5DPW | pdb_00005dpw

Crystal structure of PLEKHM1 LIR in complex with human LC3C_8-125

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)
O	d5dpwo_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	GABARAP-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
M	d5dpwm_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	GABARAP-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
K	d5dpwk_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	GABARAP-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
I	d5dpwi_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	GABARAP-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
G	d5dpwg_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	GABARAP-like	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
E	d5dpwe_	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	d5dpwc_	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	d5dpwa_	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)
O	SCOP2B Superfamily	Ubiquitin-like	8068246	3000157	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Ubiquitin-like	8068246	3000157	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Ubiquitin-like	8068246	3000157	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Ubiquitin-like	8068246	3000157	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Ubiquitin-like	8068246	3000157	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ubiquitin-like	8068246	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8068246	3000157	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ubiquitin-like	8068246	3000157	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
O	Atg8	e5dpwO1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Atg8	ECOD (1.6)
M	Atg8	e5dpwM1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Atg8	ECOD (1.6)
K	Atg8	e5dpwK1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Atg8	ECOD (1.6)
I	Atg8	e5dpwI1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Atg8	ECOD (1.6)
G	Atg8	e5dpwG1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Atg8	ECOD (1.6)
E	Atg8	e5dpwE1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Atg8	ECOD (1.6)
C	Atg8	e5dpwC1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Atg8	ECOD (1.6)
A	Atg8	e5dpwA1	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)
O	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
M	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
K	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
I	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
G	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
E	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)
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, C, E, G, I A, C, E, G, I, K, M, O	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
B, D, F, H, J B, D, F, H, J, L, N, P	Pleckstrin homology domain-containing family M member 1	cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding	membrane organization catabolic process transport macroautophagy membrane fusion organelle membrane fusion autophagy establishment of localization vesicle-mediated transport vesicle organization cellular component organization organelle fusion localization organelle organization autophagosome-lysosome fusion membrane organization catabolic process transport macroautophagy membrane fusion organelle membrane fusion autophagy establishment of localization vesicle-mediated transport vesicle organization cellular component organization organelle fusion localization organelle organization autophagosome-lysosome fusion cellular process metabolic process cellular component organization or biogenesis vesicle fusion process utilizing autophagic mechanism cellular localization late endosome to lysosome transport establishment of localization in cell vacuolar transport intracellular transport lysosomal transport organelle localization lysosome localization vacuolar localization establishment of protein localization nitrogen compound transport protein transport macromolecule localization intracellular protein localization multicellular organismal process regulation of biological process homeostatic process biological regulation positive regulation of biological process regulation of bone remodeling tissue homeostasis regulation of tissue remodeling regulation of bone resorption bone resorption multicellular organismal-level homeostasis tissue remodeling bone remodeling anatomical structure homeostasis positive regulation of multicellular organismal process regulation of multicellular organismal process positive regulation of bone resorption regulation of cellular process regulation of cellular component organization positive regulation of cellular component organization cell projection organization ruffle organization plasma membrane bounded cell projection assembly ruffle assembly cellular component biogenesis cellular component assembly positive regulation of cell projection organization positive regulation of cellular process plasma membrane bounded cell projection organization positive regulation of cellular component biogenesis regulation of cell projection organization regulation of cell projection assembly regulation of cellular component biogenesis positive regulation of ruffle assembly regulation of plasma membrane bounded cell projection assembly regulation of ruffle assembly cell projection assembly regulation of plasma membrane bounded cell projection organization positive regulation of plasma membrane bounded cell projection assembly	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membraneless organelle intracellular membrane-bounded organelle nucleolus intracellular organelle lumen intracellular organelle cellular anatomical structure organelle lumen organelle membraneless organelle nuclear lumen vacuolar membrane autolysosome membrane lytic vacuole vacuole autolysosome membrane lytic vacuole membrane bounding membrane of organelle lysosomal membrane secondary lysosome cytoplasm organelle membrane lysosome endosome membrane endosome intracellular vesicle late endosome membrane endomembrane system cytoplasmic vesicle membrane cytoplasmic vesicle vesicle membrane late endosome vesicle nucleoplasm
A, C, E, G, I A, C, E, G, I, K, M, O	Microtubule-associated proteins 1A/1B light chain 3C	phosphatidylethanolamine binding binding phospholipid binding lipid binding ubiquitin protein ligase binding protein binding ubiquitin-like protein ligase binding enzyme binding	cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress cellular process response to starvation cellular response to starvation protein exit from endoplasmic reticulum cellular localization establishment of protein localization nitrogen compound transport transport cellular response to stimulus cellular response to nutrient levels response to nutrient levels response to stimulus cellular response to stress response to stress cellular process response to starvation cellular response to starvation protein exit from endoplasmic reticulum cellular localization establishment of protein localization nitrogen compound transport transport intracellular transport establishment of localization localization protein transport establishment of localization in cell macromolecule localization intracellular protein localization intracellular protein transport catabolic process macroautophagy autophagy metabolic process process utilizing autophagic mechanism cellular component disassembly protein-containing complex organization protein-containing complex disassembly cellular component organization autophagosome maturation cellular component organization or biogenesis cellular response to nitrogen levels cellular response to nitrogen starvation autophagosome assembly organelle assembly vacuole organization autophagosome organization cellular component biogenesis organelle organization cellular component assembly aggrephagy mitophagy autophagy of mitochondrion	cellular anatomical structure endomembrane system membrane-bounded organelle intracellular organelle intracellular anatomical structure cytoplasmic vesicle organelle intracellular vesicle cytoplasm intracellular membrane-bounded organelle vesicle membraneless organelle cytoplasmic ribonucleoprotein granule intracellular membraneless organelle cellular anatomical structure endomembrane system membrane-bounded organelle intracellular organelle intracellular anatomical structure cytoplasmic vesicle organelle intracellular vesicle cytoplasm intracellular membrane-bounded organelle vesicle membraneless organelle cytoplasmic ribonucleoprotein granule intracellular membraneless organelle supramolecular complex ribonucleoprotein granule vacuole autophagosome vacuolar membrane autophagosome membrane membrane bounding membrane of organelle organelle membrane cytosol polymeric cytoskeletal fiber cytoskeleton supramolecular fiber microtubule supramolecular polymer microtubule cytoskeleton

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D, F, H, J B, D, F, H, J, L, N, P	IPR037213	RUN domain superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L, N, P	IPR025258	Rubicon Homology Domain	Domain
B, D, F, H, J B, D, F, H, J, L, N, P	IPR004012	RUN domain	Domain
B, D, F, H, J B, D, F, H, J, L, N, P	IPR002219	Protein kinase C-like, phorbol ester/diacylglycerol-binding domain	Domain
B, D, F, H, J B, D, F, H, J, L, N, P	IPR001849	Pleckstrin homology domain	Domain
B, D, F, H, J B, D, F, H, J, L, N, P	IPR047326	PLEKHM1, RUN domain	Domain
B, D, F, H, J B, D, F, H, J, L, N, P	IPR042827	PLEKHM1, PH domain	Domain
B, D, F, H, J B, D, F, H, J, L, N, P	IPR011993	PH-like domain superfamily	Homologous Superfamily
B, D, F, H, J B, D, F, H, J, L, N, P	IPR051366	Differentially Expressed in FDCP 8 Homolog	Family
A, C, E, G, I A, C, E, G, I, K, M, O	IPR004241	Autophagy protein Atg8 ubiquitin-like	Family
A, C, E, G, I A, C, E, G, I, K, M, O	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A, C, E, G, I A, C, E, G, I, K, M, O	IPR027731	Microtubule-associated protein 1A/1B light chain 3C	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D, F, H, J B, D, F, H, J, L, N, P	Pharos: Q9Y4G2	osteopetrosis autosomal recessive osteopetrosis 6 allergic rhinitis endogenous depression osteosarcoma systemic lupus erythematosus atypical teratoid rhabdoid tumor large cell medulloblastoma Osteopetrosis - intermediate type ovarian cancer lung cancer osteopetrosis, autosomal dominant 3 ovarian carcinoma
A, C, E, G, I A, C, E, G, I, K, M, O	Pharos: Q9BXW4	atypical teratoid rhabdoid tumor malignant ependymoma invasive ductal breast carcinoma osteosarcoma lung cancer psoriasis

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.