5GV3 | pdb_00005gv3

Crystal structure of the membrane-distal domain of mouse lysosome-associated membrane protein 2 (LAMP-2)

External Resource: Annotation

Domain Annotation: ECOD Classification
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)
B	ANF_receptor	e5gv3B1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ANF_receptor	ECOD (develop294)
A	Oxidored_q6	e5gv3A1	A: alpha bundles	X: TIM beta/alpha-barrel	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Oxidored_q6	ECOD (develop294)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01299	Lysosome-associated membrane glycoprotein 2-like, luminal domains (Lamp2-like_luminal)	Lysosome-associated membrane glycoprotein 2-like, luminal domains	This domain is found in a group of animal proteins that includes Lysosome-associated membrane glycoprotein 2 from humans (Lamp2). Lamp2 is an integral membrane protein that plays an important role in chaperone-mediated autophagy (CMA), targeting pert ...	This domain is found in a group of animal proteins that includes Lysosome-associated membrane glycoprotein 2 from humans (Lamp2). Lamp2 is an integral membrane protein that plays an important role in chaperone-mediated autophagy (CMA), targeting pertinent proteins for lysosomal degradation. This protein is organised into two conserved luminal domains (this entry), a single transmembrane (TM) domain (Pfam:PF21222), and a short C-terminal cytosolic tail. It adopts a trimeric configuration [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Lysosome-associated membrane glycoprotein 2	protein binding binding protein domain specific binding protein-macromolecule adaptor activity molecular adaptor activity signaling adaptor activity molecular function inhibitor activity channel regulator activity transporter inhibitor activity ion channel inhibitor activity ion channel regulator activity molecular function regulator activity transporter regulator activity channel inhibitor activity protein binding binding protein domain specific binding protein-macromolecule adaptor activity molecular adaptor activity signaling adaptor activity molecular function inhibitor activity channel regulator activity transporter inhibitor activity ion channel inhibitor activity ion channel regulator activity molecular function regulator activity transporter regulator activity channel inhibitor activity enzyme binding	monoatomic cation transmembrane transport transmembrane transport localization transport proton transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport cellular process monoatomic cation transport establishment of localization regulation of biological process positive regulation of programmed cell death regulation of cellular process biological regulation monoatomic cation transmembrane transport transmembrane transport localization transport proton transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport cellular process monoatomic cation transport establishment of localization regulation of biological process positive regulation of programmed cell death regulation of cellular process biological regulation positive regulation of biological process regulation of programmed cell death cell death positive regulation of ferroptosis regulation of ferroptosis ferroptosis programmed cell death positive regulation of cellular process homeostatic process regulation of intracellular pH cellular component organization lysosome organization intracellular monoatomic cation homeostasis regulation of pH monoatomic ion homeostasis intracellular chemical homeostasis cellular component organization or biogenesis regulation of biological quality monoatomic cation homeostasis regulation of lysosomal lumen pH regulation of cellular pH intracellular monoatomic ion homeostasis vacuole organization lytic vacuole organization lysosomal lumen pH elevation organelle organization cellular homeostasis chemical homeostasis intracellular pH elevation regulation of protein stability protein stabilization cellular component disassembly catabolic process protein-containing complex organization macroautophagy autophagy protein-containing complex disassembly autophagosome maturation metabolic process process utilizing autophagic mechanism cellular response to stimulus positive regulation of response to biotic stimulus pattern recognition receptor signaling pathway response to stimulus regulation of NLRP3 inflammasome complex assembly negative regulation of biological process regulation of signal transduction response to biotic stimulus intracellular signal transduction cell communication cellular component biogenesis immune response-activating signaling pathway cellular component assembly inflammasome-mediated signaling pathway positive regulation of immune response canonical inflammasome complex assembly regulation of immune system process signal transduction negative regulation of NLRP3 inflammasome complex assembly positive regulation of immune system process innate immune response-activating signaling pathway negative regulation of cellular component organization immune response response to other organism regulation of innate immune response response to external stimulus regulation of inflammasome-mediated signaling pathway negative regulation of protein-containing complex assembly regulation of response to stimulus defense response to other organism regulation of pattern recognition receptor signaling pathway NLRP3 inflammasome complex assembly positive regulation of defense response activation of innate immune response regulation of immune response inflammatory response activation of immune response cytoplasmic pattern recognition receptor signaling pathway regulation of defense response regulation of response to biotic stimulus biological process involved in interspecies interaction between organisms regulation of cellular component organization regulation of response to external stimulus intracellular receptor signaling pathway signaling negative regulation of signaling negative regulation of cytoplasmic pattern recognition receptor signaling pathway negative regulation of intracellular signal transduction regulation of cytoplasmic pattern recognition receptor signaling pathway negative regulation of cell communication positive regulation of response to stimulus regulation of protein-containing complex assembly positive regulation of response to external stimulus immune response-regulating signaling pathway regulation of intracellular signal transduction regulation of response to stress response to stress innate immune response negative regulation of cellular process protein-containing complex assembly response to external biotic stimulus regulation of signaling positive regulation of innate immune response defense response negative regulation of response to stimulus defense response to symbiont regulation of cellular component biogenesis negative regulation of signal transduction negative regulation of immune system process immune system process regulation of cell communication negative regulation of inflammasome-mediated signaling pathway primary metabolic process protein catabolic process protein metabolic process macromolecule metabolic process macromolecule catabolic process intracellular pH reduction vacuolar acidification lysosomal lumen acidification cellular response to nutrient levels response to nutrient levels cellular response to stress response to starvation cellular response to starvation establishment of protein localization cellular localization protein targeting to vacuole involved in autophagy protein targeting establishment of protein localization to vacuole protein targeting to lysosome involved in chaperone-mediated autophagy lysosomal transport chaperone-mediated autophagy 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 macromolecule localization vacuolar transport intracellular protein transport protein catabolic process in the vacuole lysosomal protein catabolic process muscle cell cellular homeostasis	cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle platelet dense granule membrane intracellular anatomical structure intracellular vesicle cellular anatomical structure membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle platelet dense granule membrane intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle vesicle membrane cytoplasmic vesicle platelet dense granule secretory granule secretory vesicle cytoplasm organelle membrane secretory granule membrane cell periphery plasma membrane membrane microdomain membrane raft endosome membrane endosome late endosome membrane late endosome lytic vacuole vacuole lysosome vacuolar membrane protein-containing complex chaperone-mediated autophagy translocation complex membrane protein complex lytic vacuole membrane lysosomal membrane autophagosome membrane autophagosome phagocytic vesicle phagocytic vesicle membrane endocytic vesicle membrane endocytic vesicle membrane-enclosed lumen vacuolar lumen lysosomal lumen intracellular organelle lumen organelle lumen lysosomal matrix Golgi apparatus subcompartment Golgi apparatus organelle subcompartment trans-Golgi network perinuclear region of cytoplasm autolysosome secondary lysosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR048524	Lysosome-associated membrane glycoprotein 2-like, transmembrane domain	Domain
A, B	IPR002000	Lysosome-associated membrane glycoprotein	Family
A, B	IPR048528	Lysosome-associated membrane glycoprotein 2-like, luminal domains	Domain
A, B	IPR018134	Lysosome-associated membrane glycoprotein, conserved site	Conserved Site

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.