Annotations: 9J4C

Cryo-EM structure of aPlexinA1-19-43 Fab in complex with PlexinA1 dimer

External Resource: Annotation

SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth L]	Light Chain	IGKV4	Kappa	plexin-a1	SAbDab (2026-07-10)
C [auth H]	Heavy Chain	IGHV1	-	plexin-a1	SAbDab (2026-07-10)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	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	PF24479	Plexin A/B, PSI domain (PSI_PlexinA-B)	Plexin A/B, PSI domain	This entry represents a PSI domain found in Plexin A, B and related proteins. These are neuronal receptors for the axon guidance regulators Semaphorins. Semaphorin-plexin interactions play central roles in regulating processes such as neuronal axon g ...	This entry represents a PSI domain found in Plexin A, B and related proteins. These are neuronal receptors for the axon guidance regulators Semaphorins. Semaphorin-plexin interactions play central roles in regulating processes such as neuronal axon guidance, angiogenesis and immune responses [1,2].	Domain
A	PF01403	Sema domain (Sema)	Sema domain	-	Repeat
A	PF17960	TIG domain (TIG_plexin)	TIG domain	This entry represents an TIG or IPT domain (Ig domain shared by Plexins and Transcription factors) found in plexins [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Plexin-A1	molecular transducer activity transmembrane signaling receptor activity signaling receptor activity semaphorin receptor activity	regulation of biological process regulation of cell motility regulation of cellular process regulation of locomotion regulation of cell migration biological regulation cellular process cell migration cell motility locomotion multicellular organismal process cellular developmental process cell projection organization plasma membrane bounded cell projection morphogenesis regulation of biological process regulation of cell motility regulation of cellular process regulation of locomotion regulation of cell migration biological regulation cellular process cell migration cell motility locomotion multicellular organismal process 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 nervous system development generation of neurons anatomical structure morphogenesis neuron projection guidance neuron development animal gross anatomical part developmental process gonadotrophin-releasing hormone neuronal migration to the hypothalamus hypothalamus development forebrain development central nervous system neuron development central nervous system neuron differentiation hypothalamus cell differentiation hypothalamus gonadotrophin-releasing hormone neuron development limbic system development head development neuron migration forebrain generation of neurons hypothalamus gonadotrophin-releasing hormone neuron differentiation animal organ development brain development diencephalon development forebrain neuron development central nervous system development hypothalamic tangential migration using cell-axon interactions forebrain neuron differentiation hypothalamus cell migration cellular response to stimulus cell surface receptor signaling pathway response to stimulus semaphorin-plexin signaling pathway signaling cell communication signal transduction olfactory nerve development cranial nerve formation cranial nerve morphogenesis olfactory nerve morphogenesis olfactory nerve formation nerve development cranial nerve development anatomical structure formation involved in morphogenesis cellular component biogenesis cell junction organization cellular component assembly cell junction assembly synapse organization synapse assembly 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	extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane protein-containing complex semaphorin receptor complex extracellular exosome membrane-bounded organelle extracellular vesicle cellular anatomical structure extracellular organelle extracellular region organelle vesicle extracellular membrane-bounded organelle cell periphery plasma membrane membrane protein-containing complex semaphorin receptor complex signaling receptor complex synapse cell junction glutamatergic synapse
B [auth L]	Light chain of aPlexinA1-19-43 Fab	-	-	-
C [auth H]	Heavy chain of aPlexinA1-19-43 Fab	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR042744	Plexin-A1, Sema domain	Domain
A	IPR002909	IPT domain	Domain
A	IPR041362	Plexin, TIG domain 2	Domain
A	IPR016201	PSI domain	Domain
A	IPR014756	Immunoglobulin E-set	Homologous Superfamily
A	IPR008936	Rho GTPase activation protein	Homologous Superfamily
A	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A	IPR002165	Plexin repeat	Repeat
A	IPR041019	Plexin, TIG domain 1	Domain
A	IPR031148	Plexin family	Family
A	IPR046800	Plexin, cytoplasmic RhoGTPase-binding domain	Domain
A	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
A	IPR013548	Plexin, cytoplasmic RasGAP domain	Domain
A	IPR036352	Sema domain superfamily	Homologous Superfamily
A	IPR001627	Sema domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A	: Q9UIW2	gastric carcinoma malignant mesothelioma pancreatic ductal adenocarcinoma transitional cell carcinoma juvenile dermatomyositis osteosarcoma pancreatic intraductal papillary-mucinous neoplasm ulcerative colitis lung carcinoma ovarian cancer Pick disease

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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.