3GD1 | pdb_00003gd1

Structure of an Arrestin/Clathrin complex reveals a novel clathrin binding domain that modulates receptor trafficking

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth I]	SCOP2B Superfamily	ARM repeat-like	8042013	3000116	SCOP2B (2022-06-29)
C [auth I]	SCOP2B Superfamily	Clathrin heavy-chain terminal domain-like	8042014	3001710	SCOP2B (2022-06-29)
A [auth C]	SCOP2B Superfamily	Arrestin/Vps26-like	8055051	3002071	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)
C [auth I]	HTH_3	e3gd1I1	A: alpha bundles	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: HTH_3	ECOD (develop294)
B [auth E]	ClpB_D2-small	e3gd1E1	A: alpha bundles	X: YrdC/RibB	H: SH3	T: SH3	F: ClpB_D2-small	ECOD (develop294)
A [auth C]	HTH_3	e3gd1C1	A: alpha bundles	X: HTH	H: HTH	T: tetra-helical, lambda repressor-like	F: HTH_3	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth I]	2.130.10.110	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
B [auth E]	2.60.40.640	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
A [auth C]	2.60.40.840	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)
A [auth C]	2.60.40.640	Mainly Beta	Sandwich	Immunoglobulin-like		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth I]	PF09268	Clathrin, heavy-chain linker (Clathrin-link)	Clathrin, heavy-chain linker	-	Repeat
C [auth I]	PF01394	Clathrin propeller repeat (Clathrin_propel)	Clathrin propeller repeat	-	Repeat
A [auth C], B [auth E]	PF00339	Arrestin (or S-antigen), N-terminal domain (Arrestin_N)	Arrestin (or S-antigen), N-terminal domain	Ig-like beta-sandwich fold. Scop reports duplication with C-terminal domain.	Domain
A [auth C], B [auth E]	PF02752	Arrestin (or S-antigen), C-terminal domain (Arrestin_C)	Arrestin (or S-antigen), C-terminal domain	Ig-like beta-sandwich fold. Scop reports duplication with N-terminal domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D [auth Z]	clathrin	-	-	-
C [auth I]	Clathrin heavy chain 1	clathrin binding protein binding binding clathrin light chain binding protein domain specific binding arrestin family protein binding structural molecule activity disordered domain specific binding identical protein binding	cellular process cell cycle mitotic cell cycle cell division catabolic process autophagy metabolic process process utilizing autophagic mechanism cellular component disassembly clathrin coat disassembly transport protein-containing complex organization protein-containing complex disassembly establishment of localization cellular process cell cycle mitotic cell cycle cell division catabolic process autophagy metabolic process process utilizing autophagic mechanism cellular component disassembly clathrin coat disassembly transport protein-containing complex organization protein-containing complex disassembly establishment of localization vesicle-mediated transport vesicle uncoating cellular component organization localization cellular component organization or biogenesis protein depolymerization cellular localization establishment of protein localization intracellular transport protein transport establishment of localization in cell macromolecule localization intracellular protein localization intracellular protein transport clathrin coat assembly cellular component biogenesis cellular component assembly protein-containing complex assembly regulation of cellular process glycosaminoglycan metabolic process negative regulation of biological process regulation of hyaluronan biosynthetic process carbohydrate derivative metabolic process regulation of polysaccharide metabolic process regulation of primary metabolic process negative regulation of hyaluronan biosynthetic process hyaluronan metabolic process polysaccharide metabolic process negative regulation of cellular process glycosaminoglycan biosynthetic process regulation of carbohydrate metabolic process negative regulation of carbohydrate metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process carbohydrate derivative biosynthetic process carbohydrate metabolic process regulation of biological process polysaccharide biosynthetic process negative regulation of metabolic process carbohydrate biosynthetic process biological regulation primary metabolic process regulation of macromolecule metabolic process macromolecule biosynthetic process hyaluronan biosynthetic process biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of polysaccharide biosynthetic process aminoglycan metabolic process aminoglycan biosynthetic process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of carbohydrate biosynthetic process regulation of metabolic process import into cell receptor-mediated endocytosis endocytosis	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex coated membrane membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex plasma membrane protein complex membrane plasma membrane membrane protein complex coated membrane endomembrane system clathrin coat membrane coat cell periphery clathrin-coated pit clathrin coat of coated pit pigment granule intracellular vesicle melanosome cytoplasmic vesicle vesicle clathrin complex cytoskeleton spindle membraneless organelle intracellular membraneless organelle microtubule cytoskeleton clathrin-coated endocytic vesicle clathrin-coated vesicle coated vesicle endocytic vesicle vesicle coat transport vesicle membrane clathrin coat of trans-Golgi network vesicle bounding membrane of organelle trans-Golgi network transport vesicle membrane trans-Golgi network transport vesicle vesicle membrane clathrin vesicle coat Golgi-associated vesicle clathrin-coated vesicle membrane transport vesicle Golgi apparatus coated vesicle membrane cytoplasmic vesicle membrane Golgi-associated vesicle membrane organelle membrane
A [auth C], B [auth E]	Beta-arrestin-1	clathrin binding protein binding binding protein-containing complex binding AP-2 adaptor complex binding clathrin heavy chain binding signaling receptor binding acetylcholine receptor binding small molecule binding ion binding phosphatidylinositol-3,4,5-trisphosphate binding anion binding phospholipid binding lipid binding clathrin binding protein binding binding protein-containing complex binding AP-2 adaptor complex binding clathrin heavy chain binding signaling receptor binding acetylcholine receptor binding small molecule binding ion binding phosphatidylinositol-3,4,5-trisphosphate binding anion binding phospholipid binding lipid binding phosphatidylinositol phosphate binding phosphatidylinositol binding molecular adaptor activity G protein-coupled receptor binding inositol hexakisphosphate binding alcohol binding	cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction intracellular signaling cassette cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus positive regulation of ERK1 and ERK2 cascade regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of biological process regulation of signaling positive regulation of MAPK cascade biological regulation positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of response to stimulus MAPK cascade regulation of cell communication cellular process ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade positive regulation of signaling localization import into cell receptor internalization transport receptor-mediated endocytosis endocytosis establishment of localization vesicle-mediated transport establishment of protein localization protein transport macromolecule localization intracellular protein localization regulation of localization regulation of cellular component organization positive regulation of cellular component organization regulation of receptor internalization cellular component organization positive regulation of endocytosis cellular component organization or biogenesis positive regulation of receptor-mediated endocytosis regulation of endocytosis regulation of transport regulation of receptor-mediated endocytosis regulation of vesicle-mediated transport positive regulation of receptor internalization positive regulation of transport negative adaptation of signaling pathway negative regulation of signaling negative regulation of biological process desensitization of G protein-coupled receptor signaling pathway negative regulation of G protein-coupled receptor signaling pathway negative regulation of cell communication negative regulation of cellular process regulation of G protein-coupled receptor signaling pathway negative regulation of response to stimulus negative regulation of signal transduction adaptation of signaling pathway G protein-coupled receptor signaling pathway multicellular organismal process system process sensory perception nervous system process clathrin-dependent endocytosis cell surface receptor signaling pathway Notch signaling pathway negative regulation of Notch signaling pathway regulation of Notch signaling pathway catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process ubiquitin-dependent protein catabolic process metabolic process protein metabolic process macromolecule metabolic process positive regulation of phosphorylation regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of protein modification process phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process positive regulation of protein phosphorylation phosphorus metabolic process protein modification process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process regulation of macromolecule metabolic process macromolecule modification regulation of phosphorus metabolic process regulation of phosphorylation regulation of metabolic process G protein-coupled receptor internalization	cell projection cellular anatomical structure pseudopodium plasma membrane bounded cell projection protein-containing complex intracellular anatomical structure plasma membrane protein complex membrane plasma membrane membrane protein complex coated membrane endomembrane system clathrin coat membrane coat cell projection cellular anatomical structure pseudopodium plasma membrane bounded cell projection protein-containing complex intracellular anatomical structure plasma membrane protein complex membrane plasma membrane membrane protein complex coated membrane endomembrane system clathrin coat membrane coat cell periphery clathrin-coated pit cytoplasm clathrin coat of coated pit cytosol membrane-bounded organelle intracellular organelle cytoplasmic vesicle organelle intracellular vesicle intracellular membrane-bounded organelle vesicle nucleus

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth I]	IPR016341	Clathrin, heavy chain	Family
C [auth I]	IPR015348	Clathrin, heavy chain, linker, core motif	Domain
C [auth I]	IPR016024	Armadillo-type fold	Homologous Superfamily
C [auth I]	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
C [auth I]	IPR016025	Clathrin heavy chain, N-terminal	Homologous Superfamily
C [auth I]	IPR000547	Clathrin, heavy chain/VPS, 7-fold repeat	Repeat
C [auth I]	IPR022365	Clathrin, heavy chain, propeller repeat	Repeat
C [auth I]	IPR055358	Clathrin heavy-chain repeat	Repeat
A [auth C], B [auth E]	IPR011022	Arrestin-like, C-terminal domain	Domain
A [auth C], B [auth E]	IPR000698	Arrestin	Family
A [auth C], B [auth E]	IPR011021	Arrestin-like, N-terminal	Domain
A [auth C], B [auth E]	IPR014753	Arrestin, N-terminal	Homologous Superfamily
A [auth C], B [auth E]	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A [auth C], B [auth E]	IPR017864	Arrestin, conserved site	Conserved Site
A [auth C], B [auth E]	IPR014752	Arrestin-like, C-terminal domain superfamily	Homologous Superfamily

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.