2MOM | pdb_00002mom

Structural insights of TM domain of LAMP-2A in DPC micelles

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	TibC_1st	e2momB1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: TibC_1st	ECOD (v294.1)
C	TibC_1st	e2momC1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: TibC_1st	ECOD (v294.1)
A	TibC_1st	e2momA1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: TibC_1st	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF21222	Lysosome-associated membrane glycoprotein 2, transmembrane segment (Lamp2_2nd)	Lysosome-associated membrane glycoprotein 2, transmembrane segment	This domain is found in Lysosome-associated membrane glycoprotein 2 from humans (Lamp2) and similar proteins from vertebrates. Lamp2 is an integral membrane protein that plays an important role in chaperone-mediated autophagy (CMA), targeting pertine ...	This domain is found in Lysosome-associated membrane glycoprotein 2 from humans (Lamp2) and similar proteins from vertebrates. 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, a single transmembrane domain (this entry) and a short C-terminal cytosolic tail. It adopts a trimeric configuration, and the transmembrane domains of the three monomers form a three-helix bundle structure [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	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	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 cellular process regulation of ferroptosis ferroptosis programmed cell death positive regulation of cellular process regulation of protein stability 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 cellular process regulation of ferroptosis ferroptosis programmed cell death positive regulation of cellular process regulation of protein stability regulation of biological quality protein stabilization cellular component disassembly catabolic process protein-containing complex organization macroautophagy autophagy protein-containing complex disassembly cellular component organization autophagosome maturation metabolic process cellular component organization or biogenesis 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 homeostatic process intracellular pH reduction regulation of intracellular pH vacuolar acidification lysosomal lumen acidification cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis regulation of pH monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis cellular response to nutrient levels response to nutrient levels cellular response to stress response to starvation cellular response to starvation protein import localization establishment of protein localization protein transport transport macromolecule localization intracellular protein localization establishment of 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 protein targeting to vacuole intracellular transport protein localization to vacuole protein localization to lysosome establishment of protein localization to organelle protein localization to organelle vacuolar transport intracellular protein transport protein catabolic process in the vacuole lysosomal protein catabolic process muscle cell cellular homeostasis	cellular anatomical structure 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 cellular anatomical structure 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 extracellular exosome extracellular vesicle extracellular organelle extracellular region vesicle extracellular membrane-bounded organelle intracellular vesicle endomembrane system bounding membrane of organelle vesicle membrane cytoplasmic vesicle vacuolar membrane azurophil granule lytic vacuole membrane cytoplasmic vesicle membrane lysosomal membrane secretory granule primary lysosome secretory vesicle azurophil granule membrane organelle membrane secretory granule membrane platelet dense granule membrane platelet dense granule cell periphery plasma membrane endosome membrane endosome late endosome membrane late endosome protein-containing complex chaperone-mediated autophagy translocation complex membrane protein complex autophagosome membrane autophagosome phagocytic vesicle phagocytic vesicle membrane endocytic vesicle membrane endocytic vesicle Golgi apparatus subcompartment Golgi apparatus organelle subcompartment trans-Golgi network ficolin-1-rich granule membrane ficolin-1-rich granule tertiary granule perinuclear region of cytoplasm autolysosome secondary lysosome

InterPro: Protein Family Classification InterPro Database Homepage

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

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C	Pharos: P13473	Danon disease status epilepticus hypertrophic cardiomyopathy glycogen storage disease lymphoplasmacytic lymphoma malignant mesothelioma Non-Convulsive Status Epilepticus arthrogryposis psoriasis tuberculosis Down syndrome intellectual disability large cell medulloblastoma lysosomal storage disease medulloblastoma Danon disease status epilepticus hypertrophic cardiomyopathy glycogen storage disease lymphoplasmacytic lymphoma malignant mesothelioma Non-Convulsive Status Epilepticus arthrogryposis psoriasis tuberculosis Down syndrome intellectual disability large cell medulloblastoma lysosomal storage disease medulloblastoma ovarian cancer pilocytic astrocytoma cardiomyopathy rhabdomyolysis dermatomyositis glioblastoma juvenile dermatomyositis lung cancer malignant glioma myopathy pancreatic ductal adenocarcinoma plasma cell myeloma Charcot-Marie-Tooth disease subependymal giant cell astrocytoma dilated cardiomyopathy inborn errors of metabolism

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C	OPM	Transmembrane	Bitopic proteins	Lysosome-associated membrane glycoprotein	Lysosome-associated membrane glycoprotein

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C	MemProtMD	Annotated as membrane protein by MemProtMD

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.

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