Annotations: 6VXK

Cryo-EM Structure of the full-length A39R/PlexinC1 complex

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
D	MIF4G	e6vxkD1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)
B	Cas9_a	e6vxkB01	A: beta barrels	X: Histone-like	H: all-alpha NTP pyrophosphatases	T: Hypothetical protein AF_0060	F: Cas9_a	ECOD (v294.2)
A	Glyco_transf_34	e6vxkA1	A: beta barrels	X: Tail specific protease helical domain	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: Glyco_transf_34	ECOD (v294.2)
C	C1-set	e6vxkC1	A: beta barrels	X: Tail specific protease helical domain	H: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	T: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	F: C1-set	ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (utative)
C	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D	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
B, D	PF01833	IPT/TIG domain (TIG)	IPT/TIG domain	This family consists of a domain that has an immunoglobulin like fold. These domains are found in cell surface receptors such as Met and Ron as well as in intracellular transcription factors where it is involved in DNA binding. CAUTION: This family d ...	This family consists of a domain that has an immunoglobulin like fold. These domains are found in cell surface receptors such as Met and Ron as well as in intracellular transcription factors where it is involved in DNA binding. CAUTION: This family does not currently recognise a significant number of members.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, D	Plexin-C1	protein binding binding signaling receptor binding molecular transducer activity transmembrane signaling receptor activity signaling receptor activity semaphorin receptor activity	multicellular organismal process positive regulation of nervous system development axonogenesis regulation of cellular process cell projection organization regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development positive regulation of developmental process multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation multicellular organismal process positive regulation of nervous system development axonogenesis regulation of cellular process cell projection organization regulation of cell differentiation regulation of neurogenesis neuron projection development regulation of cell development positive regulation of developmental process multicellular organism development cell projection morphogenesis neuron differentiation neuron projection morphogenesis cell differentiation anatomical structure development positive regulation of cell projection organization system development developmental process regulation of biological process regulation of cell projection organization positive regulation of cell development nervous system development generation of neurons positive regulation of multicellular organismal process regulation of neuron projection development regulation of cellular component organization positive regulation of cellular component organization cellular developmental process regulation of developmental process plasma membrane bounded cell projection morphogenesis positive regulation of biological process cell development cell morphogenesis cellular component organization regulation of nervous system development neurogenesis positive regulation of cell differentiation regulation of axonogenesis positive regulation of neurogenesis regulation of multicellular organismal process cellular component organization or biogenesis positive regulation of axonogenesis regulation of anatomical structure morphogenesis positive regulation of cellular process regulation of multicellular organismal development plasma membrane bounded cell projection organization biological regulation axon development cell morphogenesis involved in neuron differentiation anatomical structure morphogenesis neuron development cellular process regulation of plasma membrane bounded cell projection organization cellular component disassembly regulation of synapse pruning cell junction disassembly synapse pruning regulation of synapse organization cell junction organization regulation of synapse structure or activity synapse organization regulation of biological quality regulation of cell motility regulation of locomotion regulation of cell migration cell migration cell motility locomotion regulation of cell shape regulation of cell morphogenesis cellular response to stimulus cell surface receptor signaling pathway response to stimulus semaphorin-plexin signaling pathway signaling cell communication signal transduction cell adhesion cellular component biogenesis cellular component assembly cell junction assembly synapse assembly regulation of cell adhesion negative regulation of cellular process negative regulation of biological process negative regulation of cell adhesion	cellular anatomical structure membrane cell periphery plasma membrane protein-containing complex semaphorin receptor complex signaling receptor complex cerebellar climbing fiber to Purkinje cell synapse neuron to neuron synapse synapse cell junction asymmetric synapse glutamatergic synapse excitatory synapse cellular anatomical structure membrane cell periphery plasma membrane protein-containing complex semaphorin receptor complex signaling receptor complex cerebellar climbing fiber to Purkinje cell synapse neuron to neuron synapse synapse cell junction asymmetric synapse glutamatergic synapse excitatory synapse asymmetric, glutamatergic, excitatory synapse
A, C	Semaphorin-like protein 139	cell adhesion molecule binding protein-containing complex binding protein binding binding integrin binding signaling receptor binding molecular function activator activity molecular function regulator activity signaling receptor regulator activity chemorepellent activity receptor ligand activity signaling receptor activator activity semaphorin receptor binding	cellular response to stimulus regulation of biological process integrin-mediated signaling pathway regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation cell communication cellular process signal transduction semaphorin-plexin signaling pathway positive regulation of locomotion regulation of cell motility cellular response to stimulus regulation of biological process integrin-mediated signaling pathway regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling biological regulation cell communication cellular process signal transduction semaphorin-plexin signaling pathway positive regulation of locomotion regulation of cell motility positive regulation of biological process positive regulation of cell migration regulation of locomotion positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion positive regulation of cellular process	cell periphery cellular anatomical structure plasma membrane membrane extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, D	IPR002909	IPT domain	Domain
B, D	IPR016201	PSI domain	Domain
B, D	IPR008936	Rho GTPase activation protein	Homologous Superfamily
B, D	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
B, D	IPR002165	Plexin repeat	Repeat
B, D	IPR041853	Plexin-C1, Sema domain	Domain
B, D	IPR031148	Plexin family	Family
B, D	IPR046800	Plexin, cytoplasmic RhoGTPase-binding domain	Domain
B, D	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B, D	IPR013548	Plexin, cytoplasmic RasGAP domain	Domain
B, D	IPR036352	Sema domain superfamily	Homologous Superfamily
B, D	IPR001627	Sema domain	Domain
A, C	IPR036352	Sema domain superfamily	Homologous Superfamily
A, C	IPR001627	Sema domain	Domain
A, C	IPR027231	Semaphorin	Family
A, C	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, D	: O60486	endometriosis pancreatic ductal adenocarcinoma Sjogren syndrome adrenal cortex carcinoma chronic obstructive pulmonary disease Endometrioma glioblastoma invasive ductal breast carcinoma malignant mesothelioma osteosarcoma psoriasis tuberculosis atypical teratoid rhabdoid tumor Crohn disease head and neck cancer endometriosis pancreatic ductal adenocarcinoma Sjogren syndrome adrenal cortex carcinoma chronic obstructive pulmonary disease Endometrioma glioblastoma invasive ductal breast carcinoma malignant mesothelioma osteosarcoma psoriasis tuberculosis atypical teratoid rhabdoid tumor Crohn disease head and neck cancer large cell medulloblastoma malignant pancreatic neoplasm ovarian cancer sarcoidosis ulcerative colitis B-cell chronic lymphocytic leukemia diabetes mellitus gastric carcinoma interstitial cystitis lung cancer medulloblastoma

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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.