Annotations: 6WTS

CryoEM structure of the C. sordellii lethal toxin TcsL in complex with SEMA6A

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Sema domain-like	8100498	3000180	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Plexin repeat-like	8101126	3000415	SCOP2B (2022-06-29)
A	SCOP2 Family	Sema domain-like	8100497	4000934	SCOP2 (2022-06-29)
A	SCOP2 Family	Plexin repeat-like	8101125	4001807	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Sema domain-like	8100498	3000180	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Plexin repeat-like	8101126	3000415	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	CARD	e6wtsC01	A: alpha arrays	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: CARD	ECOD (v295.2)
B	Tubulin_C	e6wtsB1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Tubulin_C	ECOD (v295.2)
A	Tubulin_C	e6wtsA1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Tubulin_C	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (utative)
B	3.30.1680.10	Alpha Beta	2-Layer Sandwich	ligand-binding face of the semaphorins, domain 2	ligand-binding face of the semaphorins, domain 2	CATH (utative)
A	2.130.10.10	Mainly Beta	7 Propeller	Methylamine Dehydrogenase	Chain H	CATH (utative)
A	3.30.1680.10	Alpha Beta	2-Layer Sandwich	ligand-binding face of the semaphorins, domain 2	ligand-binding face of the semaphorins, domain 2	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	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, B	PF01403	Sema domain (Sema)	Sema domain	-	Repeat

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C	TcsL	glycosyltransferase activity transferase activity catalytic activity binding lipid binding toxin activity cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity cation binding ion binding metal ion binding small molecule binding	proteolysis metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process	cellular anatomical structure extracellular region host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane other organism part host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part host cell endosome host intracellular region cellular anatomical structure extracellular region host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane other organism part host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part host cell endosome host intracellular region host cell plasma membrane host cell cytosol
A, B	SEMA6A	protein binding binding semaphorin receptor 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	developmental process anatomical structure morphogenesis anatomical structure development animal organ development animal organ morphogenesis animal gross anatomical part developmental process multicellular organismal process regulation of sprouting angiogenesis regulation of developmental process negative regulation of biological process angiogenesis regulation of vasculature development multicellular organism development tube morphogenesis developmental process anatomical structure morphogenesis anatomical structure development animal organ development animal organ morphogenesis animal gross anatomical part developmental process multicellular organismal process regulation of sprouting angiogenesis regulation of developmental process negative regulation of biological process angiogenesis regulation of vasculature development multicellular organism development tube morphogenesis regulation of multicellular organismal process regulation of anatomical structure morphogenesis blood vessel development system development regulation of multicellular organismal development regulation of biological process blood vessel morphogenesis tube development negative regulation of blood vessel morphogenesis negative regulation of developmental process biological regulation negative regulation of angiogenesis sprouting angiogenesis vasculature development circulatory system development negative regulation of vasculature development regulation of angiogenesis anatomical structure formation involved in morphogenesis negative regulation of multicellular organismal process negative regulation of sprouting angiogenesis cellular process apoptotic process cell death programmed cell death positive regulation of locomotion regulation of cell motility regulation of cellular process cellular developmental process positive regulation of biological process regulation of neuron migration positive regulation of cell migration neurogenesis cell differentiation positive regulation of cell motility regulation of cell migration cell migration cell motility locomotion positive regulation of cellular process neuron migration nervous system development generation of neurons regulation of locomotion positive regulation of neuron migration cellular response to stimulus response to stimulus signaling negative regulation of signaling negative regulation of intracellular signal transduction regulation of signal transduction intracellular signal transduction negative regulation of cell communication cell communication regulation of intracellular signal transduction intracellular signaling cassette negative regulation of cellular process signal transduction regulation of signaling negative regulation of response to stimulus regulation of MAPK cascade negative regulation of signal transduction negative regulation of ERK1 and ERK2 cascade regulation of response to stimulus MAPK cascade regulation of cell communication ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade negative regulation of MAPK cascade stem cell development neural crest cell differentiation neural crest cell development cell development mesenchyme development tissue development mesenchymal cell migration stem cell differentiation ameboidal-type cell migration mesenchymal cell differentiation neural crest cell migration cell adhesion involved in sprouting angiogenesis negative regulation of cell adhesion cell adhesion angiogenic sprout fusion regulation of cell adhesion negative regulation of cell adhesion involved in sprouting angiogenesis cellular component organization organelle organization cellular component organization or biogenesis cytoskeleton organization cell surface receptor signaling pathway semaphorin-plexin signaling pathway axonogenesis cell projection organization plasma membrane bounded cell projection morphogenesis neuron projection development cell morphogenesis cell projection morphogenesis neuron differentiation neuron projection morphogenesis plasma membrane bounded cell projection organization axon guidance axon development cell morphogenesis involved in neuron differentiation neuron projection guidance neuron development cellular response to growth factor stimulus negative regulation of vascular endothelial growth factor signaling pathway negative regulation of cellular response to growth factor stimulus cell surface receptor protein tyrosine kinase signaling pathway cellular response to endogenous stimulus regulation of vascular endothelial growth factor signaling pathway enzyme-linked receptor protein signaling pathway regulation of cellular response to vascular endothelial growth factor stimulus response to endogenous stimulus regulation of cellular response to growth factor stimulus vascular endothelial growth factor signaling pathway cellular response to vascular endothelial growth factor stimulus response to growth factor negative regulation of cellular response to vascular endothelial growth factor stimulus	cellular anatomical structure membrane cell periphery plasma membrane axon cell projection neuron projection plasma membrane bounded cell projection

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR038383	CGT/MARTX, cysteine protease (CPD) domain superfamily	Homologous Superfamily
C	IPR024772	TcdA/TcdB toxin, N-terminal helical domain	Domain
C	IPR020974	CGT/MARTX, cysteine protease (CPD) domain	Domain
C	IPR024769	TcdA/TcdB toxin, pore forming domain	Domain
C	IPR029044	Nucleotide-diphospho-sugar transferases	Homologous Superfamily
C	IPR024770	TcdA/TcdB toxin, catalytic glycosyltransferase domain	Domain
C	IPR018337	Cell wall/choline-binding repeat	Repeat
A, B	IPR016201	PSI domain	Domain
A, B	IPR027231	Semaphorin	Family
A, B	IPR015943	WD40/YVTN repeat-like-containing domain superfamily	Homologous Superfamily
A, B	IPR002165	Plexin repeat	Repeat
A, B	IPR036352	Sema domain superfamily	Homologous Superfamily
A, B	IPR001627	Sema domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	: Q9H2E6	oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm psoriasis adrenal cortex carcinoma atypical teratoid rhabdoid tumor Crohn disease granulomatosis with polyangiitis lung adenocarcinoma malignant colon neoplasm nasopharyngeal carcinoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia ulcerative colitis astrocytic tumor breast cancer oligodendroglioma pancreatic intraductal papillary-mucinous neoplasm psoriasis adrenal cortex carcinoma atypical teratoid rhabdoid tumor Crohn disease granulomatosis with polyangiitis lung adenocarcinoma malignant colon neoplasm nasopharyngeal carcinoma osteosarcoma pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia ulcerative colitis astrocytic tumor breast cancer ductal breast carcinoma in situ invasive ductal breast carcinoma lung carcinoma malignant ependymoma non-small cell lung carcinoma ovarian cancer primitive neuroectodermal tumor atopic eczema breast carcinoma glioblastoma large cell medulloblastoma lymphoplasmacytic lymphoma 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.