5CX3 | pdb_00005cx3

Crystal structure of FYCO1 LIR in complex with LC3A

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)
D	d5cx3d_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	GABARAP-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5cx3c_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	GABARAP-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5cx3b_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	GABARAP-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5cx3a_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	GABARAP-like	automated matches	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)
D	SCOP2B Superfamily	Ubiquitin-like	8068252	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8068252	3000157	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8068252	3000157	SCOP2B (2022-06-29)
A	SCOP2 Family	GABARAP-like	8068251	4000970	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ubiquitin-like	8068252	3000157	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)
D	Atg8	e5cx3D1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Atg8	ECOD (1.6)
C	Atg8	e5cx3C1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Atg8	ECOD (1.6)
B	Atg8	e5cx3B1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Atg8	ECOD (1.6)
A	Atg8	e5cx3A1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Atg8	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
C	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
B	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
A	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF02991	Autophagy protein Atg8 ubiquitin like (ATG8)	Autophagy protein Atg8 ubiquitin like	Light chain 3 is proposed to function primarily as a subunit of microtubule associated proteins 1A and 1B and that its expression may regulate microtubule binding activity [1]. Autophagy is generally known as a process involved in the degradation of ...	Light chain 3 is proposed to function primarily as a subunit of microtubule associated proteins 1A and 1B and that its expression may regulate microtubule binding activity [1]. Autophagy is generally known as a process involved in the degradation of bulk cytoplasmic components that are non-specifically sequestered into an autophagosome, where they are sequestered into double-membrane vesicles and delivered to the degradative organelle, the lysosome/vacuole, for breakdown and eventual recycling of the resulting macromolecules. The yeast proteins are involved in the autophagosome, and Atg8 binds Atg19, via its N-terminus and the C-terminus of Atg19.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Microtubule-associated proteins 1A/1B light chain 3A	binding phospholipid binding lipid binding phosphatidylethanolamine binding cytoskeletal protein binding microtubule binding protein binding tubulin binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding	cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation p38MAPK cascade intracellular signal transduction cell communication intracellular signaling cassette MAPK cascade cellular process signal transduction cellular component disassembly cellular response to stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation p38MAPK cascade intracellular signal transduction cell communication intracellular signaling cassette MAPK cascade cellular process signal transduction 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 response to nutrient levels cellular response to nitrogen levels cellular response to starvation cellular response to nutrient levels cellular response to stress cellular response to nitrogen starvation response to stress response to starvation autophagosome assembly organelle assembly vacuole organization autophagosome organization cellular component biogenesis organelle organization cellular component assembly response to iron(II) ion response to metal ion response to iron ion response to chemical response to copper ion cellular response to metal ion cellular response to chemical stimulus cellular response to copper ion cellular response to oxidative stress response to oxygen-containing compound cellular response to chemical stress cellular response to oxygen-containing compound cellular response to hydrogen peroxide response to reactive oxygen species response to hydrogen peroxide response to oxidative stress cellular response to reactive oxygen species autophagy of mitochondrion response to lead ion cell surface receptor protein serine/threonine kinase signaling pathway cell surface receptor signaling pathway SMAD protein signal transduction enzyme-linked receptor protein signaling pathway JNK cascade cellular response to amino acid starvation response to amino acid starvation mitophagy response to decreased oxygen levels cellular response to oxygen levels cellular response to decreased oxygen levels response to oxygen levels cellular response to oxygen-glucose deprivation response to abiotic stimulus response to oxygen-glucose deprivation	membrane-bounded organelle cellular anatomical structure organelle membrane organelle membrane intracellular anatomical structure cytoplasm cytosol synapse cell junction glutamatergic synapse intracellular organelle vacuole autophagosome membrane-bounded organelle cellular anatomical structure organelle membrane organelle membrane intracellular anatomical structure cytoplasm cytosol synapse cell junction glutamatergic synapse intracellular organelle vacuole autophagosome intracellular membrane-bounded organelle vacuolar membrane autophagosome membrane bounding membrane of organelle autolysosome lytic vacuole secondary lysosome lysosome endosome intracellular vesicle endomembrane system cytoplasmic vesicle late endosome vesicle polymeric cytoskeletal fiber intracellular membraneless organelle cytoskeleton membraneless organelle supramolecular fiber microtubule supramolecular polymer supramolecular complex microtubule cytoskeleton
E, F, G, H	FYVE and coiled-coil domain-containing protein 1	cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	establishment of organelle localization vesicle cytoskeletal trafficking vesicle localization cellular localization organelle transport along microtubule transport establishment of vesicle localization intracellular transport establishment of localization plus-end-directed organelle transport along microtubule vesicle transport along microtubule localization plus-end-directed vesicle transport along microtubule organelle localization establishment of localization in cell establishment of organelle localization vesicle cytoskeletal trafficking vesicle localization cellular localization organelle transport along microtubule transport establishment of vesicle localization intracellular transport establishment of localization plus-end-directed organelle transport along microtubule vesicle transport along microtubule localization plus-end-directed vesicle transport along microtubule organelle localization establishment of localization in cell microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport cellular process microtubule-based movement microtubule-based process positive regulation of organelle organization catabolic process regulation of cellular process regulation of cellular component organization positive regulation of cellular component organization regulation of autophagosome maturation macroautophagy autophagy positive regulation of biological process protein-containing complex disassembly regulation of autophagy regulation of protein-containing complex disassembly cellular component organization positive regulation of metabolic process autophagosome maturation cellular component organization or biogenesis positive regulation of macroautophagy process utilizing autophagic mechanism positive regulation of protein-containing complex disassembly positive regulation of cellular process cellular component disassembly positive regulation of autophagy regulation of biological process protein-containing complex organization biological regulation regulation of catabolic process positive regulation of autophagosome maturation regulation of organelle organization positive regulation of catabolic process organelle organization regulation of macroautophagy metabolic process regulation of metabolic process	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle vacuole autophagosome cytoplasm intracellular membrane-bounded organelle membrane Golgi apparatus endomembrane system endosome intracellular vesicle membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle vacuole autophagosome cytoplasm intracellular membrane-bounded organelle membrane Golgi apparatus endomembrane system endosome intracellular vesicle cytoplasmic vesicle late endosome vesicle lytic vacuole lysosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR004241	Autophagy protein Atg8 ubiquitin-like	Family
A, B, C, D	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
E, F, G, H	IPR037213	RUN domain superfamily	Homologous Superfamily
E, F, G, H	IPR004012	RUN domain	Domain
E, F, G, H	IPR017455	Zinc finger, FYVE-related	Domain
E, F, G, H	IPR009038	GOLD domain	Domain
E, F, G, H	IPR013083	Zinc finger, RING/FYVE/PHD-type	Homologous Superfamily
E, F, G, H	IPR047336	FYCO1, RUN domain	Domain
E, F, G, H	IPR000306	FYVE zinc finger	Domain
E, F, G, H	IPR036598	GOLD domain superfamily	Homologous Superfamily
E, F, G, H	IPR011011	Zinc finger, FYVE/PHD-type	Homologous Superfamily
E, F, G, H	IPR047337	FYCO1, FYVE domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: Q9H492	Liver Cirrhosis, Experimental astrocytic tumor malignant glioma Pick disease skin carcinoma glioblastoma lung carcinoma melanoma pilocytic astrocytoma subependymal giant cell astrocytoma large cell medulloblastoma malignant ependymoma oligodendroglioma primitive neuroectodermal tumor
E, F, G, H	Pharos: Q9BQS8	cataract 18 cataract breast cancer Cataract, autosomal recessive congenital 2 intellectual disability malignant colon neoplasm myopathy osteosarcoma subependymal giant cell astrocytoma invasive ductal breast carcinoma malignant glioma nuclear cataract ovarian cancer tuberculosis glioblastoma cataract 18 cataract breast cancer Cataract, autosomal recessive congenital 2 intellectual disability malignant colon neoplasm myopathy osteosarcoma subependymal giant cell astrocytoma invasive ductal breast carcinoma malignant glioma nuclear cataract ovarian cancer tuberculosis glioblastoma lung cancer malignant mesothelioma pilocytic astrocytoma

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.