Annotations: 4GZ8

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Sema domain-like	8038490	3000180	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Sema domain-like	8038490	3000180	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	Sema_1	e4gz8A1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: Sema_1	ECOD (1.6)
A	PSI_1	e4gz8A2	A: few secondary structure elements	X: Trefoil/Plexin domain-like (From Topology)	H: Trefoil/Plexin domain-like (From Topology)	T: Trefoil/Plexin domain-like	F: PSI_1	ECOD (1.6)
B	Sema_1	e4gz8B1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: Sema_1	ECOD (1.6)
B	PSI_1	e4gz8B2	A: few secondary structure elements	X: Trefoil/Plexin domain-like (From Topology)	H: Trefoil/Plexin domain-like (From Topology)	T: Trefoil/Plexin domain-like	F: PSI_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
A	3.30.1680.10	Alpha Beta	2-Layer Sandwich	ligand-binding face of the semaphorins, domain 2	ligand-binding face of the semaphorins, domain 2	CATH (4.3.0)
B	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (4.3.0)
B	3.30.1680.10	Alpha Beta	2-Layer Sandwich	ligand-binding face of the semaphorins, domain 2	ligand-binding face of the semaphorins, domain 2	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01403	Sema domain (Sema)	Sema domain	-	Repeat
A, B	PF18452	Immunoglobulin domain (Ig_6)	Immunoglobulin domain	This is an immunoglobulin domain which can be found in Interleukin-18 receptor alpha (IL-18Ra). IL-18Ra ectodomain folds into three immunoglobulin (Ig)-like domains, similar to IL-1 receptors. Each domain comprises a two-layer sandwich of six to nin ...	This is an immunoglobulin domain which can be found in Interleukin-18 receptor alpha (IL-18Ra). IL-18Ra ectodomain folds into three immunoglobulin (Ig)-like domains, similar to IL-1 receptors. Each domain comprises a two-layer sandwich of six to nine beta-strands and contains at least one intra-domain disulfide bond [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Semaphorin-3A	protein binding binding semaphorin receptor binding signaling receptor binding neuropilin binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity chemorepellent activity receptor ligand activity signaling receptor activator activity	heart process multicellular organismal process system process regulation of biological process regulation of heart contraction regulation of system process biological regulation circulatory system process regulation of blood circulation regulation of multicellular organismal process regulation of biological quality heart contraction blood circulation regulation of heart rate heart process multicellular organismal process system process regulation of biological process regulation of heart contraction regulation of system process biological regulation circulatory system process regulation of blood circulation regulation of multicellular organismal process regulation of biological quality heart contraction blood circulation regulation of heart rate developmental process cranial ganglion development nervous system development tissue development ganglion development multicellular organism development nerve development cranial nerve development facioacoustic ganglion development anatomical structure development system development axon extension regulation of growth regulation of cellular process axonogenesis regulation of cellular component size developmental growth cell projection organization negative regulation of biological process regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development cell projection morphogenesis neuron differentiation negative regulation of growth neuron projection morphogenesis cell differentiation negative regulation of cellular component organization regulation of cell projection organization negative regulation of cell growth developmental growth involved in morphogenesis generation of neurons negative regulation of axonogenesis negative regulation of developmental growth negative regulation of multicellular organismal process regulation of neuron projection development regulation of cellular component organization cellular developmental process regulation of developmental process plasma membrane bounded cell projection morphogenesis cell development cell growth cell morphogenesis regulation of axon extension cellular component organization regulation of nervous system development neurogenesis negative regulation of neurogenesis regulation of extent of cell growth regulation of axonogenesis negative regulation of cellular process negative regulation of nervous system development negative regulation of cell differentiation cellular component organization or biogenesis negative regulation of cell projection organization regulation of anatomical structure morphogenesis regulation of cell size neuron projection extension regulation of multicellular organismal development regulation of developmental growth plasma membrane bounded cell projection organization developmental cell growth negative regulation of developmental process growth negative regulation of axon extension axon development regulation of cell growth cell morphogenesis involved in neuron differentiation negative regulation of neuron projection development anatomical structure morphogenesis negative regulation of cell development neuron development cellular process regulation of plasma membrane bounded cell projection organization regulation of anatomical structure size negative regulation of locomotion response to stimulus negative regulation of chemotaxis chemotaxis response to external stimulus regulation of response to stimulus regulation of response to external stimulus regulation of axon extension involved in axon guidance locomotion regulation of chemotaxis neuron projection guidance taxis neuron projection extension involved in neuron projection guidance negative regulation of axon extension involved in axon guidance response to chemical regulation of locomotion negative regulation of response to external stimulus axon extension involved in axon guidance negative regulation of response to stimulus axon guidance regulation of gonad development regulation of reproductive process reproductive process sex differentiation positive regulation of biological process developmental process involved in reproduction male gonad development male sex differentiation positive regulation of developmental process development of primary male sexual characteristics development of primary sexual characteristics positive regulation of male gonad development reproductive structure development regulation of male gonad development positive regulation of reproductive process gonad development reproductive system development animal organ development positive regulation of gonad development positive regulation of multicellular organismal process sympathetic neuron projection guidance blastoderm segmentation segmentation neural crest cell development pattern specification process mesenchyme development embryo development mesenchymal cell migration ameboidal-type cell migration cell migration cell motility neural crest cell migration stem cell development neural crest cell differentiation ventral trunk neural crest cell migration embryonic pattern specification regionalization trunk neural crest cell migration stem cell differentiation mesenchymal cell differentiation trunk segmentation maintenance of synapse structure cell junction maintenance cell junction organization cellular component maintenance synapse organization motor neuron axon guidance branchiomotor neuron axon guidance gonadotrophin-releasing hormone neuronal migration to the hypothalamus hypothalamus development forebrain development central nervous system neuron development central nervous system neuron differentiation hypothalamus cell differentiation hypothalamus gonadotrophin-releasing hormone neuron development limbic system development head development neuron migration forebrain generation of neurons hypothalamus gonadotrophin-releasing hormone neuron differentiation brain development diencephalon development forebrain neuron development central nervous system development hypothalamic tangential migration using cell-axon interactions forebrain neuron differentiation hypothalamus cell migration regulation of cell motility tissue migration negative regulation of epithelial cell migration regulation of cell migration epithelial cell migration regulation of epithelial cell migration negative regulation of cell migration epithelium migration negative regulation of cell motility negative chemotaxis neuron recognition neuron projection fasciculation axonal fasciculation cell recognition olfactory lobe development olfactory bulb development telencephalon development dendrite development dendrite arborization basal dendrite development dendrite morphogenesis basal dendrite arborization neuron projection arborization basal dendrite morphogenesis cranial nerve morphogenesis parasympathetic nervous system development cranial nerve structural organization preganglionic parasympathetic fiber development anatomical structure arrangement facial nerve morphogenesis autonomic nervous system development facial nerve structural organization facial nerve development neural crest cell migration involved in autonomic nervous system development positive regulation of locomotion regulation of neuron migration positive regulation of cell migration positive regulation of cell motility positive regulation of cellular process positive regulation of neuron migration sympathetic nervous system development sympathetic ganglion development sympathetic neuron projection extension trigeminal nerve development trigeminal nerve structural organization trigeminal nerve morphogenesis cellular response to stimulus cell surface receptor signaling pathway semaphorin-plexin signaling pathway signaling cell communication signal transduction epithelium development gland development branching involved in salivary gland morphogenesis morphogenesis of an epithelium salivary gland development dichotomous subdivision of terminal units involved in salivary gland branching tissue morphogenesis gland morphogenesis dichotomous subdivision of an epithelial terminal unit morphogenesis of a branching structure salivary gland morphogenesis animal organ morphogenesis exocrine system development morphogenesis of a branching epithelium synaptic target recognition innervation axonogenesis involved in innervation trigeminal ganglion development neural crest cell migration involved in sympathetic nervous system development	somatodendritic compartment cell projection dendrite dendritic tree neuron projection cellular anatomical entity plasma membrane bounded cell projection synapse cell junction glutamatergic synapse axon extracellular region extracellular space cerebellar climbing fiber to Purkinje cell synapse somatodendritic compartment cell projection dendrite dendritic tree neuron projection cellular anatomical entity plasma membrane bounded cell projection synapse cell junction glutamatergic synapse axon extracellular region extracellular space cerebellar climbing fiber to Purkinje cell synapse neuron to neuron synapse asymmetric synapse excitatory synapse asymmetric, glutamatergic, excitatory synapse

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR042820	Semaphorin-3A, sema domain	Domain
A, B	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
A, B	IPR041416	IL-1Ra-like, immunoglobulin domain	Domain
A, B	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A, B	IPR036352	Sema domain superfamily	Homologous Superfamily
A, B	IPR007110	Immunoglobulin-like domain	Domain
A, B	IPR003599	Immunoglobulin subtype	Domain
A, B	IPR016201	PSI domain	Domain
A, B	IPR027231	Semaphorin	Family
A, B	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, B	IPR001627	Sema domain	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.