Entry Database : PDB / ID : 2qqm Structure visualization Downloads & linksTitle Crystal Structure of the a2b1b2 Domains from Human Neuropilin-1 ComponentsNeuropilin-1 Details Keywords SIGNALING PROTEIN / VEGF receptor / semaphorin receptor / calcium-binding domain / Angiogenesis / Developmental protein / Differentiation / Glycoprotein / Heparan sulfate / Membrane / Neurogenesis / Proteoglycan / Secreted / Transmembrane / HORMONEFunction / homology Function and homology informationFunction Domain/homology Component
endothelial tip cell fate specification / basal dendrite development / protein localization to early endosome / otic placode development / basal dendrite arborization / dichotomous subdivision of terminal units involved in salivary gland branching / retina vasculature morphogenesis in camera-type eye / regulation of vascular endothelial growth factor receptor signaling pathway / vestibulocochlear nerve structural organization / dorsal root ganglion morphogenesis ... endothelial tip cell fate specification / basal dendrite development / protein localization to early endosome / otic placode development / basal dendrite arborization / dichotomous subdivision of terminal units involved in salivary gland branching / retina vasculature morphogenesis in camera-type eye / regulation of vascular endothelial growth factor receptor signaling pathway / vestibulocochlear nerve structural organization / dorsal root ganglion morphogenesis / ventral trunk neural crest cell migration / sympathetic neuron projection guidance / facioacoustic ganglion development / trigeminal ganglion development / neurofilament / postsynapse organization / trigeminal nerve structural organization / sensory neuron axon guidance / facial nerve structural organization / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / branchiomotor neuron axon guidance / renal artery morphogenesis / axon extension involved in axon guidance / VEGF-activated neuropilin signaling pathway / negative regulation of axon extension involved in axon guidance / sympathetic neuron projection extension / vascular endothelial growth factor binding / Neurophilin interactions with VEGF and VEGFR / endothelial cell chemotaxis / motor neuron migration / axonogenesis involved in innervation / sympathetic ganglion development / neural crest cell migration involved in autonomic nervous system development / positive regulation of axon extension involved in axon guidance / CHL1 interactions / vascular endothelial growth factor receptor activity / regulation of vesicle-mediated transport / Signaling by ROBO receptors / angiogenesis involved in coronary vascular morphogenesis / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / neuropilin signaling pathway / coronary artery morphogenesis / hepatocyte growth factor receptor signaling pathway / substrate-dependent cell migration, cell extension / outflow tract septum morphogenesis / semaphorin receptor activity / CRMPs in Sema3A signaling / commissural neuron axon guidance / semaphorin receptor complex / cell migration involved in sprouting angiogenesis / axonal fasciculation / regulation of Cdc42 protein signal transduction / motor neuron axon guidance / sprouting angiogenesis / neural crest cell migration / positive regulation of filopodium assembly / artery morphogenesis / retinal ganglion cell axon guidance / branching involved in blood vessel morphogenesis / positive regulation of cell migration involved in sprouting angiogenesis / cellular response to hepatocyte growth factor stimulus / positive chemotaxis / cytokine binding / positive regulation of smooth muscle cell migration / growth factor binding / sorting endosome / positive regulation of focal adhesion assembly / semaphorin-plexin signaling pathway / platelet-derived growth factor receptor signaling pathway / Sema3A PAK dependent Axon repulsion / cellular response to vascular endothelial growth factor stimulus / vasculogenesis / coreceptor activity / vascular endothelial growth factor receptor signaling pathway / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / positive regulation of endothelial cell proliferation / positive regulation of endothelial cell migration / GTPase activator activity / Signal transduction by L1 / integrin-mediated signaling pathway / mitochondrial membrane / negative regulation of extrinsic apoptotic signaling pathway / animal organ morphogenesis / axon guidance / neuron migration / response to wounding / positive regulation of angiogenesis / positive regulation of peptidyl-tyrosine phosphorylation / cell-cell signaling / heparin binding / cytoplasmic vesicle / postsynaptic membrane / angiogenesis / negative regulation of neuron apoptotic process / Attachment and Entry / positive regulation of ERK1 and ERK2 cascade / early endosome / receptor complex / symbiont entry into host cell Similarity search - Function Spermadhesin, CUB domain / Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / MAM domain signature. / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Coagulation factors 5/8 type C domain (FA58C) signature 2. ... Spermadhesin, CUB domain / Neuropilin / Neuropilin, C-terminal / C-terminal domain of neuropilin glycoprotein / MAM domain signature. / Domain in meprin, A5, receptor protein tyrosine phosphatase mu (and others) / MAM domain, meprin/A5/mu / MAM domain / MAM domain profile. / Coagulation factors 5/8 type C domain (FA58C) signature 2. / Coagulation factors 5/8 type C domain (FA58C) signature 1. / CUB domain / Domain first found in C1r, C1s, uEGF, and bone morphogenetic protein. / CUB domain / CUB domain profile. / Spermadhesin, CUB domain superfamily / Coagulation factor 5/8 C-terminal domain, discoidin domain / Coagulation factors 5/8 type C domain (FA58C) profile. / F5/8 type C domain / Coagulation factor 5/8 C-terminal domain / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta Similarity search - Domain/homologyBiological species Homo sapiens (human)Method X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution : 2 Å DetailsAuthors Appleton, B.A. / Wiesmann, C. CitationJournal : Embo J. / Year : 2007Title : Structural studies of neuropilin/antibody complexes provide insights into semaphorin and VEGF bindingAuthors: Appleton, B.A. / Wu, P. / Maloney, J. / Yin, J. / Liang, W.C. / Stawicki, S. / Mortara, K. / Bowman, K.K. / Elliott, J.M. / Desmarais, W. / Bazan, J.F. / Bagri, A. / Tessier-Lavigne, M. / ... Authors : Appleton, B.A. / Wu, P. / Maloney, J. / Yin, J. / Liang, W.C. / Stawicki, S. / Mortara, K. / Bowman, K.K. / Elliott, J.M. / Desmarais, W. / Bazan, J.F. / Bagri, A. / Tessier-Lavigne, M. / Koch, A.W. / Wu, Y. / Watts, R.J. / Wiesmann, C. History Deposition Jul 26, 2007 Deposition site : RCSB / Processing site : RCSBRevision 1.0 Nov 20, 2007 Provider : repository / Type : Initial releaseRevision 1.1 Jul 13, 2011 Group : Advisory / Version format complianceRevision 2.0 Oct 25, 2017 Group : Atomic model / Derived calculations / Refinement descriptionCategory : atom_site / pdbx_struct_assembly_gen ... atom_site / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / software / struct_conn / struct_site_gen Item : _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ... _atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.occupancy / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_site_gen.auth_asym_id / _struct_site_gen.auth_seq_id / _struct_site_gen.label_asym_id Revision 3.0 Jul 29, 2020 Group : Atomic model / Data collection ... Atomic model / Data collection / Database references / Derived calculations / Structure summary Category : atom_site / chem_comp ... atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen Item : _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ... _atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details Description : Carbohydrate remediation / Provider : repository / Type : RemediationRevision 3.1 Aug 30, 2023 Group : Data collection / Database references ... Data collection / Database references / Refinement description / Structure summary Category : chem_comp / chem_comp_atom ... chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item : _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
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