7U6V | pdb_00007u6v

Cryo-EM structure of Shiga toxin 2 in complex with the native ribosomal P-stalk

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Bacterial enterotoxins	8097164	3000434	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Bacterial enterotoxins	8097164	3000434	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Bacterial enterotoxins	8097164	3000434	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Bacterial enterotoxins	8097164	3000434	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Bacterial enterotoxins	8097164	3000434	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribosome inactivating proteins (RIP)	8099972	3001164	SCOP2B (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	MATH_2	e7u6vC1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: MATH_2	ECOD (v294.1)
D	MATH_2	e7u6vD1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: MATH_2	ECOD (v294.1)
F	MATH_2	e7u6vF1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: MATH_2	ECOD (v294.1)
E	MATH_2	e7u6vE1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: MATH_2	ECOD (v294.1)
B	MATH_2	e7u6vB1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: MATH_2	ECOD (v294.1)
A	MATH_2	e7u6vA1	A: a/b three-layered sandwiches	X: RNase A-like	H: Cytochrome P450	T: Cytochrome P450	F: MATH_2	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, C, D, E, F	PF02258	Shiga-like toxin beta subunit (SLT_beta)	Shiga-like toxin beta subunit	This family represents the B subunit of shiga-like toxin (SLT or verotoxin) produced by some strains of E.coli associated with hemorrhagic colitis and hemolytic uremic syndrome. SLT's are composed of one enzymatic A subunit and five cell binding B su ...	This family represents the B subunit of shiga-like toxin (SLT or verotoxin) produced by some strains of E.coli associated with hemorrhagic colitis and hemolytic uremic syndrome. SLT's are composed of one enzymatic A subunit and five cell binding B subunits.	Domain
A	PF00161	Ribosome inactivating protein (RIP)	Ribosome inactivating protein		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G [auth P]	C-terminal domain (CTD) from the Ribosomal P-stalk	RNA binding binding rRNA binding nucleic acid binding large ribosomal subunit rRNA binding structural molecule activity structural constituent of ribosome	primary metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process biosynthetic process cytoplasmic translation metabolic process cellular process protein metabolic process macromolecule metabolic process ribonucleoprotein complex biogenesis organelle assembly protein-containing complex organization primary metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process biosynthetic process cytoplasmic translation metabolic process cellular process protein metabolic process macromolecule metabolic process ribonucleoprotein complex biogenesis organelle assembly protein-containing complex organization membraneless organelle assembly ribosomal large subunit biogenesis protein-RNA complex assembly cellular component biogenesis cellular component organization ribosome biogenesis organelle organization protein-RNA complex organization cellular component assembly ribosomal large subunit assembly protein-containing complex assembly cellular component organization or biogenesis ribosome assembly	90S preribosome preribosome protein-containing complex ribonucleoprotein complex intracellular anatomical structure intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic large ribosomal subunit cellular anatomical structure cytosolic ribosome organelle membraneless organelle ribosome 90S preribosome preribosome protein-containing complex ribonucleoprotein complex intracellular anatomical structure intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic large ribosomal subunit cellular anatomical structure cytosolic ribosome organelle membraneless organelle ribosome cytoplasm cytosol large ribosomal subunit
B, C, D, E, F	Shiga toxin 2a subunit B (Stx2B)	toxin activity	biological process involved in interspecies interaction between organisms symbiont-mediated cytolysis of host cell symbiont-mediated hemolysis of host erythrocyte disruption of cell in another organism cytolysis biological process involved in interaction with host biological process involved in symbiotic interaction cytolysis in another organism cellular process disruption of anatomical structure in another organism symbiont-mediated killing of host cell killing of cells of another organism cell killing	cellular anatomical structure extracellular region
A	Shiga toxin 2a subunit A (Stx2A)	hydrolase activity, acting on glycosyl bonds rRNA N-glycosylase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid hydrolase activity catalytic activity, acting on a rRNA catalytic activity RNA glycosylase activity hydrolase activity, hydrolyzing N-glycosyl compounds toxin activity	regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process regulation of cellular process negative regulation of biological process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression negative regulation of translation negative regulation of cellular process protein metabolic process negative regulation of protein metabolic process negative regulation of macromolecule metabolic process regulation of biosynthetic process regulation of biological process regulation of protein metabolic process negative regulation of metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of gene expression negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process regulation of translation negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process regulation of metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
G [auth P]	IPR043141	Large ribosomal subunit protein uL10-like domain superfamily	Homologous Superfamily
G [auth P]	IPR043164	Large ribosomal subunit protein uL10-like, insertion domain superfamily	Homologous Superfamily
G [auth P]	IPR030670	Large ribosomal subunit protein uL10, eukaryota	Family
G [auth P]	IPR001790	Large ribosomal subunit protein uL10, N-terminal	Domain
G [auth P]	IPR050323	Universal ribosomal protein uL10	Family
G [auth P]	IPR040637	Large ribosomal subunit protein uL10-like, insertion domain	Domain
B, C, D, E, F	IPR008992	Enterotoxin	Homologous Superfamily
B, C, D, E, F	IPR003189	Shiga-like toxin, beta subunit	Family
A	IPR036041	Ribosome-inactivating protein superfamily	Homologous Superfamily
A	IPR016331	Shiga-like toxin, subunit A	Family
A	IPR017988	Ribosome-inactivating protein conserved site	Conserved Site
A	IPR016139	Ribosome-inactivating protein, subdomain 2	Homologous Superfamily
A	IPR016138	Ribosome-inactivating protein, subdomain 1	Homologous Superfamily
A	IPR001574	Ribosome-inactivating protein	Family

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.