glial cell proliferation behavior motor behavior antigen processing and presentation TOR signaling regulation of TOR signaling cellular respiration energy derivation by oxidation of organic compounds respiratory electron transport chain electron transport chain generation of precursor metabolites and energy autophagosome organization	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle vacuolar membrane intracellular anatomical structure membrane lytic vacuole extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle vacuolar membrane intracellular anatomical structure membrane lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle lysosomal membrane cytoplasm organelle membrane lysosome Golgi apparatus subcompartment Golgi apparatus organelle subcompartment endomembrane system trans-Golgi network membrane-enclosed lumen vacuolar lumen lysosomal lumen intracellular organelle lumen organelle lumen endoplasmic reticulum
C	Nanobody Nb1	-	-	-
D	Nanobody Nb6	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR002159	CD36 family	Family
A	IPR005429	Lysosome membrane protein II	Family
B	IPR033452	Glycosyl hydrolase family 30, beta sandwich domain	Domain
B	IPR001139	Glycoside hydrolase family 30	Family
B	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
B	IPR033453	Glycosyl hydrolase family 30, TIM-barrel domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	Pharos: Q14108	action myoclonus-renal failure syndrome Unverricht-Lundborg syndrome progressive myoclonus epilepsy malignant ependymoma medulloblastoma obesity disorder ovarian cancer platelet-type bleeding disorder 10 atherosclerosis psoriasis Down syndrome Gaucher disease glioblastoma intellectual disability lung adenocarcinoma action myoclonus-renal failure syndrome Unverricht-Lundborg syndrome progressive myoclonus epilepsy malignant ependymoma medulloblastoma obesity disorder ovarian cancer platelet-type bleeding disorder 10 atherosclerosis psoriasis Down syndrome Gaucher disease glioblastoma intellectual disability lung adenocarcinoma malignant glioma myopathy oligodendroglioma Pick disease adenoma polycystic ovary syndrome Progressive myoclonus epilepsy 4 atypical teratoid rhabdoid tumor type 2 diabetes mellitus epilepsy Gaucher disease type I hereditary spastic paraplegia juvenile dermatomyositis malaria malignant mesothelioma neurodegenerative disease osteosarcoma pilocytic astrocytoma primitive neuroectodermal tumor astrocytic tumor progressive supranuclear palsy inborn carbohydrate metabolic disorder large cell medulloblastoma
B	Pharos: P04062	Gaucher disease Parkinson disease Gaucher disease-ophthalmoplegia-cardiovascular calcification syndrome Lewy body dementia Gaucher disease perinatal lethal late-onset Parkinson disease Gaucher disease type II pulmonary hypertension Gaucher disease type III Gaucher disease type I Gaucher Disease, Type 2 (disorder) arthrogryposis mucolipidosis type IV brain aneurysm Crohn disease Gaucher disease Parkinson disease Gaucher disease-ophthalmoplegia-cardiovascular calcification syndrome Lewy body dementia Gaucher disease perinatal lethal late-onset Parkinson disease Gaucher disease type II pulmonary hypertension Gaucher disease type III Gaucher disease type I Gaucher Disease, Type 2 (disorder) arthrogryposis mucolipidosis type IV brain aneurysm Crohn disease psoriasis Riley-Day syndrome hematopoietic and lymphoid system neoplasm inborn errors of metabolism neurodegenerative disease autosomal recessive juvenile Parkinson disease 2 parkinsonian disorder cholestasis dental caries hydrops fetalis intellectual disability lysosomal storage disease Niemann-Pick disease type B diabetes mellitus gastric adenocarcinoma sphingolipidosis

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.