Annotations: 7Y4O

Rat Semaphorin 6D extracellular region

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	FAD_binding_4	e7y4oB1	A: beta barrels	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: FAD_binding_4	ECOD (v294.2)
A	FAD_binding_4	e7y4oA1	A: beta barrels	X: RNase A-like	H: RNase A-like	T: RNase A-like	F: FAD_binding_4	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF01437	Plexin repeat (PSI)	Plexin repeat	A cysteine rich repeat found in several different extracellular receptors. The function of the repeat is unknown. Three copies of the repeat are found Plexin (Swiss:P70206) [1]. Two copies of the repeat are found in mahogany protein. A related C. el ...	A cysteine rich repeat found in several different extracellular receptors. The function of the repeat is unknown. Three copies of the repeat are found Plexin (Swiss:P70206) [1]. Two copies of the repeat are found in mahogany protein. A related C. elegans protein (Swiss:Q19981) contains four copies of the repeat. The Met receptor contains a single copy of the repeat. The Pfam alignment shows 6 conserved cysteine residues that may form three conserved disulphide bridges, whereas [1] shows 8 conserved cysteines. The pattern of conservation suggests that cysteines 5 and 7 (that are not absolutely conserved) form a disulphide bridge (Personal observation. A Bateman).	Domain
A, B	PF01403	Sema domain (Sema)	Sema domain	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Semaphorin 6D	molecular function activator activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity protein binding binding semaphorin receptor binding signaling receptor binding chemorepellent activity	cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus semaphorin-plexin signaling pathway signaling biological regulation cell communication cellular process signal transduction negative regulation of locomotion regulation of cell motility regulation of smooth muscle cell migration cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus semaphorin-plexin signaling pathway signaling biological regulation cell communication cellular process signal transduction negative regulation of locomotion regulation of cell motility regulation of smooth muscle cell migration negative regulation of biological process smooth muscle cell migration muscle cell migration negative regulation of smooth muscle cell migration regulation of locomotion regulation of cell migration negative regulation of cellular process negative regulation of cell motility cell migration cell motility locomotion negative regulation of cell migration multicellular organismal process axonogenesis cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis cell development neuron projection development cell morphogenesis cellular component organization neurogenesis multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development cellular component organization or biogenesis system development developmental process plasma membrane bounded cell projection organization axon guidance nervous system development axon development cell morphogenesis involved in neuron differentiation generation of neurons anatomical structure morphogenesis neuron projection guidance neuron development positive regulation of locomotion positive regulation of biological process positive regulation of cell migration positive regulation of cell motility positive regulation of cellular process axon extension regulation of growth regulation of cellular component size developmental growth regulation of cell differentiation regulation of neurogenesis regulation of cell development negative regulation of growth regulation of biological quality negative regulation of cellular component organization regulation of cell projection organization negative regulation of cell growth developmental growth involved in morphogenesis 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 regulation of developmental process cell growth regulation of axon extension regulation of nervous system development negative regulation of neurogenesis regulation of extent of cell growth regulation of axonogenesis negative regulation of nervous system development regulation of multicellular organismal process negative regulation of cell differentiation 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 developmental cell growth negative regulation of developmental process growth negative regulation of axon extension regulation of cell growth negative regulation of neuron projection development negative regulation of cell development regulation of plasma membrane bounded cell projection organization regulation of anatomical structure size immune response cell activation lymphocyte activation cell activation involved in immune response leukocyte activation immune effector process T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell T cell activation involved in immune response T cell activation immune system process leukocyte activation involved in immune response lymphocyte activation involved in immune response head development animal organ development brain development central nervous system development ventricular system development stem cell development neural crest cell differentiation neural crest cell development mesenchyme development tissue development mesenchymal cell migration stem cell differentiation ameboidal-type cell migration mesenchymal cell differentiation neural crest cell migration positive regulation of smooth muscle cell migration	cell surface cellular anatomical structure cell periphery plasma membrane membrane intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR002165	Plexin repeat	Repeat
A, B	IPR036352	Sema domain superfamily	Homologous Superfamily
A, B	IPR001627	Sema domain	Domain
A, B	IPR027231	Semaphorin	Family
A, B	IPR015943	WD40/YVTN repeat-like-containing 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.

7Y4O | pdb_00007y4o

Rat Semaphorin 6D extracellular region

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage