1Q47 - JenaLib

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:484
 aligned with SEM3A_MOUSE | O08665 from UniProtKB/Swiss-Prot  Length:772

    Alignment length:495
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515     
          SEM3A_MOUSE    26 KNNVPRLKLSYKEMLESNNVITFNGLANSSSYHTFLLDEERSRLYVGAKDHIFSFNLVNIKDFQKIVWPVSYTRRDECKWAGKDILKECANFIKVLEAYNQTHLYACGTGAFHPICTYIEVGHHPEDNIFKLQDSHFENGRGKSPYDPKLLTASLLIDGELYSGTAADFMGRDFAIFRTLGHHHPIRTEQHDSRWLNDPRFISAHLIPESDNPEDDKVYFFFRENAIDGEHSGKATHARIGQICKNDFGGHRSLVNKWTTFLKARLICSVPGPNGIDTHFDELQDVFLMNSKDPKNPIVYGVFTTSSNIFKGSAVCMYSMSDVRRVFLGPYAHRDGPNYQWVPYQGRVPYPRPGTCPSKTFGGFDSTKDLPDDVITFARSHPAMYNPVFPINNRPIMIKTDVNYQFTQIVVDRVDAEDGQYDVMFIGTDVGTVLKVVSVPKETWHDLEEILLEEMTVFREPTTISAMELSTKQQQLYIGSTAGVAQLPLHRCDIY 520
               SCOP domains d1q47a_ A: Semaphorin 3a                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1q47A00 A:26-520 YVTN repeat-like/Quinoprotein amine dehydrogenase                                                                                                                                                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhh....eee..........eeeee....eeeeee..eeeeee......eeeee...hhhhhhhhhhh...........eeeeee....eeeeee......eeeeee..........eeeeeeeee.............eeeee..eeeeeee.......eeeeeee.....ee............eeeeeeee....hhhh.eeeeeeeee..........eeeeeeeee.................eeee...ee.......ee..eeeeeeee........eeeeeee........eeeeeehhhhhhhhhh...ee........ee......................hhhhhhhhhhhhhhh.........hhhhh..eee......eeeeeeeeee....eeeeeeeee....eeeee..-----------..eee..........eeeee....eeeee....eeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----SEMA  PDB: A:31-514 UniProt: 31-514                                                                                                                                                                                                                                                                                                                                                                                                                                                                 ------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q47 A  26 KNNVPRLKLSYKEMLESNNVITFNGLANSSSYHTFLLDEERSRLYVGAKDHIFSFNLVNIKDFQKIVWPVSYTRRDECKWAGKDILKECANFIKVLEAYNQTHLYACGTGAFHPICTYIEVGHHPEDNIFKLQDSHFENGRGKSPYDPKLLTASLLIDGELYSGTAADFMGRDFAIFRTLGHHHPIRTEQHDSRWLNDPRFISAHLIPESDNPEDDKVYFFFRENAIDGEHSGKATHARIGQICKNDFGGHRSLVNKWTTFLKARLICSVPGPNGIDTHFDELQDVFLMNSKDPKNPIVYGVFTTSSNIFKGSAVCMYSMSDVRRVFLGPYAHRDGPNYQWVPYQGRVPYPRPGTCPSKTFGGFDSTKDLPDDVITFARSHPAMYNPVFPINNRPIMIKTDVNYQFTQIVVDRVDAEDGQYDVMFIGTDVGTVLKVVSV-----------LLEEMTVFREPTTISAMELSTKQQQLYIGSTAGVAQLPLHRCDIY 520
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455        |-         -|      485       495       505       515     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                464         476

Chain B from PDB  Type:PROTEIN  Length:495
 aligned with SEM3A_MOUSE | O08665 from UniProtKB/Swiss-Prot  Length:772

    Alignment length:495
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515     
          SEM3A_MOUSE    26 KNNVPRLKLSYKEMLESNNVITFNGLANSSSYHTFLLDEERSRLYVGAKDHIFSFNLVNIKDFQKIVWPVSYTRRDECKWAGKDILKECANFIKVLEAYNQTHLYACGTGAFHPICTYIEVGHHPEDNIFKLQDSHFENGRGKSPYDPKLLTASLLIDGELYSGTAADFMGRDFAIFRTLGHHHPIRTEQHDSRWLNDPRFISAHLIPESDNPEDDKVYFFFRENAIDGEHSGKATHARIGQICKNDFGGHRSLVNKWTTFLKARLICSVPGPNGIDTHFDELQDVFLMNSKDPKNPIVYGVFTTSSNIFKGSAVCMYSMSDVRRVFLGPYAHRDGPNYQWVPYQGRVPYPRPGTCPSKTFGGFDSTKDLPDDVITFARSHPAMYNPVFPINNRPIMIKTDVNYQFTQIVVDRVDAEDGQYDVMFIGTDVGTVLKVVSVPKETWHDLEEILLEEMTVFREPTTISAMELSTKQQQLYIGSTAGVAQLPLHRCDIY 520
               SCOP domains d1q47b_ B: Semaphorin 3a                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1q47B00 B:26-520 YVTN repeat-like/Quinoprotein amine dehydrogenase                                                                                                                                                                                                                                                                                                                                                                                                                                              CATH domains
           Pfam domains (1) -------------------------------Sema-1q47B01 B:57-498                                                                                                                                                                                                                                                                                                                                                                                                                                     ---------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------Sema-1q47B02 B:57-498                                                                                                                                                                                                                                                                                                                                                                                                                                     ---------------------- Pfam domains (2)
         Sec.struct. author ......eeehhhhhhh....eee..........eeeee....eeeee...eeeeee......eeeee...hhhhhhhhhhh.........eeeeeeee....eeeeeeee....eeeeee..........eeeeeeeee.............eeeee..eeeeeee.......eeeeeee...................eeeeeeeee...hhh.eeeeeeeeee..........eeeeeeeee.................eeeee..ee.......ee..eeeeeeee........eeeeeee........eeeeeehhhhhhhhhh...ee........ee......................hhhhh.hhhhhh............hhhhh..eee......eeeeeeeeeee..eeeeeeeeee...eeeeee............eeeeeee.........eeee.....eeeeee..eeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----SEMA  PDB: B:31-514 UniProt: 31-514                                                                                                                                                                                                                                                                                                                                                                                                                                                                 ------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q47 B  26 KNNVPRLKLSYKEMLESNNVITFNGLANSSSYHTFLLDEERSRLYVGAKDHIFSFNLVNIKDFQKIVWPVSYTRRDECKWAGKDILKECANFIKVLEAYNQTHLYACGTGAFHPICTYIEVGHHPEDNIFKLQDSHFENGRGKSPYDPKLLTASLLIDGELYSGTAADFMGRDFAIFRTLGHHHPIRTEQHDSRWLNDPRFISAHLIPESDNPEDDKVYFFFRENAIDGEHSGKATHARIGQICKNDFGGHRSLVNKWTTFLKARLICSVPGPNGIDTHFDELQDVFLMNSKDPKNPIVYGVFTTSSNIFKGSAVCMYSMSDVRRVFLGPYAHRDGPNYQWVPYQGRVPYPRPGTCPSKTFGGFDSTKDLPDDVITFARSHPAMYNPVFPINNRPIMIKTDVNYQFTQIVVDRVDAEDGQYDVMFIGTDVGTVLKVVSVPKETWHDLEEVLLEEMTVFREPTTISAMELSTKQQQLYIGSTAGVAQLPLHRCDIY 520
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (SEM3A_MOUSE | O08665)

molecular function
	GO:0045499	chemorepellent activity	Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a lower concentration of that signal.
	GO:0038191	neuropilin binding	Interacting selectively and non-covalently with a member of the neuropilin family.
	GO:0030215	semaphorin receptor binding	Interacting selectively and non-covalently with semaphorin receptors.
biological process
	GO:0006915	apoptotic process	A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
	GO:0048846	axon extension involved in axon guidance	The long distance growth of a single cell process, that is involved in the migration of an axon growth cone, where the migration is directed to a specific target site by a combination of attractive and repulsive cues.
	GO:0007411	axon guidance	The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
	GO:0007413	axonal fasciculation	The collection of axons into a bundle of rods, known as a fascicle.
	GO:0060385	axonogenesis involved in innervation	The neurite development process that generates a long process of a neuron, as it invades a target tissue.
	GO:0021785	branchiomotor neuron axon guidance	The process in which a branchiomotor neuron growth cone is directed to a specific target site. Branchiomotor neurons are located in the hindbrain and innervate branchial arch-derived muscles that control jaw movements, facial expression, the larynx, and the pharynx.
	GO:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0048813	dendrite morphogenesis	The process in which the anatomical structures of a dendrite are generated and organized. A dendrite is a freely branching protoplasmic process of a nerve cell.
	GO:0060666	dichotomous subdivision of terminal units involved in salivary gland branching	The process in which a salivary epithelial cord bifurcates at its end.
	GO:0021612	facial nerve structural organization	The process that contributes to the act of creating the structural organization of the facial nerve. This process pertains to the physical shaping of a rudimentary structure. This sensory and motor nerve supplies the muscles of facial expression and the expression and taste at the anterior two-thirds of the tongue. The principal branches are the superficial opthalmic, buccal, palatine and hyomandibular. The main trunk synapses within pterygopalatine ganglion in the parotid gland and this ganglion then gives of nerve branches which supply the lacrimal gland and the mucous secreting glands of the nasal and oral cavities.
	GO:1903375	facioacoustic ganglion development	The process whose specific outcome is the progression of an acoustico-facial VII-VIII ganglion complex over time, from its formation to the mature structure.
	GO:0021828	gonadotrophin-releasing hormone neuronal migration to the hypothalamus	The directional movement of a gonadotrophin-releasing hormone producing neuron from the nasal placode to the hypothalamus.
	GO:0008045	motor neuron axon guidance	The process in which the migration of an axon growth cone of a motor neuron is directed to a specific target site in response to a combination of attractive and repulsive cues.
	GO:0007275	multicellular organism development	The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
	GO:0050919	negative chemotaxis	The directed movement of a motile cell or organism towards a lower concentration of a chemical.
	GO:0030517	negative regulation of axon extension	Any process that stops, prevents, or reduces the frequency, rate or extent of axon outgrowth.
	GO:0048843	negative regulation of axon extension involved in axon guidance	Any process that stops, prevents, or reduces the frequency, rate or extent of axon extension involved in axon guidance.
	GO:0010633	negative regulation of epithelial cell migration	Any process that stops, prevents, or reduces the frequency, rate or extent of epithelial cell migration.
	GO:0021675	nerve development	The process whose specific outcome is the progression of a nerve over time, from its formation to the mature structure.
	GO:0007399	nervous system development	The process whose specific outcome is the progression of nervous tissue over time, from its formation to its mature state.
	GO:1901166	neural crest cell migration involved in autonomic nervous system development	Any neural crest cell migration that is involved in autonomic nervous system development.
	GO:1903045	neural crest cell migration involved in sympathetic nervous system development	Any neural crest cell migration that is involved in sympathetic nervous system development.
	GO:0001764	neuron migration	The characteristic movement of an immature neuron from germinal zones to specific positions where they will reside as they mature.
	GO:0021772	olfactory bulb development	The progression of the olfactory bulb over time from its initial formation until its mature state. The olfactory bulb coordinates neuronal signaling involved in the perception of smell. It receives input from the sensory neurons and outputs to the olfactory cortex.
	GO:2000020	positive regulation of male gonad development	Any process that activates or increases the frequency, rate or extent of male gonad development.
	GO:2001224	positive regulation of neuron migration	Any process that activates or increases the frequency, rate or extent of neuron migration.
	GO:0048841	regulation of axon extension involved in axon guidance	Any process that modulates the frequency, rate or extent of axon extension involved in axon guidance.
	GO:0002027	regulation of heart rate	Any process that modulates the frequency or rate of heart contraction.
	GO:0071526	semaphorin-plexin signaling pathway	A series of molecular signals generated as a consequence of a semaphorin receptor (composed of a plexin and a neurophilin) binding to a semaphorin ligand.
	GO:1902287	semaphorin-plexin signaling pathway involved in axon guidance	Any semaphorin-plexin signaling pathway that is involved in axon guidance.
	GO:1902285	semaphorin-plexin signaling pathway involved in neuron projection guidance	Any semaphorin-plexin signaling pathway that is involved in neuron projection guidance.
	GO:0061549	sympathetic ganglion development	The process whose specific outcome is the progression of a sympathetic ganglion over time, from its formation to the mature structure.
	GO:0097490	sympathetic neuron projection extension	Long distance growth of a single sympathetic neuron projection involved in cellular development. A neuron projection is a prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
	GO:0097491	sympathetic neuron projection guidance	The process in which the migration of a sympathetic neuron projection is directed to a specific target site in response to a combination of attractive and repulsive cues.
	GO:0061551	trigeminal ganglion development	The process whose specific outcome is the progression of a trigeminal ganglion over time, from its formation to the mature structure.
	GO:0021637	trigeminal nerve structural organization	The process that contributes to the act of creating the structural organization of the oculomotor nerve. This process pertains to the physical shaping of a rudimentary structure. The trigeminal nerve is composed of three large branches. They are the ophthalmic (V1, sensory), maxillary (V2, sensory) and mandibular (V3, motor and sensory) branches. The sensory ophthalmic branch travels through the superior orbital fissure and passes through the orbit to reach the skin of the forehead and top of the head. The maxillary nerve contains sensory branches that reach the pterygopalatine fossa via the inferior orbital fissure (face, cheek and upper teeth) and pterygopalatine canal (soft and hard palate, nasal cavity and pharynx). The motor part of the mandibular branch is distributed to the muscles of mastication, the mylohyoid muscle and the anterior belly of the digastric. The mandibular nerve also innervates the tensor veli palatini and tensor tympani muscles. The sensory part of the mandibular nerve is composed of branches that carry general sensory information from the mucous membranes of the mouth and cheek, anterior two-thirds of the tongue, lower teeth, skin of the lower jaw, side of the head and scalp and meninges of the anterior and middle cranial fossae.
	GO:0036486	ventral trunk neural crest cell migration	The movement of trunk neural crest cells from the neural tube, travelling ventrally through the anterior half of each sclerotome. Trunk neural crest cells that remain in the sclerotome form the dorsal root ganglia containing the sensory neurons. Trunk neural crest cells that continue more ventrally form the sympathetic ganglia, the adrenal medulla, and the nerve clusters surrounding the aorta.
cellular component
	GO:0030424	axon	The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
	GO:0030425	dendrite	A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (7, 7)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (44, 44)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File