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(-) Description

Title :  STRUCTURAL BASIS FOR LIGAND BINDING AND HEPARIN MEDIATED ACTIVATION OF NEUROPILIN
 
Authors :  C. W. Vander Kooi, M. A. Jusino, B. Perman, D. B. Neau, H. D. Bellamy, D. J
Date :  05 Feb 07  (Deposition) - 03 Apr 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Neuropilin, Vegf, Tuftsin, Signaling Protein, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. W. Vander Kooi, M. A. Jusino, B. Perman, D. B. Neau, H. D. Bellamy, D. J. Leahy
Structural Basis For Ligand And Heparin Binding To Neuropilin B Domains.
Proc. Natl. Acad. Sci. Usa V. 104 6152 2007
PubMed-ID: 17405859  |  Reference-DOI: 10.1073/PNAS.0700043104

(-) Compounds

Molecule 1 - NEUROPILIN-1
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPT7HMT
    Expression System StrainROSETTA-GAMI-2
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneNRP1
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116
    SynonymVASCULAR ENDOTHELIAL CELL GROWTH FACTOR 165 RECEPTOR
 
Molecule 2 - TUFTSIN
    ChainsB
    EngineeredYES
    Other DetailsTUFTSIN PURCHASED FROM BACHEM
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2ORZ)

(-) Sites  (0, 0)

(no "Site" information available for 2ORZ)

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:275 -A:424
2A:431 -A:583

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ORZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ORZ)

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FA58C_3PS50022 Coagulation factors 5/8 type C domain (FA58C) profile.NRP1_RAT275-424
431-583
  2A:275-424
A:431-583
2FA58C_1PS01285 Coagulation factors 5/8 type C domain (FA58C) signature 1.NRP1_RAT314-343
470-502
  2A:314-343
A:470-502
3FA58C_2PS01286 Coagulation factors 5/8 type C domain (FA58C) signature 2.NRP1_RAT408-424
566-583
  2A:408-424
A:566-583

(-) Exons   (5, 5)

Asymmetric/Biological Unit (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSRNOT000000144921ENSRNOE00000327489chr19:58332004-5833208178NRP1_RAT-00--
1.2ENSRNOT000000144922ENSRNOE00000220561chr19:58333819-58334353535NRP1_RAT1-25250--
1.3ENSRNOT000000144923ENSRNOE00000102082chr19:58337959-58338133175NRP1_RAT25-83590--
1.4ENSRNOT000000144924ENSRNOE00000101380chr19:58395175-58395356182NRP1_RAT83-144620--
1.5ENSRNOT000000144925ENSRNOE00000101424chr19:58402081-58402308228NRP1_RAT144-220770--
1.6ENSRNOT000000144926ENSRNOE00000101477chr19:58408363-58408518156NRP1_RAT220-272530--
1.7ENSRNOT000000144927ENSRNOE00000102140chr19:58410608-58410774167NRP1_RAT272-327561A:274-32754
1.8ENSRNOT000000144928ENSRNOE00000102187chr19:58441293-58441448156NRP1_RAT328-379521A:328-37952
1.9ENSRNOT000000144929ENSRNOE00000101620chr19:58444926-58445070145NRP1_RAT380-428491A:380-42849
1.10ENSRNOT0000001449210ENSRNOE00000101661chr19:58453043-58453374332NRP1_RAT428-5381111A:428-538111
1.11ENSRNOT0000001449211ENSRNOE00000102243chr19:58460560-58460704145NRP1_RAT539-587491A:539-58648
1.12ENSRNOT0000001449212ENSRNOE00000102302chr19:58464604-58464708105NRP1_RAT587-622360--
1.13ENSRNOT0000001449213ENSRNOE00000102345chr19:58471240-5847129960NRP1_RAT622-642210--
1.14ENSRNOT0000001449214ENSRNOE00000102411chr19:58476649-58476786138NRP1_RAT642-688470--
1.15ENSRNOT0000001449215ENSRNOE00000102468chr19:58482042-58482313272NRP1_RAT688-778910--
1.16ENSRNOT0000001449216ENSRNOE00000102524chr19:58482746-5848284297NRP1_RAT779-811330--
1.17ENSRNOT0000001449217ENSRNOE00000102578chr19:58484904-5848495451NRP1_RAT811-828180--
1.18ENSRNOT0000001449218ENSRNOE00000220548chr19:58486868-58487681814NRP1_RAT828-922950--

(-) Sequences/Alignments

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
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:313
 aligned with NRP1_RAT | Q9QWJ9 from UniProtKB/Swiss-Prot  Length:922

    Alignment length:313
                                   283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583   
             NRP1_RAT   274 KCMEALGMESGEIHSDQITASSQYGTNWSVERSRLNYPENGWTPGEDSYREWIQVDLGLLRFVTAVGTQGAISKETKKKYYVKTYRVDISSNGEDWITLKEGNKAIIFQGNTNPTDVVFGVFPKPLITRFVRIKPASWETGISMRFEVYGCKITDYPCSGMLGMVSGLISDSQITASNQGDRNWMPENIRLVTSRTGWALPPSPHPYINEWLQVDLGDEKIVRGVIIQGGKHRENKVFMRKFKIAYSNNGSDWKMIMDDSKRKAKSFEGNNNYDTPELRAFTPLSTRFIRIYPERATHSGLGLRMELLGCEVE 586
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2orzA01 A:274-427 Galactose-binding domain-like                                                                                                           2orzA02 A:428-586 Galactose-binding domain-like                                                                                                                 CATH domains
           Pfam domains (1) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------F5_F8_type_C-2orzA01 A:446-580                                                                                                         ------ Pfam domains (1)
           Pfam domains (2) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------F5_F8_type_C-2orzA02 A:446-580                                                                                                         ------ Pfam domains (2)
         Sec.struct. author ...ee........hhh.eee....hhhhhhhhh...................eeeeeeeeeeeeeeeee.ee......eeeeeeeeeeee......ee.ee..ee..ee........eeeeeeeeeeeeeeeeeeeeee.....eeeeeeehhhhh.........ee.hhhheeee........hhhhhh.......eee...........eeeeeeeeeeeeeeeee.eee..eee.eeeeeeeee......ee...........ee........eeeeeeeeeeeeeeeeeeee....eeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -FA58C_3  PDB: A:275-424 UniProt: 275-424                                                                                                              ------FA58C_3  PDB: A:431-583 UniProt: 431-583                                                                                                                 --- PROSITE (1)
                PROSITE (2) ----------------------------------------FA58C_1  PDB: A:314-343       ----------------------------------------------------------------FA58C_2          ---------------------------------------------FA58C_1  PDB: A:470-502          ---------------------------------------------------------------FA58C_2           --- PROSITE (2)
           Transcript 1 (1) Exon 1.7  PDB: A:274-327 UniProt: 272-327 [INCOMPLETE]Exon 1.8  PDB: A:328-379 UniProt: 328-379           ------------------------------------------------Exon 1.10  PDB: A:428-538 UniProt: 428-538                                                                     Exon 1.11  PDB: A:539-586 UniProt: 539-587       Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------------------Exon 1.9  PDB: A:380-428 UniProt: 380-428        -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript 1 (2)
                 2orz A 274 KCMEALGMESGEIHSDQITASSQYGTNWSVERSRLNYPENGWTPGEDSYREWIQVDLGLLRFVTAVGTQGAISKETKKKYYVKTYRVDISSNGEDWITLKEGNKAIIFQGNTNPTDVVFGVFPKPLITRFVRIKPASWETGISMRFEVYGCKITDYPCSGMLGMVSGLISDSQITASNQGDRNWMPENIRLVTSRTGWALPPSPHPYINEWLQVDLGDEKIVRGVIIQGGKHRENKVFMRKFKIAYSNNGSDWKMIMDDSKRKAKSFEGNNNYDTPELRAFTPLSTRFIRIYPERATHSGLGLRMELLGCEVE 586
                                   283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583   

Chain B from PDB  Type:PROTEIN  Length:3
                                   
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 2orz B   2 KPR   4

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2ORZ)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: GBD (153)

(-) Gene Ontology  (90, 90)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NRP1_RAT | Q9QWJ9)
molecular function
    GO:0019838    growth factor binding    Interacting selectively and non-covalently with any growth factor, proteins or polypeptides that stimulate a cell or organism to grow or proliferate.
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0017154    semaphorin receptor activity    Combining with a semaphorin, and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity.
    GO:0038085    vascular endothelial growth factor binding    Interacting selectively and non-covalently with a vascular endothelial growth factor.
    GO:0005021    vascular endothelial growth factor-activated receptor activity    Combining with a vascular endothelial growth factor (VEGF) and transmitting the signal across the plasma membrane to initiate a change in cell activity.
biological process
    GO:0038190    VEGF-activated neuropilin signaling pathway    A series of molecular signals initiated by the binding of vascular endothelial growth factor (VEGF) to a neuropilin protein on the surface of a target cell, followed by transmission of the signal, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:1902378    VEGF-activated neuropilin signaling pathway involved in axon guidance    Any VEGF-activated neuropilin signaling pathway that is involved in axon guidance.
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0060978    angiogenesis involved in coronary vascular morphogenesis    Blood vessel formation in the heart when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0009887    animal organ morphogenesis    Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    GO:0048844    artery morphogenesis    The process in which the anatomical structures of arterial blood vessels are generated and organized. Arteries are blood vessels that transport blood from the heart to the body and its organs.
    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:0001569    branching involved in blood vessel morphogenesis    The process of coordinated growth and sprouting of blood vessels giving rise to the organized vascular system.
    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:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0002042    cell migration involved in sprouting angiogenesis    The orderly movement of endothelial cells into the extracellular matrix in order to form new blood vessels involved in sprouting angiogenesis.
    GO:0035729    cellular response to hepatocyte growth factor stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hepatocyte growth factor stimulus.
    GO:0035924    cellular response to vascular endothelial growth factor stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a vascular endothelial growth factor stimulus.
    GO:0071679    commissural neuron axon guidance    The process in which the migration of an axon growth cone of a commissural neuron is directed to its target in the brain in response to a combination of attractive and repulsive cues.
    GO:0060982    coronary artery morphogenesis    The process in which the anatomical structures of coronary arteries are generated and organized. Coronary arteries are blood vessels that transport blood to the heart muscle.
    GO:0016358    dendrite development    The process whose specific outcome is the progression of the dendrite over time, from its formation to the mature structure. 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:1904835    dorsal root ganglion morphogenesis    The developmental process by which a dorsal root ganglion is generated and organized.
    GO:0035767    endothelial cell chemotaxis    The directed movement of an endothelial cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    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:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0048012    hepatocyte growth factor receptor signaling pathway    The series of molecular signals generated as a consequence of the hepatocyte growth factor receptor binding to one of its physiological ligands.
    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: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:2001237    negative regulation of extrinsic apoptotic signaling pathway    Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway.
    GO:0043524    negative regulation of neuron apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons.
    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:0048666    neuron development    The process whose specific outcome is the progression of a neuron over time, from initial commitment of the cell to a specific fate, to the fully functional differentiated cell.
    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:0043049    otic placode formation    The initial developmental process that will lead to the formation of the vertebrate inner ear. The otic placode forms as a thickening of the head ectoderm adjacent to the developing hindbrain.
    GO:0048008    platelet-derived growth factor receptor signaling pathway    The series of molecular signals generated as a consequence of a platelet-derived growth factor receptor binding to one of its physiological ligands.
    GO:0050918    positive chemotaxis    The directed movement of a motile cell or organism towards a higher concentration of a chemical.
    GO:0070374    positive regulation of ERK1 and ERK2 cascade    Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the ERK1 and ERK2 cascade.
    GO:0048842    positive regulation of axon extension involved in axon guidance    Any process that activates, maintains or increases the frequency, rate or extent of axon extension involved in axon guidance.
    GO:0050731    positive regulation of peptidyl-tyrosine phosphorylation    Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
    GO:1902336    positive regulation of retinal ganglion cell axon guidance    Any process that activates or increases the frequency, rate or extent of retinal ganglion cell axon guidance.
    GO:1902946    protein localization to early endosome    A process in which a protein is transported to, or maintained in, a location within an early endosome.
    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:0090259    regulation of retinal ganglion cell axon guidance    Any process that modulates the frequency, rate, or extent of retinal ganglion cell axon guidance, the process in which the migration of an axon growth cone of a retinal ganglion cell (RGC) is directed to its target in the brain in response to a combination of attractive and repulsive cues.
    GO:0061441    renal artery morphogenesis    The process in which the anatomical structure of a renal artery is generated and organized. Renal arteries supply the kidneys with blood.
    GO:0009611    response to wounding    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to the organism.
    GO:0061299    retina vasculature morphogenesis in camera-type eye    The process in which the vasculature of the retina is generated and organized.
    GO:0031290    retinal ganglion cell axon guidance    The process in which the migration of an axon growth cone of a retinal ganglion cell (RGC) is directed to its target in the brain in response to a combination of attractive and repulsive cues.
    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:0097374    sensory neuron axon guidance    The process in which the migration of an axon growth cone of a sensory neuron is directed to a specific target site in response to a combination of attractive and repulsive cues. A sensory neuron is an afferent neuron conveying sensory impulses.
    GO:0002040    sprouting angiogenesis    The extension of new blood vessels from existing capillaries into avascular tissues resulting from the proliferation of blood vessel endothelial cells.
    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:0048485    sympathetic nervous system development    The process whose specific outcome is the progression of the sympathetic nervous system over time, from its formation to the mature structure. The sympathetic nervous system is one of the two divisions of the vertebrate autonomic nervous system (the other being the parasympathetic nervous system). The sympathetic preganglionic neurons have their cell bodies in the thoracic and lumbar regions of the spinal cord and connect to the paravertebral chain of sympathetic ganglia. Innervate heart and blood vessels, sweat glands, viscera and the adrenal medulla. Most sympathetic neurons, but not all, use noradrenaline as a post-ganglionic neurotransmitter.
    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:1901998    toxin transport    The directed movement of a toxin into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    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:0021636    trigeminal nerve morphogenesis    The process in which the anatomical structure of the trigeminal nerve is generated and organized. 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: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:0048010    vascular endothelial growth factor receptor signaling pathway    Any series of molecular signals initiated by the binding of an extracellular ligand to a vascular endothelial growth factor receptor (VEGFR) located on the surface of the receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0038084    vascular endothelial growth factor signaling pathway    A series of molecular signals initiated by the binding of a vascular endothelial growth factor (VEGF) to a receptor on the surface of the target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    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.
    GO:0021649    vestibulocochlear nerve structural organization    The process that contributes to the act of creating the structural organization of the vestibulocochlear nerve. This process pertains to the physical shaping of a rudimentary structure. This sensory nerve innervates the membranous labyrinth of the inner ear. The vestibular branch innervates the vestibular apparatus that senses head position changes relative to gravity. The auditory branch innervates the cochlear duct, which is connected to the three bony ossicles which transduce sound waves into fluid movement in the cochlea.
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:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005769    early endosome    A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
    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.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0030426    growth cone    The migrating motile tip of a growing nerve cell axon or dendrite.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005883    neurofilament    A type of intermediate filament found in the core of neuronal axons. Neurofilaments are heteropolymers composed of three type IV polypeptides: NF-L, NF-M, and NF-H (for low, middle, and high molecular weight). Neurofilaments are responsible for the radial growth of an axon and determine axonal diameter.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0097443    sorting endosome    A multivesicular body surrounded by and connected with multiple tubular compartments with associated vesicles.

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