6Y09 | pdb_00006y09

Crystal structure of Atg16L in complex with GTP-bound Rab33B (Q92L)

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)
C [auth B]	d6y09b_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d6y09a_	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	automated matches	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)
C [auth B]	SCOP2B Superfamily	Ras-like P-loop GTPases	8100496	3002022	SCOP2B (2022-06-29)
A	SCOP2 Family	Ras-like monodomain GTPases	8100495	4004043	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Ras-like P-loop GTPases	8100496	3002022	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)
C [auth B]	Ras	e6y09B1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ras	ECOD (1.6)
A	Ras	e6y09A1	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Ras	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth B]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth C], D	PF08614	Autophagy protein 16 (ATG16) (ATG16)	Autophagy protein 16 (ATG16)	-	Coiled-coil
A, C [auth B]	PF00071	Ras family (Ras)	Ras family	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motili ...	Includes sub-families Ras, Rab, Rac, Ral, Ran, Rap Ypt1 and more. Shares P-loop motif with GTP_EFTU, arf and myosin_head. See Pfam:PF00009 Pfam:PF00025, Pfam:PF00063. As regards Rab GTPases, these are important regulators of vesicle formation, motility and fusion. They share a fold in common with all Ras GTPases: this is a six-stranded beta-sheet surrounded by five alpha-helices [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth C], D	Autophagy-related protein 16-1	protein binding binding enzyme binding GTPase binding protein-membrane adaptor activity protein-macromolecule adaptor activity molecular adaptor activity identical protein binding	developmental process corpus callosum development multicellular organismal process head development forebrain development animal organ development brain development nervous system development multicellular organism development central nervous system development anatomical structure development telencephalon development system development cellular developmental process developmental process corpus callosum development multicellular organismal process head development forebrain development animal organ development brain development nervous system development multicellular organism development central nervous system development anatomical structure development telencephalon development system development cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis dendrite development cell differentiation cellular component organization or biogenesis plasma membrane bounded cell projection organization dendrite arborization dendrite morphogenesis cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron projection arborization neuron development cellular process pallium development hippocampus development limbic system development autophagosome assembly catabolic process organelle assembly vacuole organization macroautophagy autophagy autophagosome organization cellular component biogenesis organelle organization cellular component assembly metabolic process process utilizing autophagic mechanism localization establishment of protein localization nitrogen compound transport protein transport transport macromolecule localization intracellular protein localization establishment of localization cellular localization intracellular transport axonal transport axo-dendritic transport establishment of localization in cell microtubule-based transport transport along microtubule cytoskeleton-dependent intracellular transport microtubule-based movement microtubule-based process biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response xenophagy response to external stimulus response to biotic stimulus defense response to other organism response to stress response to external biotic stimulus microautophagy defense response to virus response to virus regulation of growth regulation of cellular process developmental growth negative regulation of biological process regulation of cell morphogenesis negative regulation of growth negative regulation of dendrite extension regulation of biological process negative regulation of cell growth developmental growth involved in morphogenesis negative regulation of developmental growth regulation of cellular component organization regulation of developmental process cell growth negative regulation of cellular process dendrite extension regulation of anatomical structure morphogenesis neuron projection extension regulation of developmental growth developmental cell growth negative regulation of developmental process growth biological regulation regulation of dendrite extension regulation of cell growth RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process negative stranded viral RNA replication viral genome replication biosynthetic process viral RNA genome replication viral process macromolecule metabolic process positive regulation of autophagy positive regulation of biological process regulation of catabolic process regulation of autophagy positive regulation of catabolic process positive regulation of metabolic process regulation of metabolic process positive regulation of cellular process protein localization to phagophore assembly site	organelle membrane contact site cellular anatomical structure organelle vacuole-isolation membrane contact site membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium intracellular membraneless organelle cytoplasmic region plasma membrane bounded cell projection cytoplasm plasma membrane bounded cell projection intracellular organelle organelle membrane contact site cellular anatomical structure organelle vacuole-isolation membrane contact site membrane-bounded organelle intracellular anatomical structure axoneme ciliary plasm cilium intracellular membraneless organelle cytoplasmic region plasma membrane bounded cell projection cytoplasm plasma membrane bounded cell projection intracellular organelle cell projection cytoskeleton membraneless organelle cytoplasm endosome membrane endolysosome membrane intracellular vesicle lytic vacuole endomembrane system bounding membrane of organelle endolysosome vesicle membrane cytoplasmic vesicle vesicle lysosome vacuolar membrane membrane endosome vacuole intracellular membrane-bounded organelle lytic vacuole membrane cytoplasmic vesicle membrane lysosomal membrane organelle membrane cytosol phagophore assembly site membrane phagophore assembly site sperm midpiece 9+2 motile cilium sperm flagellum motile cilium synapse cell junction glutamatergic synapse protein-containing complex catalytic complex Atg12-Atg5-Atg16 complex transferase complex autophagosome autophagosome membrane axon neuron projection
A, C [auth B]	Ras-related protein Rab-33B	pyrophosphatase activity GTPase activity G protein activity ribonucleoside triphosphate phosphatase activity molecular function regulator activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding pyrophosphatase activity GTPase activity G protein activity ribonucleoside triphosphate phosphatase activity molecular function regulator activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding	localization transport cellular process establishment of localization Golgi vesicle transport vesicle-mediated transport intra-Golgi vesicle-mediated transport developmental process multicellular organism development multicellular organismal process anatomical structure morphogenesis skeletal system development anatomical structure development animal organ development localization transport cellular process establishment of localization Golgi vesicle transport vesicle-mediated transport intra-Golgi vesicle-mediated transport developmental process multicellular organism development multicellular organismal process anatomical structure morphogenesis skeletal system development anatomical structure development animal organ development skeletal system morphogenesis animal organ morphogenesis system development autophagosome assembly catabolic process organelle assembly vacuole organization macroautophagy autophagy autophagosome organization cellular component biogenesis cellular component organization organelle organization cellular component assembly metabolic process cellular component organization or biogenesis process utilizing autophagic mechanism regulation of localization regulation of cellular process regulation of constitutive secretory pathway negative regulation of biological process negative regulation of transport secretion by cell regulation of secretion by cell negative regulation of secretion negative regulation of exocytosis negative regulation of cellular process negative regulation of secretion by cell regulation of biological process secretion regulation of transport biological regulation export from cell regulation of vesicle-mediated transport regulation of secretion exocytosis constitutive secretory pathway regulation of exocytosis negative regulation of constitutive secretory pathway protein localization to Golgi apparatus protein localization to organelle macromolecule localization intracellular protein localization establishment of protein localization nitrogen compound transport protein transport regulation of retrograde vesicle-mediated transport, Golgi to ER retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum cellular response to stimulus small GTPase-mediated signal transduction response to stimulus signaling intracellular signal transduction cell communication intracellular signaling cassette Rab protein signal transduction signal transduction regulation of cellular component organization regulation of organelle organization regulation of Golgi organization Golgi organization endomembrane system organization protein localization to phagophore assembly site	membrane-bounded organelle intracellular anatomical structure Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen Golgi lumen intracellular organelle cellular anatomical structure organelle lumen organelle cytoplasm endosome membrane-bounded organelle intracellular anatomical structure Golgi apparatus membrane-enclosed lumen intracellular membrane-bounded organelle endomembrane system intracellular organelle lumen Golgi lumen intracellular organelle cellular anatomical structure organelle lumen organelle cytoplasm endosome intracellular vesicle cytoplasmic vesicle vesicle Golgi membrane membrane bounding membrane of organelle organelle membrane phagophore assembly site membrane phagophore assembly site presynapse synapse cell junction

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth C], D	IPR045160	Autophagy-related protein 16	Family
B [auth C], D	IPR019775	WD40 repeat, conserved site	Conserved Site
B [auth C], D	IPR020472	PAC1/LIS1-like, WD-40 repeat	Repeat
B [auth C], D	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
B [auth C], D	IPR013923	Autophagy-related protein 16 domain	Domain
B [auth C], D	IPR036322	WD40-repeat-containing domain superfamily	Homologous Superfamily
B [auth C], D	IPR001680	WD40 repeat	Repeat
A, C [auth B]	IPR041822	Rab33A/B	Family
A, C [auth B]	IPR005225	Small GTP-binding domain	Domain
A, C [auth B]	IPR001806	Small GTPase	Family
A, C [auth B]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, C [auth B]	Pharos: Q9H082	Smith-McCort dysplasia 2 cystic fibrosis pancreatic ductal adenocarcinoma osteosarcoma psoriasis ovarian cancer Smith-McCort dysplasia

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.