1JCH | pdb_00001jch

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
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	Ribonuclease domain of colicin E3	8032534	3000525	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cloacin translocation domain	8037676	3000374	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	Cloacin	e1jchA1	A: a/b three-layered sandwiches	X: Cloacin translocation domain	H: Cloacin translocation domain	T: Cloacin translocation domain	F: Cloacin	ECOD (v294.1)
A	PABP	e1jchA2	A: a/b three-layered sandwiches	X: HTH	H: PABC(PABP) domain	T: PABC(PABP) domain	F: PABP	ECOD (v294.1)
C	Cloacin	e1jchC1	A: a/b three-layered sandwiches	X: Cloacin translocation domain	H: Cloacin translocation domain	T: Cloacin translocation domain	F: Cloacin	ECOD (v294.1)
C	PABP	e1jchC2	A: a/b three-layered sandwiches	X: HTH	H: PABC(PABP) domain	T: PABC(PABP) domain	F: PABP	ECOD (v294.1)
B	RWD	e1jchB1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: RWD	ECOD (v294.1)
D	RWD	e1jchD1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: RWD	ECOD (v294.1)

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)

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 RNA binding rRNA binding nucleic acid binding ribonucleoprotein complex binding protein-containing complex binding ribosome binding lyase activity catalytic activity endonuclease activity nuclease activity catalytic activity, acting on a nucleic acid protein binding binding transmembrane transporter binding RNA binding rRNA binding nucleic acid binding ribonucleoprotein complex binding protein-containing complex binding ribosome binding lyase activity catalytic activity endonuclease activity nuclease activity catalytic activity, acting on a nucleic acid hydrolase activity, acting on ester bonds hydrolase activity tRNA 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 defense response to bacterium response to stimulus response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus 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 defense response to bacterium response to stimulus response to other organism defense response response to bacterium response to stress response to external stimulus response to external biotic stimulus response to biotic stimulus	cellular anatomical structure extracellular region intracellular anatomical structure extrachromosomal circular DNA extrachromosomal DNA
B, D	COLICIN E3 IMMUNITY PROTEIN	binding toxic substance binding	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 EC: 4.6.1 (UniProt) Search M-CSA Motif + EC 4.6.1

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.