9V55 | pdb_00009v55

Structure of TolC, YbjP, and AcrA complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
AMR Gene: CARD Annotation
AMR Gene Family: CARD Annotation
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 [auth C3]	SCOP2B Superfamily	Outer membrane efflux proteins (OEP)	8037933	3000246	SCOP2B (2022-06-29)
B [auth C2]	SCOP2B Superfamily	Outer membrane efflux proteins (OEP)	8037933	3000246	SCOP2B (2022-06-29)
A [auth C1]	SCOP2B Superfamily	Outer membrane efflux proteins (OEP)	8037933	3000246	SCOP2B (2022-06-29)

AMR Gene: CARD Annotation CARD Database Homepage

Chains	Accession	Short Name	Description	Provenance Source (Version)
A [auth C1], B [auth C2], C [auth C3]	ARO:3000237	TolC	TolC is a protein subunit of many multidrug efflux complexes in Gram negative bacteria. It is an outer membrane efflux protein and is constitutively open. Regulation of efflux activity is often at its periplasmic entrance by other components of the efflux complex.	CARD (4.0.1)
G [auth A1], H [auth A2], I [auth A3], J [auth a2], K [auth a1], G [auth A1], H [auth A2], I [auth A3], J [auth a2], K [auth a1], L [auth a3]	ARO:3004043	Escherichia coli acrA	AcrA is a subunit of the AcrAB-TolC multidrug efflux system found in E. coli.	CARD (4.0.1)

AMR Gene Family: CARD Annotation CARD Database Homepage

Chains	Accession	Gene Family	Drug Class	Resistance Machanism	Provenance Source (Version)
A [auth C1], B [auth C2], C [auth C3]	ARO:0010004	resistance-nodulation-cell division (RND) antibiotic efflux pump	macrolide antibiotic, fluoroquinolone antibiotic, aminoglycoside antibiotic, carbapenem, cephalosporin, glycylcycline, penicillin beta-lactam, tetracycline antibiotic, peptide antibiotic, aminocoumarin antibiotic, rifamycin antibiotic, phenicol antibiotic, disinfecting agents and antiseptics	antibiotic efflux	CARD (4.0.1)
A [auth C1], B [auth C2], C [auth C3]	ARO:0010004	resistance-nodulation-cell division (RND) antibiotic efflux pump	macrolide antibiotic, fluoroquinolone antibiotic, aminoglycoside antibiotic, carbapenem, cephalosporin, glycylcycline, penicillin beta-lactam, tetracycline antibiotic, peptide antibiotic, aminocoumarin antibiotic, rifamycin antibiotic, phenicol antibiotic, disinfecting agents and antiseptics	antibiotic efflux	CARD (4.0.1)
G [auth A1], H [auth A2], I [auth A3], J [auth a2], K [auth a1], G [auth A1], H [auth A2], I [auth A3], J [auth a2], K [auth a1], L [auth a3]	ARO:0010004	resistance-nodulation-cell division (RND) antibiotic efflux pump	fluoroquinolone antibiotic, cephalosporin, glycylcycline, penicillin beta-lactam, tetracycline antibiotic, rifamycin antibiotic, phenicol antibiotic, disinfecting agents and antiseptics	antibiotic efflux	CARD (4.0.1)
G [auth A1], H [auth A2], I [auth A3], J [auth a2], K [auth a1], G [auth A1], H [auth A2], I [auth A3], J [auth a2], K [auth a1], L [auth a3]	ARO:0010004	resistance-nodulation-cell division (RND) antibiotic efflux pump	fluoroquinolone antibiotic, cephalosporin, glycylcycline, penicillin beta-lactam, tetracycline antibiotic, rifamycin antibiotic, phenicol antibiotic, disinfecting agents and antiseptics	antibiotic efflux	CARD (4.0.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth C1], B [auth C2], C [auth C3]	PF02321	Outer membrane efflux protein (OEP)	Outer membrane efflux protein	-	Family
D [auth P1], E [auth P2], F [auth P3]	PF12883	Protein of unknown function (DUF3828) (DUF3828)	Protein of unknown function (DUF3828)	This is a family of bacterial proteins of unknown function.	Domain
G [auth A1], H [auth A2], I [auth A3], J [auth a2], K [auth a1], G [auth A1], H [auth A2], I [auth A3], J [auth a2], K [auth a1], L [auth a3]	PF25876	RND MFP, alpha-helical hairpin domain (HH_MFP_RND)	RND MFP, alpha-helical hairpin domain	This domain is found in the periplasmic membrane fusion proteins (MFPs) that are components of the RND tripartite drug efflux pumps. MFPs bridge the outer membrane factor and an inner membrane transporter. The most characterized MFP AcrA connects the ...	This domain is found in the periplasmic membrane fusion proteins (MFPs) that are components of the RND tripartite drug efflux pumps. MFPs bridge the outer membrane factor and an inner membrane transporter. The most characterized MFP AcrA connects the outer membrane factor TolC and the resistance- nodulation-division-type efflux transporter AcrB, which is a major multidrug efflux pump in Escherichia coli [1]. The alpha -helical hairpin domain of AcrA shows conformational flexibility, which has potential mechanistic significance in coupling between AcrA conformations and TolC channel opening [1].	Domain
G [auth A1], H [auth A2], I [auth A3], J [auth a2], K [auth a1], G [auth A1], H [auth A2], I [auth A3], J [auth a2], K [auth a1], L [auth a3]	PF25917	RND MFP, barrel-sandwich hybrid domain (BSH_RND)	RND MFP, barrel-sandwich hybrid domain	This domain is found in the periplasmic membrane fusion proteins (MFPs) that are components of the RND tripartite drug efflux pumps. MFPs bridge the outer membrane factor and an inner membrane transporter. The most characterized MFP AcrA connects the ...	This domain is found in the periplasmic membrane fusion proteins (MFPs) that are components of the RND tripartite drug efflux pumps. MFPs bridge the outer membrane factor and an inner membrane transporter. The most characterized MFP AcrA connects the outer membrane factor TolC and the resistance-nodulation-division-type efflux transporter AcrB, which is a major multidrug efflux pump in Escherichia coli [1]. The barrel-sandwich hybrid domain is an important structural feature found in membrane fusion proteins. This domain plays a crucial role in the assembly and function of tripartite drug efflux systems [2]. It is involved in interactions with the other components of the RND pumps.	Domain
G [auth A1], H [auth A2], I [auth A3], J [auth a2], K [auth a1], G [auth A1], H [auth A2], I [auth A3], J [auth a2], K [auth a1], L [auth a3]	PF25967	RND MFPs, C-terminal permuted SH3 domain (RND-MFP_C)	RND MFPs, C-terminal permuted SH3 domain	This domain is found in the periplasmic membrane fusion proteins (MFPs) that are components of the RND tripartite drug efflux pumps. MFPs bridge the outer membrane factor and an inner membrane transporter. The most characterized MFP AcrA connects the ...	This domain is found in the periplasmic membrane fusion proteins (MFPs) that are components of the RND tripartite drug efflux pumps. MFPs bridge the outer membrane factor and an inner membrane transporter. The most characterized MFP AcrA connects the outer membrane factor TolC and the resistance- nodulation-division-type efflux transporter AcrB, which is a major multidrug efflux pump in Escherichia coli [1]. Another member MexA, a Pseudomonas aeruginosa homolog of AcrA, is a component of the tripartite multidrug efflux system MexAB-OprM which is a major factor for antibiotic resistance by exporting a large variety of antimicrobial compounds [2]. The domain represented by this entry folds into an open barrel with a circularly permuted topology of SH3-like barrels. This domain is involved in interactions with efflux pump membrane transporter.	Domain
G [auth A1], H [auth A2], I [auth A3], J [auth a2], K [auth a1], G [auth A1], H [auth A2], I [auth A3], J [auth a2], K [auth a1], L [auth a3]	PF25944	RND MFPs, beta-barrel domain (Beta-barrel_RND)	RND MFPs, beta-barrel domain	This domain is found in the periplasmic membrane fusion proteins (MFPs) that are components of the RND tripartite drug efflux pumps. MFPs bridge the outer membrane factor and an inner membrane transporter. The most characterized MFP AcrA connects the ...	This domain is found in the periplasmic membrane fusion proteins (MFPs) that are components of the RND tripartite drug efflux pumps. MFPs bridge the outer membrane factor and an inner membrane transporter. The most characterized MFP AcrA connects the outer membrane factor TolC and the resistance- nodulation-division-type efflux transporter AcrB, which is a major multidrug efflux pump in Escherichia coli [1,2]. The domain represented in this entry folds into a six-stranded closed beta-barrel with a greek-key topology which has a structural similarity to the C-terminal domain of alanine racemase. This domain is interrupted by the barrel-sandwich hybrid domain which is inserted after the first beta-strand of the barrel. This model does not include the N-terminal strand.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth C1], B [auth C2], C [auth C3]	Outer membrane protein TolC	wide pore channel activity passive transmembrane transporter activity channel activity porin activity transporter activity transmembrane transporter activity lipid transporter activity lipid transmembrane transporter activity monocarboxylic acid transmembrane transporter activity carboxylic acid transmembrane transporter activity bile acid transmembrane transporter activity monoatomic ion channel activity monoatomic ion transmembrane transporter activity efflux transmembrane transporter activity wide pore channel activity passive transmembrane transporter activity channel activity porin activity transporter activity transmembrane transporter activity lipid transporter activity lipid transmembrane transporter activity monocarboxylic acid transmembrane transporter activity carboxylic acid transmembrane transporter activity bile acid transmembrane transporter activity monoatomic ion channel activity monoatomic ion transmembrane transporter activity efflux transmembrane transporter activity identical protein binding protein binding binding enterobactin transmembrane transporter activity siderophore-iron transmembrane transporter activity iron chelate transmembrane transporter activity	response to stimulus response to chemical response to xenobiotic stimulus xenobiotic transport transport detoxification export across cell outer membrane xenobiotic detoxification by transmembrane export across the cell outer membrane establishment of localization response to toxic substance transmembrane transport localization cellular process response to antibiotic response to stimulus response to chemical response to xenobiotic stimulus xenobiotic transport transport detoxification export across cell outer membrane xenobiotic detoxification by transmembrane export across the cell outer membrane establishment of localization response to toxic substance transmembrane transport localization cellular process response to antibiotic monoatomic ion transmembrane transport monoatomic ion transport organic anion transport carboxylic acid transport lipid localization bile acid and bile salt transport lipid transport organic hydroxy compound transport organic acid transport monocarboxylic acid transport macromolecule localization siderophore transport iron ion transport metal ion transport enterobactin transport transition metal ion transport monoatomic cation transport iron coordination entity transport xenobiotic export from cell xenobiotic detoxification by transmembrane export across the plasma membrane export from cell export across plasma membrane	cellular anatomical structure membrane protein-containing complex efflux pump complex transmembrane transporter complex membrane protein complex transporter complex cell periphery cell surface periplasmic side of plasma membrane plasma membrane external side of plasma membrane side of membrane MacAB-TolC complex cellular anatomical structure membrane protein-containing complex efflux pump complex transmembrane transporter complex membrane protein complex transporter complex cell periphery cell surface periplasmic side of plasma membrane plasma membrane external side of plasma membrane side of membrane MacAB-TolC complex macrolide transmembrane transporter complex cell outer membrane external encapsulating structure cell envelope outer membrane
D [auth P1], E [auth P2], F [auth P3]	Uncharacterized lipoprotein YbjP	-	-	cell periphery cellular anatomical structure plasma membrane membrane
G [auth A1], H [auth A2], I [auth A3], J [auth a2], K [auth a1], G [auth A1], H [auth A2], I [auth A3], J [auth a2], K [auth a1], L [auth a3]	Multidrug efflux pump subunit AcrA	alkane transmembrane transporter activity transporter activity transmembrane transporter activity lipid transporter activity lipid transmembrane transporter activity monocarboxylic acid transmembrane transporter activity carboxylic acid transmembrane transporter activity bile acid transmembrane transporter activity identical protein binding protein binding binding	response to stimulus response to chemical response to xenobiotic stimulus xenobiotic transport transport detoxification export across cell outer membrane xenobiotic detoxification by transmembrane export across the cell outer membrane establishment of localization response to toxic substance transmembrane transport localization cellular process organic anion transport response to stimulus response to chemical response to xenobiotic stimulus xenobiotic transport transport detoxification export across cell outer membrane xenobiotic detoxification by transmembrane export across the cell outer membrane establishment of localization response to toxic substance transmembrane transport localization cellular process organic anion transport carboxylic acid transport lipid localization lipid transport organic acid transport monocarboxylic acid transport fatty acid transport macromolecule localization alkane transport response to antibiotic bile acid and bile salt transport organic hydroxy compound transport	protein-containing complex cellular anatomical structure efflux pump complex transmembrane transporter complex membrane membrane protein complex transporter complex cell periphery plasma membrane cell surface periplasmic side of plasma membrane external side of plasma membrane side of membrane outer membrane-bounded periplasmic space protein-containing complex cellular anatomical structure efflux pump complex transmembrane transporter complex membrane membrane protein complex transporter complex cell periphery plasma membrane cell surface periplasmic side of plasma membrane external side of plasma membrane side of membrane outer membrane-bounded periplasmic space cell envelope periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth C1], B [auth C2], C [auth C3]	IPR058622	Outer membrane channel protein TolC	Family
A [auth C1], B [auth C2], C [auth C3]	IPR010130	Type I secretion outer membrane protein, TolC	Family
A [auth C1], B [auth C2], C [auth C3]	IPR051906	Outer membrane protein TolC-like	Family
A [auth C1], B [auth C2], C [auth C3]	IPR003423	Outer membrane efflux protein	Family
D [auth P1], E [auth P2], F [auth P3]	IPR024289	Domain of unknown function DUF3828	Domain
G [auth A1], H [auth A2], I [auth A3], J [auth a2], K [auth a1], G [auth A1], H [auth A2], I [auth A3], J [auth a2], K [auth a1], L [auth a3]	IPR058627	Multidrug resistance protein MdtA-like, C-terminal permuted SH3 domain	Domain
G [auth A1], H [auth A2], I [auth A3], J [auth a2], K [auth a1], G [auth A1], H [auth A2], I [auth A3], J [auth a2], K [auth a1], L [auth a3]	IPR006143	RND efflux pump, membrane fusion protein	Family
G [auth A1], H [auth A2], I [auth A3], J [auth a2], K [auth a1], G [auth A1], H [auth A2], I [auth A3], J [auth a2], K [auth a1], L [auth a3]	IPR058625	Multidrug resistance protein MdtA-like, barrel-sandwich hybrid domain	Domain
G [auth A1], H [auth A2], I [auth A3], J [auth a2], K [auth a1], G [auth A1], H [auth A2], I [auth A3], J [auth a2], K [auth a1], L [auth a3]	IPR058628	Multidrug efflux pump subunit AcrA	Family
G [auth A1], H [auth A2], I [auth A3], J [auth a2], K [auth a1], G [auth A1], H [auth A2], I [auth A3], J [auth a2], K [auth a1], L [auth a3]	IPR058626	Multidrug resistance protein MdtA-like, beta-barrel domain	Domain
G [auth A1], H [auth A2], I [auth A3], J [auth a2], K [auth a1], G [auth A1], H [auth A2], I [auth A3], J [auth a2], K [auth a1], L [auth a3]	IPR058624	Multidrug resistance protein MdtA-like, alpha-helical hairpin 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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.