3NE5 | pdb_00003ne5

Crystal structure of the CusBA heavy-metal efflux complex from Escherichia coli

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B [auth C]	SCOP2B Superfamily	Single hybrid motif	8092212	3001880	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	Single hybrid motif	8092212	3001880	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	HlyD C-terminal domain-like	8092213	3002572	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	HlyD beta-barrel domain-like	8092211	3002000	SCOP2B (2022-06-29)
B [auth C]	SCOP2B Superfamily	HlyD beta-barrel domain-like	8092211	3002000	SCOP2B (2022-06-29)
A [auth B]	SCOP2 Family	HlyD-like secretion proteins	8045801	4003003	SCOP2 (2022-06-29)
A [auth B]	SCOP2 Superfamily	HlyD beta-barrel domain-like	8092211	3002000	SCOP2 (2022-06-29)
A [auth B]	SCOP2 Superfamily	Single hybrid motif	8092212	3001880	SCOP2 (2022-06-29)
A [auth B]	SCOP2 Superfamily	HlyD C-terminal domain-like	8092213	3002572	SCOP2 (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 [auth A]	ACR_tran_4th	e3ne5A1	A: alpha bundles	X: Multidrug efflux transporter AcrB transmembrane domain (From Topology)	H: Multidrug efflux transporter AcrB transmembrane domain (From Topology)	T: Multidrug efflux transporter AcrB transmembrane domain	F: ACR_tran_4th	ECOD (1.6)
C [auth A]	ACR_tran_3rd_1	e3ne5A4	A: a+b two layers	X: Alpha-beta plaits	H: Ferredoxin domains in multidrug efflux transporter	T: Multidrug efflux transporter AcrB pore domain	F: ACR_tran_3rd_1	ECOD (1.6)
C [auth A]	ACR_tran_1st	e3ne5A3	A: a+b two layers	X: Alpha-beta plaits	H: Ferredoxin domains in multidrug efflux transporter	T: Multidrug efflux transporter AcrB pore domain	F: ACR_tran_1st	ECOD (1.6)
C [auth A]	ACR_tran_6th	e3ne5A5	A: a+b two layers	X: Alpha-beta plaits	H: Ferredoxin domains in multidrug efflux transporter	T: Multidrug efflux transporter AcrB pore domain	F: ACR_tran_6th	ECOD (1.6)
C [auth A]	ACR_tran_5th_1	e3ne5A6	A: a+b two layers	X: Alpha-beta plaits	H: Ferredoxin domains in multidrug efflux transporter	T: Multidrug efflux transporter AcrB pore domain	F: ACR_tran_5th_1	ECOD (1.6)
C [auth A]	ACR_tran_6th_1	e3ne5A7	A: a+b two layers	X: Alpha-beta plaits	H: Ferredoxin domains in multidrug efflux transporter	T: Multidrug efflux transporter AcrB TolC docking domain	F: ACR_tran_6th_1	ECOD (1.6)
B [auth C]	PRK15030_2nd	e3ne5C2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: PRK15030_2nd	ECOD (1.6)
B [auth C]	HlyD_D23_C	e3ne5C3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: HlyD_D23_C	ECOD (1.6)
B [auth C]	HlyD_D4	e3ne5C4	A: alpha bundles	X: Helical bundle domain in CusB (From Topology)	H: Helical bundle domain in CusB (From Topology)	T: Helical bundle domain in CusB	F: HlyD_D4	ECOD (1.6)
B [auth C]	HlyD_D23_N	e3ne5C5	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: HlyD_D23_N	ECOD (1.6)
A [auth B]	PRK15030_2nd	e3ne5B3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: PRK15030_2nd	ECOD (1.6)
A [auth B]	HlyD_D23_C	e3ne5B2	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: HlyD_D23_C	ECOD (1.6)
A [auth B]	HlyD_D4	e3ne5B4	A: alpha bundles	X: Helical bundle domain in CusB (From Topology)	H: Helical bundle domain in CusB (From Topology)	T: Helical bundle domain in CusB	F: HlyD_D4	ECOD (1.6)
A [auth B]	HlyD_D23_N	e3ne5B1	A: a+b complex topology	X: alpha/beta-Hammerhead/Barrel-sandwich hybrid	H: alpha/beta-Hammerhead/Barrel-sandwich hybrid	T: Single hybrid motif	F: HlyD_D23_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth C]	2.40.420.20	Mainly Beta	Beta Barrel	conserved putative lor/sdh protein from methanococcus maripaludis s2 fold		CATH (4.2.0)
B [auth C]	2.40.30.170	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.2.0)
B [auth C]	2.40.50.100	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain	CATH (4.2.0)
B [auth C]	6.10.140.730	Special	Helix non-globular	Helix Hairpins		CATH (4.2.0)
A [auth B]	2.40.420.20	Mainly Beta	Beta Barrel	conserved putative lor/sdh protein from methanococcus maripaludis s2 fold		CATH (4.2.0)
A [auth B]	2.40.30.170	Mainly Beta	Beta Barrel	Elongation Factor Tu (Ef-tu)	domain 3	CATH (4.2.0)
A [auth B]	2.40.50.100	Mainly Beta	Beta Barrel	OB fold (Dihydrolipoamide Acetyltransferase, E2P)	RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain	CATH (4.2.0)
A [auth B]	6.10.140.730	Special	Helix non-globular	Helix Hairpins		CATH (4.2.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth B], B [auth C]	PF25954	CusB-like, beta-barrel domain (Beta-barrel_RND_2)	CusB-like, 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. One characterized member is the Cation efflu ...	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. One characterized member is the Cation efflux system protein CusB which is an essential component of the CusCBA tripartite efflux system from Escherichia coli. This protein plays an essential role in bridging the inner membrane efflux pump CusA and the outer membrane channel CusC to mediate resistance to Cu+ and Ag+ ions. CusB is a multidomain protein and assembles into homohexamer that forms a narrow channel defined by an alpha-helical domain and a barrel-sandwich hybrid domain in which it is inserted [1,2]. The remaining two domains, one of which is represented by this entry, form a cap-like structure that engages in interactions with the CusA trimer. 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
A [auth B], B [auth C]	PF25919	CusB, barrel-sandwich hybrid domain (BSH_CusB)	CusB, barrel-sandwich hybrid domain	-	Family
A [auth B], B [auth C]	PF25869	CusB, three alpha-helical bundle domain (3HB_CusB)	CusB, three alpha-helical bundle domain	This domain is found in the Cation efflux system protein CusB and related proteins. CusB is an essential component of the CusCBA tripartite efflux system from Escherichia coli. This protein plays an essential role in bridging the inner membrane efflu ...	This domain is found in the Cation efflux system protein CusB and related proteins. CusB is an essential component of the CusCBA tripartite efflux system from Escherichia coli. This protein plays an essential role in bridging the inner membrane efflux pump CusA and the outer membrane channel CusC to mediate resistance to Cu+ and Ag+ ions. CusB is a multidomain protein and assembles into homohexamer that forms a narrow channel defined by the domain represented by this entry and the barrel-sandwich hybrid domain in which it is inserted [1,2]. The remaining two domains form a cap-like structure that engages in interactions with the CusA trimer. This domain is also predicted to interact with CusC [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth A]	Cation efflux system protein cusA	monoatomic cation transmembrane transporter activity copper ion transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transition metal ion transmembrane transporter activity metal ion transmembrane transporter activity transmembrane transporter activity silver ion transmembrane transporter activity cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding monoatomic cation transmembrane transporter activity copper ion transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transition metal ion transmembrane transporter activity metal ion transmembrane transporter activity transmembrane transporter activity silver ion transmembrane transporter activity cation binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding xenobiotic transmembrane transporter activity	response to stimulus response to metal ion response to chemical response to silver ion response to copper ion transport monoatomic ion transmembrane transport silver ion transport establishment of localization metal ion transport monoatomic cation transmembrane transport transmembrane transport localization silver ion transmembrane transport response to stimulus response to metal ion response to chemical response to silver ion response to copper ion transport monoatomic ion transmembrane transport silver ion transport establishment of localization metal ion transport monoatomic cation transmembrane transport transmembrane transport localization silver ion transmembrane transport transition metal ion transport monoatomic ion transport cellular process monoatomic cation transport detoxification of inorganic compound detoxification of copper ion detoxification stress response to copper ion response to toxic substance response to stress stress response to metal ion inorganic ion homeostasis homeostatic process intracellular copper ion homeostasis copper ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis copper ion transmembrane transport copper ion transport copper ion export plasma membrane copper ion transport	cellular anatomical structure membrane cell periphery plasma membrane
A [auth B], B [auth C]	Cation efflux system protein cusB	monoatomic cation transmembrane transporter activity copper ion transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transition metal ion transmembrane transporter activity metal ion transmembrane transporter activity transmembrane transporter activity cation binding transition metal ion binding ion binding binding metal ion binding small molecule binding copper ion binding	response to stimulus response to metal ion response to chemical response to silver ion response to copper ion transport monoatomic ion transmembrane transport silver ion transport establishment of localization metal ion transport monoatomic cation transmembrane transport transmembrane transport localization silver ion transmembrane transport response to stimulus response to metal ion response to chemical response to silver ion response to copper ion transport monoatomic ion transmembrane transport silver ion transport establishment of localization metal ion transport monoatomic cation transmembrane transport transmembrane transport localization silver ion transmembrane transport transition metal ion transport monoatomic ion transport cellular process monoatomic cation transport detoxification of inorganic compound detoxification of copper ion detoxification stress response to copper ion response to toxic substance response to stress stress response to metal ion inorganic ion homeostasis homeostatic process intracellular copper ion homeostasis copper ion homeostasis cellular homeostasis chemical homeostasis intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis copper ion transmembrane transport copper ion transport copper ion export plasma membrane copper ion transport	cellular anatomical structure membrane outer membrane-bounded periplasmic space cell envelope periplasmic space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth A]	IPR027463	Multidrug efflux transporter AcrB TolC docking domain, DN/DC subdomains	Homologous Superfamily
C [auth A]	IPR004763	Cation efflux system CusA-like	Family
C [auth A]	IPR001036	Acriflavin resistance protein	Family
A [auth B], B [auth C]	IPR045800	Heavy metal binding domain	Domain
A [auth B], B [auth C]	IPR051909	Membrane Fusion Protein Cation Efflux System	Family
A [auth B], B [auth C]	IPR006143	RND efflux pump, membrane fusion protein	Family
A [auth B], B [auth C]	IPR043602	CusB-like_dom_1	Unknown
A [auth B], B [auth C]	IPR032317	CusB_D23	Unknown

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A [auth B], B [auth C], C [auth A]	OPM	Transmembrane	Alpha-helical polytopic	Resistance-nodulation-cell division	Heavy metal efflux family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A [auth B], B [auth C], C [auth A]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A [auth B], B [auth C], C [auth A]	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth B], B [auth C], C [auth A]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Multi-Drug Efflux Transporters	CusBA heavy-metal efflux complex

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.

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