5Y3B | pdb_00005y3b

Crystal structure of mouse Ccd1 DIX domain

External Resource: Annotation

Domain Annotation: SCOP/SCOPe 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)
G	d5y3bg_	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	d5y3bf1	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	d5y3bf2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
E	d5y3be_	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	d5y3bd_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d5y3bc1	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C	d5y3bc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B	d5y3bb_	Alpha and beta proteins (a+b)	beta-Grasp (ubiquitin-like)	Ubiquitin-like	automated matches	automated matches	Mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
A	d5y3ba_	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: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
G	DIX	e5y3bG1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: DIX	ECOD (1.6)
F	DIX	e5y3bF1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: DIX	ECOD (1.6)
E	DIX	e5y3bE1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: DIX	ECOD (1.6)
D	DIX	e5y3bD1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: DIX	ECOD (1.6)
C	DIX	e5y3bC1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: DIX	ECOD (1.6)
B	DIX	e5y3bB1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: DIX	ECOD (1.6)
A	DIX	e5y3bA1	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)
G	2.40.240.130	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	CATH (utative)
F	2.40.240.130	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	CATH (utative)
E	2.40.240.130	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	CATH (utative)
D	2.40.240.130	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	CATH (utative)
C	2.40.240.130	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	CATH (utative)
B	2.40.240.130	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	CATH (utative)
A	2.40.240.130	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G	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	Dixin	cytoskeletal protein binding protein binding binding gamma-tubulin binding tubulin binding protein domain specific binding actin binding	multicellular organismal process regulation of cellular process regulation of developmental process cellular developmental process negative regulation of biological process regulation of cell differentiation neurogenesis multicellular organism development neuron differentiation cell differentiation negative regulation of cellular process anatomical structure development negative regulation of cell differentiation system development multicellular organismal process regulation of cellular process regulation of developmental process cellular developmental process negative regulation of biological process regulation of cell differentiation neurogenesis multicellular organism development neuron differentiation cell differentiation negative regulation of cellular process anatomical structure development negative regulation of cell differentiation system development developmental process regulation of biological process negative regulation of developmental process biological regulation nervous system development generation of neurons cellular process negative regulation of neuron differentiation regulation of neuron differentiation cellular component organization cell junction organization modification of postsynaptic actin cytoskeleton synapse organization cellular component organization or biogenesis modification of postsynaptic structure modification of synaptic structure cellular response to stimulus positive regulation of cell communication positive regulation of signal transduction response to stimulus signaling positive regulation of biological process regulation of signal transduction cell communication positive regulation of response to stimulus positive regulation of Wnt signaling pathway signal transduction Wnt signaling pathway positive regulation of cellular process regulation of signaling cell surface receptor signaling pathway regulation of Wnt signaling pathway regulation of response to stimulus regulation of cell communication positive regulation of signaling cell proliferation in forebrain head development cell population proliferation forebrain development animal organ development brain development central nervous system development neural precursor cell proliferation canonical Wnt signaling pathway regulation of cytoskeleton organization regulation of cellular component 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 cerebral cortex cell migration pallium development cerebral cortex development telencephalon cell migration forebrain cell migration cell migration telencephalon development cell motility forebrain ventricular zone progenitor cell division cell division cerebral cortex radially oriented cell migration microtubule cytoskeleton organization regulation of microtubule-based process microtubule-based process regulation of microtubule cytoskeleton organization	cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction intracellular anatomical structure actin filament bundle intracellular membraneless organelle actin cytoskeleton actomyosin intracellular organelle cytoskeleton organelle membraneless organelle cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction intracellular anatomical structure actin filament bundle intracellular membraneless organelle actin cytoskeleton actomyosin intracellular organelle cytoskeleton organelle membraneless organelle stress fiber contractile actin filament bundle cytoplasm cytosol postsynapse synapse glutamatergic synapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G	IPR001158	DIX domain	Domain
A, B, C, D, E A, B, C, D, E, F, G	IPR015506	Dishevelled-related protein	Family
A, B, C, D, E A, B, C, D, E, F, G	IPR036872	CH domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G	IPR001715	Calponin homology domain	Domain
A, B, C, D, E A, B, C, D, E, F, G	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G	IPR038207	DIX 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.