Entry Database : PDB / ID : 3ol2 Structure visualization Downloads & linksTitle Receptor-ligand structure of Human Semaphorin 4D with Plexin B1. Components Details Keywords SIGNALING PROTEIN / Beta-Propeller / Signalling / ExtacellularFunction / homology Function and homology informationFunction Domain/homology Component
leukocyte aggregation / positive regulation of inhibitory synapse assembly / regulation of cell projection organization / semaphorin receptor binding / negative regulation of peptidyl-tyrosine phosphorylation / Other semaphorin interactions / semaphorin-plexin signaling pathway involved in axon guidance / negative regulation of axon extension involved in axon guidance / negative regulation of osteoblast proliferation / bone trabecula morphogenesis ... leukocyte aggregation / positive regulation of inhibitory synapse assembly / regulation of cell projection organization / semaphorin receptor binding / negative regulation of peptidyl-tyrosine phosphorylation / Other semaphorin interactions / semaphorin-plexin signaling pathway involved in axon guidance / negative regulation of axon extension involved in axon guidance / negative regulation of osteoblast proliferation / bone trabecula morphogenesis / inhibitory synapse assembly / semaphorin receptor complex / positive regulation of collateral sprouting / chemorepellent activity / semaphorin receptor activity / negative regulation of cell adhesion / RHOD GTPase cycle / Sema4D induced cell migration and growth-cone collapse / GTPase activating protein binding / Sema4D mediated inhibition of cell attachment and migration / ossification involved in bone maturation / neural crest cell migration / regulation of cytoskeleton organization / positive regulation of Rho protein signal transduction / negative chemotaxis / positive regulation of axonogenesis / regulation of dendrite morphogenesis / semaphorin-plexin signaling pathway / negative regulation of osteoblast differentiation / regulation of cell migration / GTPase activator activity / neuron projection morphogenesis / axon guidance / positive regulation of GTPase activity / G alpha (12/13) signalling events / positive regulation of peptidyl-tyrosine phosphorylation / cell migration / transmembrane signaling receptor activity / signaling receptor activity / regulation of cell shape / receptor ligand activity / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / cell adhesion / positive regulation of cell migration / intracellular signal transduction / immune response / positive regulation of protein phosphorylation / signaling receptor binding / negative regulation of apoptotic process / negative regulation of transcription by RNA polymerase II / extracellular space / extracellular region / identical protein binding / plasma membrane Similarity search - Function Semaphorin / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain / ligand-binding face of the semaphorins, domain 2 ... Semaphorin / Plexin, TIG domain 2 / TIG domain found in plexin / Plexin, TIG domain 1 / TIG domain / Plexin, cytoplasmic RhoGTPase-binding domain / Plexin cytoplasmic RhoGTPase-binding domain / Plexin, cytoplasmic RasGAP domain / Plexin cytoplasmic RasGAP domain / ligand-binding face of the semaphorins, domain 2 / ligand-binding face of the semaphorins, domain 2 / Plexin family / Plexin repeat / Plexin repeat / Sema domain / semaphorin domain / Sema domain / Sema domain superfamily / Sema domain profile. / IPT/TIG domain / ig-like, plexins, transcription factors / Rho GTPase activation protein / PSI domain / domain found in Plexins, Semaphorins and Integrins / IPT domain / Immunoglobulin / Immunoglobulin domain / YVTN repeat-like/Quinoprotein amine dehydrogenase / 7 Propeller / Methylamine Dehydrogenase; Chain H / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Immunoglobulin E-set / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / 2-Layer Sandwich / Mainly Beta / Alpha Beta Similarity search - Domain/homologyBiological species Homo sapiens (human)Method X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution : 2.99 Å DetailsAuthors Janssen, B.J.C. / Robinson, R.A. / Perez-Branguli, F. / Bell, C.H. / Mitchell, C.J. / Siebold, C. / Jones, E.Y. CitationJournal : Nature / Year : 2010Title : Structural basis of semaphorin-plexin signalling.Authors : Janssen, B.J. / Robinson, R.A. / Perez-Branguli, F. / Bell, C.H. / Mitchell, K.J. / Siebold, C. / Jones, E.Y. History Deposition Aug 25, 2010 Deposition site : RCSB / Processing site : RCSBRevision 1.0 Oct 13, 2010 Provider : repository / Type : Initial releaseRevision 1.1 Jul 13, 2011 Group : Version format complianceRevision 1.2 Jan 24, 2018 Group : Structure summary / Category : audit_author / Item : _audit_author.nameRevision 2.0 Jul 29, 2020 Group : Advisory / Atomic model ... Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary Category : atom_site / atom_site_anisotrop ... atom_site / atom_site_anisotrop / 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_validate_close_contact / 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 / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_comp_id / _struct_ref_seq_dif.details Description : Carbohydrate remediation / Provider : repository / Type : Remediation
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