3ML6 | pdb_00003ml6

a complex between Dishevelled2 and clathrin adaptor AP-2

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)
F	SCOP2B Superfamily	mu adaptin domain-like	8036010	3000810	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	mu adaptin domain-like	8036010	3000810	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	mu adaptin domain-like	8036010	3000810	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	mu adaptin domain-like	8036010	3000810	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	mu adaptin domain-like	8036010	3000810	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	mu adaptin domain-like	8036010	3000810	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)
F	Sdh_cyt	e3ml6F1	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: Sdh_cyt	ECOD (v295.2)
E	Sdh_cyt	e3ml6E1	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: Sdh_cyt	ECOD (v295.2)
D	Sdh_cyt	e3ml6D1	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: Sdh_cyt	ECOD (v295.2)
C	Sdh_cyt	e3ml6C1	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: Sdh_cyt	ECOD (v295.2)
C	SpaA	e3ml6C4	A: alpha arrays	X: Fusion glycoprotein F2	H: Fusion glycoprotein F2	T: Fusion glycoprotein F2	F: SpaA	ECOD (v295.2)
B	Sdh_cyt	e3ml6B1	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: Sdh_cyt	ECOD (v295.2)
A	Sdh_cyt	e3ml6A1	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: Sdh_cyt	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
E	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
D	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
C	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
B	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)
A	1.10.10.10	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF00928	Adaptor complexes medium subunit family (Adap_comp_sub)	Adaptor complexes medium subunit family	-	Family
A, B, C, D, E A, B, C, D, E, F	PF00610	Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP) (DEP)	Domain found in Dishevelled, Egl-10, and Pleckstrin (DEP)	The DEP domain [1] is responsible for mediating intracellular protein targeting and regulation of protein stability in the cell [2-3]. The DEP domain is present in a number of signaling molecules, including Regulator of G protein Signaling (RGS) prot ...	The DEP domain [1] is responsible for mediating intracellular protein targeting and regulation of protein stability in the cell [2-3]. The DEP domain is present in a number of signaling molecules, including Regulator of G protein Signaling (RGS) proteins, and has been implicated in membrane targeting [4-5]. New findings in yeast, however, demonstrate a major role for a DEP domain in mediating the interaction of an RGS protein to the C-terminal tail of a GPCR, thus placing RGS in close proximity with its substrate G protein alpha subunit [6-7].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Chimeric complex between protein Dishevelled2 homolog dvl-2 and clathrin adaptor AP-2 complex subunit mu	signal sequence receptor activity protein binding binding transmembrane transporter binding lipid binding cargo adaptor activity protein-macromolecule adaptor activity molecular adaptor activity clathrin-cargo adaptor activity low-density lipoprotein particle receptor binding signaling receptor binding lipoprotein particle receptor binding disordered domain specific binding protein domain specific binding signal sequence receptor activity protein binding binding transmembrane transporter binding lipid binding cargo adaptor activity protein-macromolecule adaptor activity molecular adaptor activity clathrin-cargo adaptor activity low-density lipoprotein particle receptor binding signaling receptor binding lipoprotein particle receptor binding disordered domain specific binding protein domain specific binding small GTPase binding enzyme binding GTPase binding G protein-coupled receptor binding frizzled binding identical protein binding kinase binding protein kinase binding	cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis synaptic vesicle endocytosis import into cell cellular localization transport synaptic vesicle cycle establishment of localization vesicle-mediated transport cellular component organization cellular component biogenesis cellular component assembly protein-containing complex organization protein-containing complex assembly cellular process cellular component organization or biogenesis synaptic vesicle endocytosis import into cell cellular localization transport synaptic vesicle cycle establishment of localization vesicle-mediated transport presynaptic endocytosis vesicle-mediated transport in synapse synaptic vesicle recycling localization establishment of localization in cell endocytosis post-Golgi vesicle-mediated transport intracellular transport Golgi to vacuole transport vacuolar transport Golgi vesicle transport regulation of localization regulation of cellular process regulation of protein localization negative regulation of biological process negative regulation of protein localization to plasma membrane negative regulation of cellular process intracellular protein localization regulation of protein localization to membrane negative regulation of protein localization regulation of biological process protein localization to cell periphery protein localization to plasma membrane biological regulation regulation of protein localization to cell periphery localization within membrane protein localization to membrane negative regulation of protein localization to membrane regulation of cellular localization macromolecule localization negative regulation of protein localization to cell periphery regulation of protein localization to plasma membrane receptor internalization receptor-mediated endocytosis regulation of cellular component organization positive regulation of cellular component organization positive regulation of biological process regulation of receptor internalization positive regulation of endocytosis positive regulation of receptor-mediated endocytosis positive regulation of cellular process 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 clathrin-dependent endocytosis postsynaptic neurotransmitter receptor internalization neurotransmitter receptor internalization regulation of postsynaptic membrane neurotransmitter receptor levels postsynaptic endocytosis regulation of biological quality regulation of cellular component size regulation of vesicle size regulation of anatomical structure size membrane organization vesicle budding from membrane vesicle organization organelle organization establishment of protein localization protein transport intracellular protein transport positive regulation of synaptic vesicle recycling regulation of synaptic vesicle recycling regulation of synaptic vesicle endocytosis positive regulation of synaptic vesicle endocytosis developmental process multicellular organism development multicellular organismal process segmentation anatomical structure development pattern specification process regionalization segment specification cellular response to stimulus positive regulation of cell communication positive regulation of signal transduction response to stimulus signaling regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction regulation of signal transduction by p53 class mediator positive regulation of signal transduction by p53 class mediator signal transduction regulation of signaling positive regulation of intracellular signal transduction signal transduction by p53 class mediator regulation of response to stimulus regulation of cell communication positive regulation of signaling heart development animal organ development animal gross anatomical part developmental process circulatory system development system development epithelium development convergent extension involved in organogenesis morphogenesis of an epithelium tissue development tissue morphogenesis anatomical structure morphogenesis convergent extension cell surface receptor signaling pathway canonical Wnt signaling pathway Wnt signaling pathway regulation of protein modification process positive regulation of phosphorylation regulation of catalytic activity regulation of protein phosphorylation positive regulation of protein metabolic process regulation of transferase activity positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of molecular function positive regulation of protein modification process positive regulation of peptidyl-tyrosine phosphorylation phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process protein metabolic process positive regulation of protein kinase activity protein modification process positive regulation of protein phosphorylation protein phosphorylation positive regulation of protein tyrosine kinase activity phosphorylation regulation of protein metabolic process regulation of peptidyl-tyrosine phosphorylation positive regulation of catalytic activity primary metabolic process regulation of protein kinase activity regulation of macromolecule metabolic process regulation of molecular function positive regulation of kinase activity regulation of protein tyrosine kinase activity regulation of kinase activity macromolecule modification regulation of phosphorylation metabolic process macromolecule metabolic process peptidyl-tyrosine phosphorylation regulation of metabolic process heart morphogenesis animal organ morphogenesis embryonic epithelial tube formation chordate embryonic development tube formation embryo development epithelial tube formation tube morphogenesis primary neural tube formation embryo development ending in birth or egg hatching epithelial tube morphogenesis morphogenesis of embryonic epithelium neural tube development tube development embryonic morphogenesis nervous system development neural tube closure neural tube formation anatomical structure formation involved in morphogenesis tube closure positive regulation of JNK cascade JNK cascade intracellular signaling cassette positive regulation of MAPK cascade regulation of JNK cascade regulation of MAPK cascade MAPK cascade Wnt signaling pathway, planar cell polarity pathway non-canonical Wnt signaling pathway RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of gene expression biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription neural plate development convergent extension involved in gastrulation morphogenesis of an epithelial sheet gastrulation convergent extension involved in neural plate elongation neural plate elongation neural plate morphogenesis regulation of developmental process cellular developmental process regulation of neuron projection arborization cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis regulation of cell morphogenesis positive regulation of developmental process neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation positive regulation of cell projection organization regulation of anatomical structure morphogenesis plasma membrane bounded cell projection organization regulation of cell projection organization positive regulation of neuron projection arborization generation of neurons neuron projection arborization neuron development positive regulation of DNA-templated transcription positive regulation of macromolecule biosynthetic process transcription by RNA polymerase II positive regulation of biosynthetic process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process embryonic heart tube development embryonic heart tube morphogenesis heart looping determination of bilateral symmetry embryonic organ development determination of left/right symmetry specification of symmetry embryonic organ morphogenesis determination of heart left/right asymmetry left/right pattern formation ear morphogenesis ear development sensory organ development sensory organ morphogenesis inner ear development cochlea development inner ear morphogenesis cochlea morphogenesis cell population proliferation regulation of cell population proliferation small GTPase-mediated signal transduction outflow tract morphogenesis	cellular anatomical structure clathrin-coated pit membrane endomembrane system axon synapse neuron projection axon terminus plasma membrane bounded cell projection presynapse cell projection distal axon terminal bouton cell junction cellular anatomical structure clathrin-coated pit membrane endomembrane system axon synapse neuron projection axon terminus plasma membrane bounded cell projection presynapse cell projection distal axon terminal bouton cell junction neuron projection terminus intracellular anatomical structure cytoplasm cytosol membrane-bounded organelle protein-containing complex vesicle coat intracellular vesicle membrane protein complex transport vesicle membrane clathrin coat of trans-Golgi network vesicle intracellular organelle membrane coat bounding membrane of organelle trans-Golgi network transport vesicle membrane trans-Golgi network transport vesicle AP-type membrane coat adaptor complex AP-1 adaptor complex vesicle membrane cytoplasmic vesicle clathrin-coated vesicle clathrin vesicle coat coated vesicle Golgi-associated vesicle vesicle clathrin-coated vesicle membrane transport vesicle Golgi apparatus intracellular membrane-bounded organelle coated membrane clathrin coat coated vesicle membrane cytoplasmic vesicle membrane organelle Golgi-associated vesicle membrane organelle membrane clathrin adaptor complex cell periphery plasma membrane AP-2 adaptor complex endocytic vesicle membrane endocytic vesicle clathrin coat of coated pit clathrin coat of endocytic vesicle clathrin-coated endocytic vesicle membrane plasma membrane protein complex clathrin-coated endocytic vesicle glutamatergic synapse extrinsic component of plasma membrane presynaptic endocytic zone presynaptic membrane extrinsic component of presynaptic endocytic zone membrane synaptic membrane extrinsic component of synaptic membrane presynaptic endocytic zone membrane extrinsic component of presynaptic membrane plasma membrane region extrinsic component of membrane postsynapse synaptic vesicle secretory vesicle exocytic vesicle apical part of cell cytoskeleton membraneless organelle intracellular membraneless organelle cell cortex inclusion body aggresome nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen lateral plasma membrane nuclear body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR043512	Mu2, C-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR050431	Adaptor complexes medium subunit	Family
A, B, C, D, E A, B, C, D, E, F	IPR036168	AP-2 complex subunit mu, C-terminal superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR028565	Mu homology domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR018240	Clathrin adaptor, mu subunit, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F	IPR001392	Clathrin adaptor, mu subunit	Family
A, B, C, D, E A, B, C, D, E, F	IPR011012	Longin-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR043532	AP-2 complex subunit mu, N-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR022775	AP complex, mu/sigma subunit	Domain
A, B, C, D, E A, B, C, D, E, F	IPR000591	DEP domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR008339	Dishevelled family	Family
A, B, C, D, E A, B, C, D, E, F	IPR024580	Dishevelled C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR015506	Dishevelled-related protein	Family
A, B, C, D, E A, B, C, D, E, F	IPR038207	DIX domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR003351	Dishevelled protein domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR008341	Dishevelled-2	Family
A, B, C, D, E A, B, C, D, E, F	IPR001158	DIX domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR036034	PDZ superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR001478	PDZ domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

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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.