5SUY | pdb_00005suy

Domain-swapped dimer of human Dishevelled2 DEP domain: monoclinic crystal form crystallised from dimeric fraction

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	d5suya1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	DEP domain	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d5suya2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5suyb1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	DEP domain	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d5suyb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5suyc1	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	DEP domain	automated matches	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d5suyc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d5suyd_	All alpha proteins	DNA/RNA-binding 3-helical bundle	'Winged helix' DNA-binding domain	DEP domain	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)
A	SCOP2B Superfamily	Winged helix DNA-binding domain	8081795	3000034	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Winged helix DNA-binding domain	8081795	3000034	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Winged helix DNA-binding domain	8081795	3000034	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Winged helix DNA-binding domain	8081795	3000034	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	DEP	e5suyA1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: DEP	ECOD (1.6)
B	DEP	e5suyB1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: DEP	ECOD (1.6)
C	DEP	e5suyC1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: DEP	ECOD (1.6)
D	DEP	e5suyD1	A: alpha arrays	X: HTH	H: HTH	T: winged	F: DEP	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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 (utative)
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 (utative)
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 (utative)
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 (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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	Segment polarity protein dishevelled homolog DVL-2	small GTPase binding protein binding binding enzyme binding GTPase binding signaling receptor binding G protein-coupled receptor binding frizzled binding protein-macromolecule adaptor activity molecular adaptor activity identical protein binding protein domain specific binding kinase binding protein kinase binding	developmental process multicellular organism development multicellular organismal process segmentation anatomical structure development pattern specification process regionalization segment specification heart development animal organ development circulatory system development system development protein localization localization developmental process multicellular organism development multicellular organismal process segmentation anatomical structure development pattern specification process regionalization segment specification heart development animal organ development circulatory system development system development protein localization localization cellular localization cellular macromolecule localization macromolecule localization cellular process cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling canonical Wnt signaling pathway biological regulation cell communication signal transduction Wnt signaling pathway positive regulation of DNA-binding transcription factor activity RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process positive regulation of molecular function 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 primary metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of molecular function regulation of gene expression biosynthetic process regulation of DNA-binding transcription factor activity metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process 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 epithelium development neural tube development tube development embryonic morphogenesis morphogenesis of an epithelium nervous system development tissue development anatomical structure morphogenesis tissue morphogenesis neural tube closure neural tube formation anatomical structure formation involved in morphogenesis tube closure 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 Wnt signaling pathway, planar cell polarity pathway non-canonical Wnt signaling pathway neural plate development convergent extension involved in gastrulation convergent extension involved in organogenesis morphogenesis of an epithelial sheet gastrulation convergent extension involved in neural plate elongation neural plate elongation convergent extension neural plate morphogenesis positive regulation of phosphorylation regulation of catalytic activity regulation of transferase activity positive regulation of phosphate metabolic process regulation of MAP kinase activity positive regulation of protein serine/threonine kinase activity positive regulation of metabolic process regulation of phosphate metabolic process phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process phosphorus metabolic process protein modification process positive regulation of protein phosphorylation positive regulation of MAP kinase activity protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation regulation of protein metabolic process positive regulation of JUN kinase activity positive regulation of kinase activity regulation of kinase activity regulation of protein serine/threonine kinase activity macromolecule modification regulation of phosphorus metabolic process regulation of protein modification process regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of protein modification process protein metabolic process positive regulation of protein kinase activity positive regulation of transferase activity positive regulation of catalytic activity regulation of protein kinase activity regulation of JUN kinase activity regulation of phosphorylation regulation of cellular component organization positive regulation of cellular component organization 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 cellular component organization positive regulation of developmental process neurogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation positive regulation of cell projection organization cellular component organization or biogenesis 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 nucleobase-containing compound metabolic process positive regulation of transcription by RNA polymerase II positive regulation of RNA metabolic process positive regulation of RNA biosynthetic process heart morphogenesis embryonic heart tube development embryonic heart tube morphogenesis heart looping determination of bilateral symmetry animal organ morphogenesis embryonic organ development determination of left/right symmetry specification of symmetry embryonic organ morphogenesis determination of heart left/right asymmetry left/right pattern formation regulation of cytoskeleton organization regulation of actin filament-based process actin cytoskeleton organization regulation of organelle organization organelle organization regulation of actin cytoskeleton organization actin filament-based process cytoskeleton organization 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 outflow tract morphogenesis	cellular anatomical structure apical part of cell intracellular anatomical structure cytoplasm cytosol inclusion body aggresome membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm cellular anatomical structure apical part of cell intracellular anatomical structure cytoplasm cytosol inclusion body aggresome membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen cytoplasmic vesicle intracellular vesicle vesicle clathrin-coated endocytic vesicle clathrin-coated vesicle coated vesicle endocytic vesicle cell periphery plasma membrane membrane lateral plasma membrane nuclear body

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR000591	DEP domain	Domain
A, B, C, D	IPR008339	Dishevelled family	Family
A, B, C, D	IPR024580	Dishevelled C-terminal	Domain
A, B, C, D	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
A, B, C, D	IPR015506	Dishevelled-related protein	Family
A, B, C, D	IPR038207	DIX domain superfamily	Homologous Superfamily
A, B, C, D	IPR003351	Dishevelled protein domain	Domain
A, B, C, D	IPR008341	Dishevelled-2	Family
A, B, C, D	IPR001158	DIX domain	Domain
A, B, C, D	IPR036034	PDZ superfamily	Homologous Superfamily
A, B, C, D	IPR001478	PDZ domain	Domain
A, B, C, D	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: O14641	malignant mesothelioma osteosarcoma vascular disease medulloblastoma ovarian cancer oligodendroglioma psoriasis

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.