1XPR

Structural mechanism of inhibition of the Rho transcription termination factor by the antibiotic 5a-formylbicyclomycin (FB)

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
G [auth A]	d1xpra1	All alpha proteins	LEM/SAP HeH motif	Rho N-terminal domain-like	Rho termination factor, N-terminal domain	Rho termination factor, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
G [auth A]	d1xpra2	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	Rho termination factor, RNA-binding domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
G [auth A]	d1xpra3	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	RecA protein-like (ATPase-domain)	Transcription termination factor Rho, ATPase domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
H [auth B]	d1xprb1	All alpha proteins	LEM/SAP HeH motif	Rho N-terminal domain-like	Rho termination factor, N-terminal domain	Rho termination factor, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
H [auth B]	d1xprb2	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	Rho termination factor, RNA-binding domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
H [auth B]	d1xprb3	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	RecA protein-like (ATPase-domain)	Transcription termination factor Rho, ATPase domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
I [auth C]	d1xprc1	All alpha proteins	LEM/SAP HeH motif	Rho N-terminal domain-like	Rho termination factor, N-terminal domain	Rho termination factor, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
I [auth C]	d1xprc2	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	Rho termination factor, RNA-binding domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
I [auth C]	d1xprc3	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	RecA protein-like (ATPase-domain)	Transcription termination factor Rho, ATPase domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
J [auth D]	d1xprd1	All alpha proteins	LEM/SAP HeH motif	Rho N-terminal domain-like	Rho termination factor, N-terminal domain	Rho termination factor, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
J [auth D]	d1xprd2	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	Rho termination factor, RNA-binding domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
J [auth D]	d1xprd3	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	RecA protein-like (ATPase-domain)	Transcription termination factor Rho, ATPase domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
K [auth E]	d1xpre1	All alpha proteins	LEM/SAP HeH motif	Rho N-terminal domain-like	Rho termination factor, N-terminal domain	Rho termination factor, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
K [auth E]	d1xpre2	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	Rho termination factor, RNA-binding domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
K [auth E]	d1xpre3	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	RecA protein-like (ATPase-domain)	Transcription termination factor Rho, ATPase domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
L [auth F]	d1xprf1	All alpha proteins	LEM/SAP HeH motif	Rho N-terminal domain-like	Rho termination factor, N-terminal domain	Rho termination factor, N-terminal domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
L [auth F]	d1xprf2	All beta proteins	OB-fold	Nucleic acid-binding proteins	Cold shock DNA-binding domain-like	Rho termination factor, RNA-binding domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)
L [auth F]	d1xprf3	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	RecA protein-like (ATPase-domain)	Transcription termination factor Rho, ATPase domain	(Escherichia coli ) [TaxId: 562 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
G [auth A]	SCOP2B Superfamily	RecA-like P-loop NTPases	8057376	3002019	SCOP2B (2022-06-29)
G [auth A]	SCOP2B Superfamily	Rho N-terminal domain-like	8057372	3001774	SCOP2B (2022-06-29)
G [auth A]	SCOP2B Superfamily	Nucleic acid-binding proteins	8057374	3000135	SCOP2B (2022-06-29)
H [auth B]	SCOP2B Superfamily	Nucleic acid-binding proteins	8057374	3000135	SCOP2B (2022-06-29)
H [auth B]	SCOP2B Superfamily	RecA-like P-loop NTPases	8057376	3002019	SCOP2B (2022-06-29)
H [auth B]	SCOP2B Superfamily	Rho N-terminal domain-like	8057372	3001774	SCOP2B (2022-06-29)
I [auth C]	SCOP2B Superfamily	RecA-like P-loop NTPases	8057376	3002019	SCOP2B (2022-06-29)
I [auth C]	SCOP2B Superfamily	Rho N-terminal domain-like	8057372	3001774	SCOP2B (2022-06-29)
I [auth C]	SCOP2B Superfamily	Nucleic acid-binding proteins	8057374	3000135	SCOP2B (2022-06-29)
J [auth D]	SCOP2B Superfamily	Rho N-terminal domain-like	8057372	3001774	SCOP2B (2022-06-29)
J [auth D]	SCOP2B Superfamily	RecA-like P-loop NTPases	8057376	3002019	SCOP2B (2022-06-29)
J [auth D]	SCOP2B Superfamily	Nucleic acid-binding proteins	8057374	3000135	SCOP2B (2022-06-29)
K [auth E]	SCOP2B Superfamily	RecA-like P-loop NTPases	8057376	3002019	SCOP2B (2022-06-29)
K [auth E]	SCOP2B Superfamily	Rho N-terminal domain-like	8057372	3001774	SCOP2B (2022-06-29)
K [auth E]	SCOP2B Superfamily	Nucleic acid-binding proteins	8057374	3000135	SCOP2B (2022-06-29)
L [auth F]	SCOP2B Superfamily	Rho N-terminal domain-like	8057372	3001774	SCOP2B (2022-06-29)
L [auth F]	SCOP2B Superfamily	Nucleic acid-binding proteins	8057374	3000135	SCOP2B (2022-06-29)
L [auth F]	SCOP2B Superfamily	RecA-like P-loop NTPases	8057376	3002019	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)
G [auth A]	Rho_RNA_bind	e1xprA1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Rho_RNA_bind	ECOD (1.6)
G [auth A]	Rho_N	e1xprA2	A: alpha arrays	X: LEM/SAP HeH motif-like	H: LEM/SAP HeH motif	T: LEM/SAP HeH motif	F: Rho_N	ECOD (1.6)
G [auth A]	ATP-synt_ab	e1xprA3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ATP-synt_ab	ECOD (1.6)
H [auth B]	Rho_RNA_bind	e1xprB1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Rho_RNA_bind	ECOD (1.6)
H [auth B]	Rho_N	e1xprB2	A: alpha arrays	X: LEM/SAP HeH motif-like	H: LEM/SAP HeH motif	T: LEM/SAP HeH motif	F: Rho_N	ECOD (1.6)
H [auth B]	ATP-synt_ab	e1xprB3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ATP-synt_ab	ECOD (1.6)
I [auth C]	Rho_RNA_bind	e1xprC1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Rho_RNA_bind	ECOD (1.6)
I [auth C]	Rho_N	e1xprC2	A: alpha arrays	X: LEM/SAP HeH motif-like	H: LEM/SAP HeH motif	T: LEM/SAP HeH motif	F: Rho_N	ECOD (1.6)
I [auth C]	ATP-synt_ab	e1xprC3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ATP-synt_ab	ECOD (1.6)
J [auth D]	Rho_RNA_bind	e1xprD1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Rho_RNA_bind	ECOD (1.6)
J [auth D]	Rho_N	e1xprD2	A: alpha arrays	X: LEM/SAP HeH motif-like	H: LEM/SAP HeH motif	T: LEM/SAP HeH motif	F: Rho_N	ECOD (1.6)
J [auth D]	ATP-synt_ab	e1xprD3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ATP-synt_ab	ECOD (1.6)
K [auth E]	Rho_RNA_bind	e1xprE5	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Rho_RNA_bind	ECOD (1.6)
K [auth E]	Rho_N	e1xprE6	A: alpha arrays	X: LEM/SAP HeH motif-like	H: LEM/SAP HeH motif	T: LEM/SAP HeH motif	F: Rho_N	ECOD (1.6)
K [auth E]	ATP-synt_ab	e1xprE4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ATP-synt_ab	ECOD (1.6)
L [auth F]	Rho_RNA_bind	e1xprF1	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Rho_RNA_bind	ECOD (1.6)
L [auth F]	Rho_N	e1xprF2	A: alpha arrays	X: LEM/SAP HeH motif-like	H: LEM/SAP HeH motif	T: LEM/SAP HeH motif	F: Rho_N	ECOD (1.6)
L [auth F]	ATP-synt_ab	e1xprF3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: ATP-synt_ab	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
G [auth A]	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
G [auth A]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
H [auth B]	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
H [auth B]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
I [auth C]	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
I [auth C]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
J [auth D]	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
J [auth D]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
K [auth E]	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
K [auth E]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
L [auth F]	2.40.50.140	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	Nucleic acid-binding proteins	CATH (4.3.0)
L [auth F]	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	PF00006	ATP synthase alpha/beta family, nucleotide-binding domain (ATP-synt_ab)	ATP synthase alpha/beta family, nucleotide-binding domain	This entry includes the ATP synthase alpha and beta subunits, the ATP synthase associated with flagella and the termination factor Rho.	Domain
G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	PF07498	Rho termination factor, N-terminal domain (Rho_N)	Rho termination factor, N-terminal domain	The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It it thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [1]. This domain is found to the N- ...	The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It it thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [1]. This domain is found to the N-terminus of the RNA binding domain (Pfam:PF07497).	Domain
G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	PF07497	Rho termination factor, RNA-binding domain (Rho_RNA_bind)	Rho termination factor, RNA-binding domain	The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It it thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth G], B [auth M], C [auth H], D [auth J], E [auth K], A [auth G], B [auth M], C [auth H], D [auth J], E [auth K], F [auth L]	5'-R(CPUPCPUPCPUPCPU)-3'	-	-	-
G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	Rho transcription termination factor	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity ATP-dependent activity, acting on RNA pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides RNA binding nucleic acid binding identical protein binding protein binding	cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression DNA-templated transcription termination macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process cellular biosynthetic process cellular metabolic process RNA metabolic process primary metabolic process nucleobase-containing compound biosynthetic process gene expression DNA-templated transcription termination macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process DNA-templated transcription nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process	membrane cellular anatomical entity intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	IPR011129	Cold-shock domain	Domain
G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	IPR004665	Transcription termination factor Rho	Family
G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	IPR000194	ATPase, F1/V1/A1 complex, alpha/beta subunit, nucleotide-binding domain	Domain
G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	IPR003593	AAA+ ATPase domain	Domain
G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	IPR036269	Rho termination factor, N-terminal domain superfamily	Homologous Superfamily
G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily
G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	IPR011112	Rho termination factor-like, N-terminal	Domain
G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	IPR011113	Rho termination factor, RNA-binding domain	Domain
G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], G [auth A], H [auth B], I [auth C], J [auth D], K [auth E], L [auth F]	IPR041703	Transcription termination factor Rho, ATP binding domain	Domain

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.