7EAA | pdb_00007eaa

crystal structure of NDP52 SKICH domain in complex with RB1CC1 coiled-coil domain

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C [auth B]	CALCOCO1	e7eaaB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: CALCOCO1	ECOD (1.6)
D [auth A]	CALCOCO1	e7eaaA1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: CALCOCO1	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth B], D [auth A]	PF17751	SKICH domain (SKICH)	SKICH domain	The SKICH domains of SKIP and PIPP mediate plasma membrane localisation. The functions of the SKICH domains of NDP52 and CALCOCO1 are not known.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C], B [auth D]	RB1-inducible coiled-coil protein 1	protein-membrane adaptor activity protein-macromolecule adaptor activity molecular adaptor activity protein binding binding kinase binding enzyme binding protein kinase binding	carbohydrate metabolic process catabolic process glucan catabolic process energy derivation by oxidation of organic compounds macroautophagy glycogen metabolic process carbohydrate catabolic process autophagy primary metabolic process generation of precursor metabolites and energy macromolecule catabolic process polysaccharide metabolic process glucan metabolic process glycogen catabolic process glycophagy carbohydrate metabolic process catabolic process glucan catabolic process energy derivation by oxidation of organic compounds macroautophagy glycogen metabolic process carbohydrate catabolic process autophagy primary metabolic process generation of precursor metabolites and energy macromolecule catabolic process polysaccharide metabolic process glucan metabolic process glycogen catabolic process glycophagy polysaccharide catabolic process metabolic process cellular process energy reserve metabolic process macromolecule metabolic process process utilizing autophagic mechanism developmental process multicellular organism development multicellular organismal process hepaticobiliary system development gland development animal organ development anatomical structure development liver development system development heart development circulatory system development autophagosome assembly organelle assembly vacuole organization autophagosome organization cellular component biogenesis cellular component organization organelle organization cellular component assembly cellular component organization or biogenesis piecemeal microautophagy of the nucleus microautophagy nucleophagy biological process involved in interspecies interaction between organisms response to stimulus immune response response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway signaling biological regulation cell death extrinsic apoptotic signaling pathway cell communication apoptotic signaling pathway signal transduction apoptotic process programmed cell death autophagy of peroxisome pexophagy ribophagy positive regulation of cell communication positive regulation of signal transduction positive regulation of biological process regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus positive regulation of JNK cascade regulation of intracellular signal transduction JNK cascade intracellular signaling cassette positive regulation of cellular process regulation of signaling positive regulation of MAPK cascade regulation of JNK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of response to stimulus MAPK cascade regulation of cell communication positive regulation of signaling autophagy of mitochondrion negative regulation of cell population proliferation cell population proliferation regulation of cell population proliferation negative regulation of cellular process negative regulation of biological process negative regulation of signaling regulation of programmed cell death negative regulation of cell communication negative regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic signaling pathway negative regulation of response to stimulus negative regulation of programmed cell death regulation of apoptotic process negative regulation of signal transduction regulation of extrinsic apoptotic signaling pathway negative regulation of apoptotic process regulation of apoptotic signaling pathway positive regulation of cell size regulation of cellular component size regulation of biological quality regulation of cell size regulation of anatomical structure size regulation of protein modification process lipoprotein biosynthetic process lipoprotein metabolic process regulation of primary metabolic process protein lipidation regulation of lipoprotein metabolic process protein metabolic process protein modification process regulation of biosynthetic process regulation of protein lipidation regulation of protein metabolic process regulation of macromolecule metabolic process macromolecule biosynthetic process biosynthetic process macromolecule modification regulation of macromolecule biosynthetic process regulation of metabolic process defense response to virus response to virus positive regulation of autophagy regulation of catabolic process regulation of autophagy positive regulation of catabolic process positive regulation of metabolic process reticulophagy	membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope organelle membrane protein kinase complex membrane-bounded organelle intracellular anatomical structure nuclear membrane membrane nucleus intracellular membrane-bounded organelle endomembrane system intracellular organelle organelle envelope cellular anatomical structure organelle nuclear envelope organelle membrane protein kinase complex transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex serine/threonine protein kinase complex Atg1/ULK1 kinase complex cytoplasm transferase complex cytosol phagophore assembly site membrane phagophore assembly site lytic vacuole vacuole lysosome organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane vacuolar membrane autophagosome membrane autophagosome bounding membrane of organelle
C [auth B], D [auth A]	Calcium-binding and coiled-coil domain-containing protein 2	identical protein binding protein binding binding protein homodimerization activity protein dimerization activity cation binding ion binding metal ion binding small molecule binding	biological process involved in interspecies interaction between organisms response to stimulus immune response response to other organism defense response response to type II interferon response to cytokine defense response to symbiont response to external stimulus response to biotic stimulus response to peptide response to chemical immune system process defense response to other organism response to stress biological process involved in interspecies interaction between organisms response to stimulus immune response response to other organism defense response response to type II interferon response to cytokine defense response to symbiont response to external stimulus response to biotic stimulus response to peptide response to chemical immune system process defense response to other organism response to stress innate immune response response to external biotic stimulus viral 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 cellular process metabolic process regulation of metabolic process xenophagy	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure cytoplasmic vesicle organelle intracellular vesicle cytoplasm intracellular membrane-bounded organelle vesicle vacuole autophagosome vacuolar membrane autophagosome membrane membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure cytoplasmic vesicle organelle intracellular vesicle cytoplasm intracellular membrane-bounded organelle vesicle vacuole autophagosome vacuolar membrane autophagosome membrane membrane bounding membrane of organelle organelle membrane cytoskeleton membraneless organelle intracellular membraneless organelle cytosol perinuclear region of cytoplasm nucleus membrane-enclosed lumen intracellular organelle lumen nuclear body nucleoplasm organelle lumen PML body nuclear lumen

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth C], B [auth D]	IPR019460	Autophagy-related protein 11, C-terminal	Domain
A [auth C], B [auth D]	IPR040040	Autophagy-related protein 11	Family
C [auth B], D [auth A]	IPR041611	SKICH domain	Domain
C [auth B], D [auth A]	IPR051002	Ubiquitin-binding and autophagy-associated domain-containing protein	Family
C [auth B], D [auth A]	IPR041641	CALCOCO1/2, zinc finger UBZ1-type	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A [auth C], B [auth D]	Pharos: Q8TDY2	schizophrenia breast carcinoma Alzheimer disease breast adenocarcinoma glioblastoma limb-girdle muscular dystrophy Malignant neoplasm of breast ovarian cancer astrocytic tumor breast cancer hereditary breast carcinoma malignant glioma plasma cell myeloma spina bifida atypical teratoid rhabdoid tumor schizophrenia breast carcinoma Alzheimer disease breast adenocarcinoma glioblastoma limb-girdle muscular dystrophy Malignant neoplasm of breast ovarian cancer astrocytic tumor breast cancer hereditary breast carcinoma malignant glioma plasma cell myeloma spina bifida atypical teratoid rhabdoid tumor hereditary spastic paraplegia malignant mesothelioma sarcoidosis
C [auth B], D [auth A]	Pharos: Q13137	colorectal cancer breast cancer Colorectal Neoplasms lung cancer plasma cell myeloma heart disease malignant glioma colorectal carcinoma large cell medulloblastoma ovarian cancer

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.