3PZ8 | pdb_00003pz8

Crystal structure of Dvl1-DIX(Y17D) mutant

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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
H	d3pz8h_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
G	d3pz8g_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
F	d3pz8f1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
F	d3pz8f2	Artifacts	Tags	Tags	Tags	N-terminal Tags	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E	d3pz8e1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E	d3pz8e2	Artifacts	Tags	Tags	Tags	N-terminal Tags	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D	d3pz8d1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
D	d3pz8d2	Artifacts	Tags	Tags	Tags	N-terminal Tags	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d3pz8c_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d3pz8b1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d3pz8b2	Artifacts	Tags	Tags	Tags	N-terminal Tags	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d3pz8a_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	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)
H	SCOP2B Superfamily	Ubiquitin-like	8066814	3000157	SCOP2B (2022-06-29)
G	SCOP2 Family	DIX domain	8066813	4002651	SCOP2 (2022-06-29)
G	SCOP2 Superfamily	Ubiquitin-like	8066814	3000157	SCOP2 (2022-06-29)
F	SCOP2B Superfamily	Ubiquitin-like	8066814	3000157	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ubiquitin-like	8066814	3000157	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ubiquitin-like	8066814	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8066814	3000157	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8066814	3000157	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ubiquitin-like	8066814	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)
H	DIX	e3pz8H1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: DIX	ECOD (1.6)
G	DIX	e3pz8G1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: DIX	ECOD (1.6)
F	DIX	e3pz8F1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: DIX	ECOD (1.6)
E	DIX	e3pz8E1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: DIX	ECOD (1.6)
D	DIX	e3pz8D1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: DIX	ECOD (1.6)
C	DIX	e3pz8C1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: DIX	ECOD (1.6)
B	DIX	e3pz8B1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: DIX	ECOD (1.6)
A	DIX	e3pz8A1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: DIX	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	2.40.240.130	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	CATH (4.3.0)
G	2.40.240.130	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	CATH (4.3.0)
F	2.40.240.130	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	CATH (4.3.0)
E	2.40.240.130	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	CATH (4.3.0)
D	2.40.240.130	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	CATH (4.3.0)
C	2.40.240.130	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	CATH (4.3.0)
B	2.40.240.130	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	CATH (4.3.0)
A	2.40.240.130	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	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, G, H	PF00778	DIX domain (DIX)	DIX domain	-	Family

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, G, H	Segment polarity protein dishevelled homolog DVL-1	small GTPase binding protein binding binding enzyme binding GTPase binding signaling receptor binding G protein-coupled receptor binding frizzled binding identical protein binding kinase binding protein kinase binding beta-catenin binding	cellular response to stimulus positive regulation of cell communication multicellular organismal process regulation of postsynaptic membrane potential system process regulation of cellular process positive regulation of signal transduction response to stimulus signaling modulation of chemical synaptic transmission regulation of system process positive regulation of excitatory postsynaptic potential positive regulation of biological process regulation of signal transduction chemical synaptic transmission, postsynaptic cellular response to stimulus positive regulation of cell communication multicellular organismal process regulation of postsynaptic membrane potential system process regulation of cellular process positive regulation of signal transduction response to stimulus signaling modulation of chemical synaptic transmission regulation of system process positive regulation of excitatory postsynaptic potential positive regulation of biological process regulation of signal transduction chemical synaptic transmission, postsynaptic cell communication positive regulation of response to stimulus synaptic signaling modulation of excitatory postsynaptic potential regulation of multicellular organismal process signal transduction regulation of biological quality positive regulation of cellular process trans-synaptic signaling regulation of biological process regulation of signaling cell surface receptor signaling pathway nervous system process biological regulation cell-cell signaling chemical synaptic transmission regulation of nervous system process regulation of trans-synaptic signaling regulation of response to stimulus anterograde trans-synaptic signaling regulation of cell communication cellular process excitatory postsynaptic potential regulation of membrane potential positive regulation of signaling developmental process tissue morphogenesis anatomical structure morphogenesis epithelium development convergent extension involved in organogenesis convergent extension animal organ development anatomical structure development morphogenesis of an epithelium tissue development regulation of protein stability protein stabilization canonical Wnt signaling pathway Wnt signaling pathway positive regulation of proteasomal protein catabolic process catabolic process positive regulation of protein metabolic process proteolysis involved in protein catabolic process proteasome-mediated ubiquitin-dependent protein catabolic process macromolecule catabolic process regulation of ubiquitin-dependent protein catabolic process regulation of primary metabolic process positive regulation of metabolic 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 positive regulation of macromolecule metabolic process protein metabolic process regulation of protein metabolic process primary metabolic process proteasomal protein catabolic process regulation of macromolecule metabolic 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 metabolic process ubiquitin-dependent protein catabolic process macromolecule metabolic process regulation of metabolic process regulation of protein catabolic process cellular component organization cell junction organization postsynapse organization synapse organization cellular component organization or biogenesis axonogenesis cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation system development plasma membrane bounded cell projection organization nervous system development axon development cell morphogenesis involved in neuron differentiation generation of neurons neuron development regulation of neuron projection development regulation of cellular component organization positive regulation of cellular component organization positive regulation of neuron projection development positive regulation of cell projection organization regulation of cell projection organization regulation of plasma membrane bounded cell projection organization startle response regulation of response to external stimulus neuromuscular process negative regulation of response to stimulus negative regulation of biological process prepulse inhibition response to external stimulus negative regulation of response to external stimulus Wnt signaling pathway, planar cell polarity pathway non-canonical Wnt signaling pathway protein localization to microtubule cytoskeleton protein localization to microtubule localization protein localization to cytoskeleton protein localization to organelle macromolecule localization intracellular protein localization dendrite development dendritic spine morphogenesis dendritic spine development dendritic spine organization dendrite morphogenesis neuron projection organization chordate embryonic development embryo development neural plate development embryo development ending in birth or egg hatching morphogenesis of embryonic epithelium convergent extension involved in gastrulation embryonic morphogenesis morphogenesis of an epithelial sheet gastrulation convergent extension involved in neural plate elongation neural plate elongation neural plate morphogenesis axon extension developmental growth cell growth neuron projection extension developmental cell growth growth developmental growth involved in morphogenesis cellular localization regulated exocytosis transport synaptic vesicle cycle synaptic vesicle exocytosis vesicle-mediated transport vesicle-mediated transport in synapse secretion by cell signal release establishment of localization in cell neurotransmitter secretion secretion export from cell neurotransmitter transport establishment of localization signal release from synapse exocytosis regulation of developmental process regulation of neuron projection arborization regulation of cell morphogenesis positive regulation of developmental process regulation of anatomical structure morphogenesis positive regulation of neuron projection arborization neuron projection arborization receptor clustering localization within membrane protein localization to membrane positive regulation of DNA-templated transcription RNA metabolic process positive regulation of macromolecule biosynthetic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process transcription by RNA polymerase II positive regulation of biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of transcription by RNA polymerase II positive regulation of transcription by RNA polymerase II nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process positive regulation of RNA metabolic process regulation of gene expression biosynthetic process positive regulation of RNA biosynthetic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription regulation of postsynapse organization regulation of synapse organization regulation of synapse structure or activity regulation of localization regulation of regulated secretory pathway regulation of secretion by cell regulation of transport regulation of neurotransmitter transport regulation of synaptic vesicle exocytosis regulation of vesicle-mediated transport regulation of secretion regulation of neurotransmitter secretion regulation of exocytosis membrane organization skeletal muscle acetylcholine-gated channel clustering neuromuscular junction development postsynaptic membrane organization heart morphogenesis pattern specification process embryonic heart tube development tube morphogenesis embryonic heart tube morphogenesis heart looping determination of bilateral symmetry animal organ morphogenesis epithelial tube morphogenesis embryonic organ development determination of left/right symmetry specification of symmetry embryonic organ morphogenesis heart development tube development determination of heart left/right asymmetry regionalization circulatory system development left/right pattern formation presynapse organization cellular component biogenesis cellular component assembly cell junction assembly synapse assembly presynapse assembly collateral sprouting organelle organization microtubule cytoskeleton organization microtubule-based process cytoplasmic microtubule organization supramolecular fiber organization cytoskeleton organization ear morphogenesis ear development sensory organ development sensory organ morphogenesis inner ear development cochlea development inner ear morphogenesis cochlea morphogenesis axon guidance neuron projection guidance regulation of protein localization behavior biological process involved in intraspecies interaction between organisms social behavior neural tube development intracellular signal transduction protein localization to nucleus outflow tract morphogenesis	membrane-bounded organelle intracellular anatomical structure dense core granule intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle membrane-bounded organelle intracellular anatomical structure dense core granule intracellular vesicle intracellular membrane-bounded organelle endomembrane system intracellular organelle cellular anatomical structure cytoplasmic vesicle organelle secretory granule secretory vesicle cytoplasm vesicle neuronal dense core vesicle cytosol synapse cell junction glutamatergic synapse neuron spine neuron projection dendritic spine plasma membrane bounded cell projection somatodendritic compartment cell projection postsynapse dendrite dendritic tree cell body neuronal cell body axon polymeric cytoskeletal fiber intracellular membraneless organelle cytoskeleton membraneless organelle supramolecular fiber microtubule supramolecular polymer supramolecular complex microtubule cytoskeleton clathrin-coated vesicle coated vesicle cell periphery plasma membrane membrane presynapse growth cone distal axon site of polarized growth protein-containing complex Wnt signalosome postsynaptic density neuron to neuron synapse postsynaptic specialization asymmetric synapse Schaffer collateral - CA1 synapse lateral plasma membrane

InterPro: Protein Family Classification InterPro Database Homepage

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