7ML7

Structural basis for CSPG4 as a receptor for TcdB and a therapeutic target in Clostridioides difficile infection

External Resource: Annotation

Domain Annotation: SCOP2 Classification
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)
A	SCOP2B Superfamily	Nucleotide-diphospho-sugar transferases	8033597	3000077	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF12919	TcdA/TcdB catalytic glycosyltransferase domain (TcdA_TcdB)	TcdA/TcdB catalytic glycosyltransferase domain	This domain represents the N-terminal glycosyltransferase from a set of toxins found in some bacteria. This domain in TcdB glycosylates the host RhoA protein.	Domain
A	PF12918	TcdB toxin N-terminal helical domain (TcdB_N)	TcdB toxin N-terminal helical domain	This is a short helical bundle domain found associated with the catalytic domain of the TcdB toxin from C. difficile [1]. The function of this domain is unknown, but it may be involved in substrate recognition.	Domain
A	PF01473	Putative cell wall binding repeat (Choline_bind_1)	Putative cell wall binding repeat	-	Repeat
A	PF11647	Membrane Localization Domain (MLD)	Membrane Localization Domain	This is a membrane localization domain found in multiple families of bacterial toxins including all of the clostridial glucosyltransferase toxins and various MARTX toxins (multifunctional-autoprocessing RTX toxins) [1,4]. In the Pasteurella multocida ...	This is a membrane localization domain found in multiple families of bacterial toxins including all of the clostridial glucosyltransferase toxins and various MARTX toxins (multifunctional-autoprocessing RTX toxins) [1,4]. In the Pasteurella multocida toxin (PMT) C-terminal fragment, structural analysis have indicated that the C1 domain possesses a signal that leads the toxin to the cell membrane. Furthermore, the C1 domain was found to structurally resemble the phospholipid-binding domain of C. difficile toxin B [2]. Functional studies in Vibrio cholera indicate that the subdomain at the N terminus of RID (Rho-inactivation domain), homologous to the membrane targeting C1 domain of Pasteurella multocida toxin, is a conserved membrane localization domain essential for proper localization [1]. The Rho-inactivation domain (RID) of MARTX (Multifunctional Autoprocessing RTX toxin) is responsible for inactivating the Rho-family of small GTPases in Vibrio cholerae. It is a bacterial toxin that self-process by a cysteine peptidase mechanism [3]. The Vibrio cholerae RTX toxin is an autoprocessing cysteine protease whose activity is stimulated by the intracellular environment [3]. This cysteine peptidase belongs to MEROPS peptidase family G6.	Domain
A	PF11713	Peptidase C80 family (Peptidase_C80)	Peptidase C80 family	This family belongs to cysteine peptidase family C80.	Domain
A	PF12920	TcdA/TcdB pore forming domain (TcdA_TcdB_pore)	TcdA/TcdB pore forming domain	-	Family
B	PF16184	Cadherin-like (Cadherin_3)	Cadherin-like	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Toxin B	binding lipid binding toxin activity glycosyltransferase activity transferase activity glucosyltransferase activity hexosyltransferase activity catalytic activity cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity cation binding ion binding binding lipid binding toxin activity glycosyltransferase activity transferase activity glucosyltransferase activity hexosyltransferase activity catalytic 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	organic substance metabolic process organonitrogen compound metabolic process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	membrane cellular anatomical entity extracellular region host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane host cell cytoplasm part host intracellular organelle host cell endosome membrane host cell cytoplasm host cell part host cell endosome host intracellular region membrane cellular anatomical entity extracellular region host intracellular membrane-bounded organelle host cellular component host intracellular part host cell membrane 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
B	Chondroitin sulfate proteoglycan 4	molecular transducer activity coreceptor activity signaling receptor activity protein binding binding kinase binding enzyme binding protein kinase binding	developmental process multicellular organismal process blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development multicellular organism development anatomical structure morphogenesis tube morphogenesis anatomical structure development anatomical structure formation involved in morphogenesis blood vessel development system development developmental process multicellular organismal process blood vessel morphogenesis tube development angiogenesis vasculature development circulatory system development multicellular organism development anatomical structure morphogenesis tube morphogenesis anatomical structure development anatomical structure formation involved in morphogenesis blood vessel development system development tissue remodeling cellular response to stimulus regulation of biological process regulation of cellular process cell surface receptor signaling pathway response to stimulus signaling platelet-derived growth factor receptor signaling pathway biological regulation cell surface receptor protein tyrosine kinase signaling pathway cell communication cellular process signal transduction enzyme-linked receptor protein signaling pathway substrate-dependent cell migration cell migration cell motility positive regulation of cell communication positive regulation of signal transduction positive regulation of biological process regulation of signal transduction intracellular signal transduction positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette positive regulation of cellular process regulation of signaling positive regulation of MAPK cascade positive regulation of intracellular signal transduction regulation of MAPK cascade regulation of response to stimulus MAPK cascade regulation of cell communication positive regulation of signaling plasma membrane bounded cell projection organization ruffle organization cell projection organization plasma membrane bounded cell projection assembly ruffle assembly cellular component organization cellular component biogenesis cellular component assembly cellular component organization or biogenesis cell projection assembly cellular developmental process glial cell migration nervous system development neurogenesis gliogenesis cell differentiation regulation of protein modification process positive regulation of phosphorylation regulation of protein phosphorylation positive regulation of protein metabolic process positive regulation of cellular metabolic process peptidyl-tyrosine modification positive regulation of phosphate metabolic process regulation of primary metabolic process positive regulation of metabolic process positive regulation of peptidyl-tyrosine phosphorylation positive regulation of protein modification process organic substance metabolic process regulation of phosphate metabolic process peptidyl-amino acid modification phosphate-containing compound metabolic process positive regulation of macromolecule metabolic process protein metabolic process protein modification process phosphorus metabolic process positive regulation of protein phosphorylation organonitrogen compound metabolic process protein phosphorylation positive regulation of phosphorus metabolic process phosphorylation cellular metabolic process regulation of protein metabolic process regulation of peptidyl-tyrosine phosphorylation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process macromolecule modification metabolic process regulation of phosphorylation regulation of phosphorus metabolic process macromolecule metabolic process peptidyl-tyrosine phosphorylation regulation of metabolic process	anchoring junction cell junction cellular anatomical entity focal adhesion cell-substrate junction cell periphery apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane membrane-bounded organelle intracellular anatomical structure lytic vacuole anchoring junction cell junction cellular anatomical entity focal adhesion cell-substrate junction cell periphery apical part of cell membrane plasma membrane plasma membrane region apical plasma membrane membrane-bounded organelle intracellular anatomical structure lytic vacuole membrane-enclosed lumen vacuolar lumen vacuole intracellular membrane-bounded organelle lysosomal lumen intracellular organelle lumen intracellular organelle organelle lumen organelle cytoplasm lysosome extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space vesicle extracellular membrane-bounded organelle extracellular matrix external encapsulating structure collagen-containing extracellular matrix cell surface nucleus nucleoplasm nuclear lumen cell leading edge leading edge membrane plasma membrane bounded cell projection cell projection lamellipodium membrane cell projection membrane lamellipodium Golgi apparatus endomembrane system Golgi lumen ruffle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR038383	CGT/MARTX, cysteine protease (CPD) domain superfamily	Homologous Superfamily
A	IPR024772	TcdA/TcdB toxin, N-terminal helical domain	Domain
A	IPR020974	CGT/MARTX, cysteine protease (CPD) domain	Domain
A	IPR024769	TcdA/TcdB toxin, pore forming domain	Domain
A	IPR029044	Nucleotide-diphospho-sugar transferases	Homologous Superfamily
A	IPR020972	Dermonecrotic/RTX toxin, membrane localization domain	Domain
A	IPR024770	TcdA/TcdB toxin, catalytic glycosyltransferase domain	Domain
A	IPR018337	Cell wall/choline-binding repeat	Repeat
B	IPR013320	Concanavalin A-like lectin/glucanase domain superfamily	Homologous Superfamily
B	IPR001791	Laminin G domain	Domain
B	IPR039005	CSPG repeat	Repeat

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B	Pharos: Q6UVK1	astrocytic tumor hepatocellular carcinoma lung cancer malignant glioma osteosarcoma diabetes mellitus invasive ductal breast carcinoma malignant colon neoplasm medulloblastoma pilocytic astrocytoma glioblastoma lung adenocarcinoma malignant ependymoma oligodendroglioma psoriasis

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.