5YIR

Crystal Structure of AnkB LIR/GABARAP complex

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)
A [auth D]	d5yird_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	GABARAP-like	GABA(A) receptor associated protein GABARAP	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth A]	d5yira_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	GABARAP-like	GABA(A) receptor associated protein GABARAP	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth B]	d5yirb_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	GABARAP-like	GABA(A) receptor associated protein GABARAP	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth D]	SCOP2 Family	GABARAP-like	8100479	4000970	SCOP2 (2022-06-29)
A [auth D]	SCOP2 Superfamily	Ubiquitin-like	8100480	3000157	SCOP2 (2022-06-29)
B [auth A]	SCOP2B Superfamily	Ubiquitin-like	8100480	3000157	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Ubiquitin-like	8100480	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)
A [auth D]	PF02991	e5yirD1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF02991	ECOD (1.6)
B [auth A]	PF02991	e5yirA1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF02991	ECOD (1.6)
C [auth B]	PF02991	e5yirB1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF02991	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth D]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
B [auth A]	3.10.20.90	Alpha Beta	Roll	Ubiquitin-like (UB roll)	Phosphatidylinositol 3-kinase Catalytic Subunit	CATH (4.3.0)
C [auth B]	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 [auth D], B [auth A], C [auth B]	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
D [auth C], E [auth G], F [auth H]	Ankyrin-2	protein-macromolecule adaptor activity molecular adaptor activity ATPase binding protein binding binding enzyme binding cytoskeletal protein binding spectrin binding protein-containing complex binding transmembrane transporter binding kinase binding protein kinase binding structural constituent of cytoskeleton structural molecule activity protein-macromolecule adaptor activity molecular adaptor activity ATPase binding protein binding binding enzyme binding cytoskeletal protein binding spectrin binding protein-containing complex binding transmembrane transporter binding kinase binding protein kinase binding structural constituent of cytoskeleton structural molecule activity cytoskeletal anchor activity phosphorylation-dependent protein binding modification-dependent protein binding	heart process multicellular organismal process system process regulation of biological process regulation of heart contraction regulation of system process biological regulation circulatory system process regulation of blood circulation regulation of multicellular organismal process regulation of biological quality heart contraction blood circulation regulation of heart rate heart process multicellular organismal process system process regulation of biological process regulation of heart contraction regulation of system process biological regulation circulatory system process regulation of blood circulation regulation of multicellular organismal process regulation of biological quality heart contraction blood circulation regulation of heart rate regulation of protein stability protein stabilization protein localization localization cellular localization cellular macromolecule localization macromolecule localization cellular process regulation of calcium ion transport regulation of localization transport regulation of transport regulation of monoatomic ion transport establishment of localization metal ion transport calcium ion transport monoatomic ion transport regulation of metal ion transport monoatomic cation transport response to organic substance response to stimulus response to chemical response to methylmercury protein localization to cell periphery protein localization to plasma membrane localization within membrane protein localization to membrane protein localization to T-tubule regulation of cellular process cellular biosynthetic process positive regulation of biological process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process positive regulation of metabolic process organic substance metabolic process positive regulation of biosynthetic process organic substance biosynthetic process positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of biosynthetic process cellular metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process positive regulation of gene expression regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process regulation of metabolic process positive regulation of cellular biosynthetic process cardiac muscle cell membrane repolarization membrane repolarization regulation of membrane repolarization ventricular cardiac muscle cell membrane repolarization regulation of cardiac muscle cell membrane repolarization regulation of ventricular cardiac muscle cell membrane repolarization regulation of membrane potential protein localization to organelle inorganic ion homeostasis intracellular calcium ion homeostasis homeostatic process calcium ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis SA node cell to atrial cardiac muscle cell signaling signaling cell-cell signaling involved in cardiac conduction SA node cell to atrial cardiac muscle cell communication cell communication regulation of cardiac muscle cell action potential cell communication involved in cardiac conduction regulation of action potential SA node cell action potential cell-cell signaling action potential cardiac conduction regulation of SA node cell action potential regulation of cell communication cardiac muscle cell action potential positive regulation of cation transmembrane transport regulation of potassium ion transport monoatomic ion transmembrane transport potassium ion transmembrane transport regulation of transmembrane transporter activity regulation of monoatomic ion transmembrane transport regulation of transporter activity monoatomic cation transmembrane transport positive regulation of molecular function positive regulation of monoatomic ion transport positive regulation of transmembrane transport positive regulation of monoatomic ion transmembrane transport regulation of potassium ion transmembrane transporter activity regulation of monoatomic ion transmembrane transporter activity inorganic ion transmembrane transport regulation of potassium ion transmembrane transport inorganic cation transmembrane transport transmembrane transport regulation of molecular function positive regulation of potassium ion transport regulation of transmembrane transport positive regulation of transport positive regulation of potassium ion transmembrane transport positive regulation of transporter activity positive regulation of ion transmembrane transporter activity potassium ion transport regulation of monoatomic cation transmembrane transport positive regulation of potassium ion transmembrane transporter activity positive regulation of calcium ion transport cellular response to stimulus negative regulation of biological process sarcoplasmic reticulum calcium ion transport release of sequestered calcium ion into cytosol by sarcoplasmic reticulum cardiac muscle contraction intracellular signal transduction intracellular signaling cassette signal transduction release of sequestered calcium ion into cytosol by endoplasmic reticulum regulation of release of sequestered calcium ion into cytosol regulation of cardiac muscle contraction muscle contraction maintenance of location release of sequestered calcium ion into cytosol regulation of striated muscle contraction calcium-mediated signaling regulation of muscle contraction negative regulation of sequestering of calcium ion regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion maintenance of location in cell striated muscle contraction regulation of calcium ion transmembrane transport negative regulation of cellular process regulation of sequestering of calcium ion calcium ion transmembrane import into cytosol regulation of cardiac muscle contraction by calcium ion signaling sequestering of calcium ion muscle system process regulation of muscle system process calcium ion transmembrane transport regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum membrane organization developmental process cellular developmental process cell development muscle cell differentiation cellular component organization muscle structure development T-tubule organization muscle cell development cell differentiation plasma membrane organization anatomical structure development cellular component organization or biogenesis endomembrane system organization actin filament-based process cardiac muscle cell contraction regulation of actin filament-based movement regulation of atrial cardiac muscle cell action potential cardiac muscle cell action potential involved in contraction regulation of actin filament-based process regulation of cardiac conduction atrial cardiac muscle cell to AV node cell signaling atrial cardiac muscle cell to AV node cell communication atrial cardiac muscle cell action potential actin filament-based movement regulation of cardiac muscle cell contraction actin-mediated cell contraction regulation of heart rate by cardiac conduction ventricular cardiac muscle cell action potential positive regulation of cation channel activity regulation of cation channel activity protein localization to cell surface import into cell endocytosis vesicle-mediated transport establishment of protein localization nitrogen compound transport organic substance transport protein transport regulation of calcium ion transmembrane transporter activity membrane depolarization during cardiac muscle cell action potential membrane depolarization during action potential membrane depolarization membrane depolarization during SA node cell action potential positive regulation of calcium ion transmembrane transporter activity positive regulation of calcium ion transmembrane transport heart development animal organ development cardiac atrium development circulatory system development multicellular organism development cardiac septum development cardiac chamber development atrial septum development system development protein localization to endoplasmic reticulum cellular component assembly involved in morphogenesis myelin assembly cellular component biogenesis cellular anatomical entity morphogenesis cellular component assembly cell junction assembly axon ensheathment ensheathment of neurons cell-cell junction assembly cell-cell junction organization nervous system development myelination anatomical structure morphogenesis cell junction organization anatomical structure formation involved in morphogenesis paranodal junction assembly protein localization to M-band	cell periphery postsynapse postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region cellular anatomical entity synaptic membrane sarcolemma T-tubule M band intracellular anatomical structure cell periphery postsynapse postsynaptic membrane synapse cell junction membrane plasma membrane plasma membrane region cellular anatomical entity synaptic membrane sarcolemma T-tubule M band intracellular anatomical structure sarcomere intracellular organelle organelle intracellular non-membrane-bounded organelle contractile muscle fiber A band cytoplasm supramolecular fiber myofibril supramolecular polymer supramolecular complex non-membrane-bounded organelle Z disc I band cytosol costamere basal part of cell basal plasma membrane basolateral plasma membrane cell projection neuron projection plasma membrane bounded cell projection cytoskeleton membrane-bounded organelle endosome intracellular vesicle intracellular membrane-bounded organelle recycling endosome endomembrane system cytoplasmic vesicle vesicle cell-cell junction intercalated disc anchoring junction cell-cell contact zone mitochondrion apical part of cell apical plasma membrane lytic vacuole vacuole lysosome early endosome
A [auth D], B [auth A], C [auth B]	Gamma-aminobutyric acid receptor-associated protein	protein binding binding signaling receptor binding GABA receptor binding phosphatidylethanolamine binding phospholipid binding lipid binding cytoskeletal protein binding microtubule binding tubulin binding ubiquitin protein ligase binding ubiquitin-like protein ligase binding enzyme binding beta-tubulin binding	cellular response to stimulus regulation of biological process regulation of signaling small GTPase-mediated signal transduction regulation of cellular process response to stimulus signaling regulation of small GTPase mediated signal transduction Rac protein signal transduction biological regulation regulation of signal transduction intracellular signal transduction regulation of Rac protein signal transduction cell communication regulation of intracellular signal transduction cellular response to stimulus regulation of biological process regulation of signaling small GTPase-mediated signal transduction regulation of cellular process response to stimulus signaling regulation of small GTPase mediated signal transduction Rac protein signal transduction biological regulation regulation of signal transduction intracellular signal transduction regulation of Rac protein signal transduction cell communication regulation of intracellular signal transduction regulation of response to stimulus intracellular signaling cassette regulation of cell communication cellular process signal transduction 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 catabolic process organelle assembly vacuole organization macroautophagy cellular metabolic process autophagy autophagosome organization cellular component biogenesis cellular component organization cellular catabolic process organelle organization cellular component assembly metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism protein localization establishment of protein localization cellular localization nitrogen compound transport transport organic substance transport establishment of localization localization protein transport cellular macromolecule localization macromolecule localization positive regulation of protein K48-linked ubiquitination regulation of protein K48-linked ubiquitination regulation of protein modification process positive regulation of protein metabolic process positive regulation of biological process regulation of protein ubiquitination positive regulation of post-translational protein modification regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process organic substance metabolic process protein ubiquitination positive regulation of macromolecule metabolic process protein metabolic process protein modification process regulation of protein modification by small protein conjugation or removal positive regulation of protein modification by small protein conjugation or removal positive regulation of protein ubiquitination regulation of protein polyubiquitination organonitrogen compound metabolic process regulation of post-translational protein modification regulation of protein metabolic process protein polyubiquitination primary metabolic process regulation of macromolecule metabolic process positive regulation of protein polyubiquitination macromolecule modification macromolecule metabolic process post-translational protein modification protein modification by small protein conjugation regulation of metabolic process protein K48-linked ubiquitination protein modification by small protein conjugation or removal positive regulation of proteasomal protein catabolic process proteolysis involved in protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of ubiquitin-dependent protein catabolic process positive regulation of ubiquitin-dependent protein catabolic process regulation of proteolysis regulation of proteolysis involved in protein catabolic process modification-dependent macromolecule catabolic process proteolysis organonitrogen compound catabolic process proteasomal protein catabolic process protein catabolic process regulation of catabolic process positive regulation of protein catabolic process positive regulation of proteolysis involved in protein catabolic process positive regulation of catabolic process regulation of proteasomal ubiquitin-dependent protein catabolic process modification-dependent protein catabolic process positive regulation of proteolysis regulation of proteasomal protein catabolic process positive regulation of proteasomal ubiquitin-dependent protein catabolic process ubiquitin-dependent protein catabolic process organic substance catabolic process regulation of protein catabolic process extrinsic apoptotic signaling pathway via death domain receptors cell surface receptor signaling pathway cell death extrinsic apoptotic signaling pathway apoptotic signaling pathway apoptotic process programmed cell death microtubule cytoskeleton organization microtubule-based process cytoskeleton organization	membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium cellular anatomical entity cytoplasmic region plasma membrane bounded cell projection cytoplasm plasma membrane bounded cell projection intracellular organelle cell projection cytoskeleton organelle intracellular non-membrane-bounded organelle membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium cellular anatomical entity cytoplasmic region plasma membrane bounded cell projection cytoplasm plasma membrane bounded cell projection intracellular organelle cell projection cytoskeleton organelle intracellular non-membrane-bounded organelle cytoplasm non-membrane-bounded organelle actin cytoskeleton cytosol cell periphery plasma membrane membrane endoplasmic reticulum smooth endoplasmic reticulum intracellular membrane-bounded organelle endomembrane system sperm midpiece 9+2 motile cilium sperm flagellum motile cilium lytic vacuole vacuole lysosome cytoplasmic vesicle intracellular vesicle vesicle autophagosome vacuolar membrane autophagosome membrane bounding membrane of organelle organelle membrane Golgi apparatus Golgi membrane perinuclear region of cytoplasm cell body protein-containing complex microtubule associated complex microtubule cytoskeleton polymeric cytoskeletal fiber supramolecular fiber microtubule supramolecular polymer supramolecular complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth C], E [auth G], F [auth H]	IPR040745	Ankyrin, UPA domain	Domain
D [auth C], E [auth G], F [auth H]	IPR000906	ZU5 domain	Domain
D [auth C], E [auth G], F [auth H]	IPR002110	Ankyrin repeat	Repeat
D [auth C], E [auth G], F [auth H]	IPR000488	Death domain	Domain
D [auth C], E [auth G], F [auth H]	IPR036770	Ankyrin repeat-containing domain superfamily	Homologous Superfamily
D [auth C], E [auth G], F [auth H]	IPR011029	Death-like domain superfamily	Homologous Superfamily
A [auth D], B [auth A], C [auth B]	IPR004241	Autophagy protein Atg8 ubiquitin-like	Family
A [auth D], B [auth A], C [auth B]	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
D [auth C], E [auth G], F [auth H]	Pharos: Q01484	cardiac arrhythmia, ankyrin-B-related long QT syndrome cerebrovascular disorder Neurodevelopmental Disorders familial long QT syndrome invasive ductal breast carcinoma long QT syndrome 1 lung carcinoma malignant glioma medulloblastoma atopic eczema non-small cell lung carcinoma autosomal dominant cardiac arrhythmia (Kuhn) pancreatic intraductal papillary-mucinous carcinoma Brugada syndrome cardiac arrhythmia, ankyrin-B-related long QT syndrome cerebrovascular disorder Neurodevelopmental Disorders familial long QT syndrome invasive ductal breast carcinoma long QT syndrome 1 lung carcinoma malignant glioma medulloblastoma atopic eczema non-small cell lung carcinoma autosomal dominant cardiac arrhythmia (Kuhn) pancreatic intraductal papillary-mucinous carcinoma Brugada syndrome catecholaminergic polymorphic ventricular tachycardia Pick disease primitive neuroectodermal tumor Down syndrome glioblastoma large cell medulloblastoma malignant colon neoplasm malignant mesothelioma acute myeloid leukemia nephrosclerosis atypical teratoid rhabdoid tumor oligodendroglioma B-cell chronic lymphocytic leukemia pancreatic intraductal papillary-mucinous neoplasm catecholaminergic polymorphic ventricular tachycardia 1 pilocytic astrocytoma colorectal cancer psoriasis ductal breast carcinoma in situ hereditary spastic paraplegia lung cancer malignant ependymoma adrenal cortex carcinoma autism spectrum disorder ovarian cancer breast carcinoma cardiomyopathy pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia pituitary cancer dermatomyositis

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.