1JCH

Crystal Structure of Colicin E3 in Complex with its Immunity Protein

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1jcha1	All beta proteins	Ribonuclease domain of colicin E3	Ribonuclease domain of colicin E3	Ribonuclease domain of colicin E3	Ribonuclease domain of colicin E3	(Escherichia coli str. K-12 substr. W3110 ) [TaxId: 316407 ],	SCOPe (2.08)
A	d1jcha2	All beta proteins	Cloacin translocation domain	Cloacin translocation domain	Cloacin translocation domain	Colicin E3 N-terminal domain	(Escherichia coli str. K-12 substr. W3110 ) [TaxId: 316407 ],	SCOPe (2.08)
A	d1jcha3	Coiled coil proteins	Antiparallel coiled-coil	Colicin E3 receptor domain	Colicin E3 receptor domain	Colicin E3 receptor domain	(Escherichia coli str. K-12 substr. W3110 ) [TaxId: 316407 ],	SCOPe (2.08)
C	d1jchc1	All beta proteins	Ribonuclease domain of colicin E3	Ribonuclease domain of colicin E3	Ribonuclease domain of colicin E3	Ribonuclease domain of colicin E3	(Escherichia coli str. K-12 substr. W3110 ) [TaxId: 316407 ],	SCOPe (2.08)
C	d1jchc2	All beta proteins	Cloacin translocation domain	Cloacin translocation domain	Cloacin translocation domain	Colicin E3 N-terminal domain	(Escherichia coli str. K-12 substr. W3110 ) [TaxId: 316407 ],	SCOPe (2.08)
C	d1jchc3	Coiled coil proteins	Antiparallel coiled-coil	Colicin E3 receptor domain	Colicin E3 receptor domain	Colicin E3 receptor domain	(Escherichia coli str. K-12 substr. W3110 ) [TaxId: 316407 ],	SCOPe (2.08)
B	d1jchb_	Alpha and beta proteins (a+b)	FKBP-like	Colicin E3 immunity protein	Colicin E3 immunity protein	Colicin E3 immunity protein	(Escherichia coli str. K-12 substr. W3110 ) [TaxId: 316407 ],	SCOPe (2.08)
D	d1jchd_	Alpha and beta proteins (a+b)	FKBP-like	Colicin E3 immunity protein	Colicin E3 immunity protein	Colicin E3 immunity protein	(Escherichia coli str. K-12 substr. W3110 ) [TaxId: 316407 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Cloacin translocation domain	8037676	3000374	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease domain of colicin E3	8032534	3000525	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Colicin E3 receptor domain	8037679	3001221	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribonuclease domain of colicin E3	8032534	3000525	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cloacin translocation domain	8037676	3000374	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Colicin E3 receptor domain	8037679	3001221	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Colicin E3 immunity protein	8034875	3000656	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Colicin E3 immunity protein	8034875	3000656	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)
A	Cytotoxic	e1jchA2	A: beta meanders	X: Colicin E3 ribonuclease domain-like	H: Ribonuclease domain of colicin E3 (From Topology)	T: Ribonuclease domain of colicin E3	F: Cytotoxic	ECOD (1.6)
A	Cloacin	e1jchA1	A: beta complex topology	X: Cloacin translocation domain (From Topology)	H: Cloacin translocation domain (From Topology)	T: Cloacin translocation domain	F: Cloacin	ECOD (1.6)
C	Cytotoxic	e1jchC2	A: beta meanders	X: Colicin E3 ribonuclease domain-like	H: Ribonuclease domain of colicin E3 (From Topology)	T: Ribonuclease domain of colicin E3	F: Cytotoxic	ECOD (1.6)
C	Cloacin	e1jchC1	A: beta complex topology	X: Cloacin translocation domain (From Topology)	H: Cloacin translocation domain (From Topology)	T: Cloacin translocation domain	F: Cloacin	ECOD (1.6)
B	Cloacin_immun	e1jchB1	A: a+b two layers	X: FKBP-like	H: Colicin E3 immunity protein (From Topology)	T: Colicin E3 immunity protein	F: Cloacin_immun	ECOD (1.6)
D	Cloacin_immun	e1jchD1	A: a+b two layers	X: FKBP-like	H: Colicin E3 immunity protein (From Topology)	T: Colicin E3 immunity protein	F: Cloacin_immun	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.287.620	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix Hairpins	CATH (4.3.0)
A	3.10.380.10	Alpha Beta	Roll	Ribonuclease domain of colicin e3 (Residues 456-551)	Colicin E3-like ribonuclease domain	CATH (4.3.0)
C	1.10.287.620	Mainly Alpha	Orthogonal Bundle	Helix Hairpins	Helix Hairpins	CATH (4.3.0)
C	3.10.380.10	Alpha Beta	Roll	Ribonuclease domain of colicin e3 (Residues 456-551)	Colicin E3-like ribonuclease domain	CATH (4.3.0)
B	3.10.50.20	Alpha Beta	Roll	Chitinase A	domain 3	CATH (4.3.0)
D	3.10.50.20	Alpha Beta	Roll	Chitinase A	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, C	PF06958	S-type Pyocin (Pyocin_S)	S-type Pyocin	-	Family
A, C	PF09000	Cytotoxic (Cytotoxic)	Cytotoxic	The cytotoxic domain confers cytotoxic activity to proteins, enabling the formation of nucleolytic breaks in 16S ribosomal RNA. The structure of the domain reveals a highly twisted central beta-sheet elaborated with a short N-terminal alpha-helix [1] ...	The cytotoxic domain confers cytotoxic activity to proteins, enabling the formation of nucleolytic breaks in 16S ribosomal RNA. The structure of the domain reveals a highly twisted central beta-sheet elaborated with a short N-terminal alpha-helix [1].	Domain
A, C	PF11570	Coiled-coil receptor-binding R-domain of colicin E2 (E2R135)	Coiled-coil receptor-binding R-domain of colicin E2	-	Coiled-coil
B, D	PF03513	Cloacin immunity protein (Cloacin_immun)	Cloacin immunity protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, C	COLICIN E3	protein binding binding transmembrane transporter binding ribonucleoprotein complex binding protein-containing complex binding ribosome binding endonuclease activity nuclease activity hydrolase activity, acting on ester bonds hydrolase activity catalytic activity RNA binding organic cyclic compound binding nucleic acid binding	biological process involved in interspecies interaction between organisms cellular process disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing regulation of localization negative regulation of ion transmembrane transporter activity regulation of cellular process transport negative regulation of monoatomic ion transport monoatomic ion transmembrane transport negative regulation of biological process regulation of transmembrane transporter activity biological process involved in interspecies interaction between organisms cellular process disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing regulation of localization negative regulation of ion transmembrane transporter activity regulation of cellular process transport negative regulation of monoatomic ion transport monoatomic ion transmembrane transport negative regulation of biological process regulation of transmembrane transporter activity negative regulation of transport regulation of monoatomic ion transmembrane transport negative regulation of transmembrane transport regulation of transporter activity localization negative regulation of monoatomic ion transmembrane transport negative regulation of cellular process monoatomic ion transport regulation of monoatomic ion transmembrane transporter activity regulation of biological process regulation of transport regulation of monoatomic ion transport negative regulation of transporter activity biological regulation negative regulation of molecular function establishment of localization transmembrane transport regulation of molecular function regulation of transmembrane transport response to stimulus response to other organism defense response response to external stimulus response to biotic stimulus defense response to bacterium defense response to other organism response to stress response to bacterium response to external biotic stimulus	intracellular anatomical structure extrachromosomal circular DNA cellular anatomical entity extrachromosomal DNA
B, D	COLICIN E3 IMMUNITY PROTEIN	binding toxic substance binding	cellular metabolic process metabolic process cellular process bacteriocin immunity toxin metabolic process secondary metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, C	IPR024575	Cloacin/colicin	Family
A, C	IPR009105	Colicin E3-like ribonuclease domain	Domain
A, C	IPR016128	Pyosin/cloacin translocation domain	Domain
A, C	IPR024566	Colicin, receptor domain	Domain
A, C	IPR036725	Colicin E3-like ribonuclease domain superfamily	Homologous Superfamily
A, C	IPR036302	Pyosin/cloacin translocation domain superfamily	Homologous Superfamily
B, D	IPR036528	Cloacin immunity protein superfamily	Homologous Superfamily
B, D	IPR003063	Cloacin immunity protein family	Family

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	colicin-E3 M-CSA #530	Colicin E3 kills Escherichia coli cells by binding to a surface receptor, entering the cell and inactivating protein biosynthetic machinery by ribonucleolytic cleavage of the ribosomal subunit 16S rRNA. The mechanism shows homology to ribonuclease T1.	Defined by 4 residues: ASP:A-510HIS:A-513GLU:A-517ARG:A-545 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 3.1.21 (PDB Primary Data) Search M-CSA Motif + EC 3.1.21

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.