3H90 | pdb_00003h90

Structural basis for the autoregulation of the zinc transporter YiiP

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
Membrane Protein Annotation: OPM
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD
Membrane Protein Annotation: mpstruc

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d3h90d2	Alpha and beta proteins (a+b)	Alpha-lytic protease prodomain-like	Cation efflux protein cytoplasmic domain-like	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D	d3h90d1	Membrane and cell surface proteins and peptides	Cation efflux protein transmembrane domain-like	Cation efflux protein transmembrane domain-like	Cation efflux protein transmembrane domain-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d3h90c2	Alpha and beta proteins (a+b)	Alpha-lytic protease prodomain-like	Cation efflux protein cytoplasmic domain-like	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d3h90c1	Membrane and cell surface proteins and peptides	Cation efflux protein transmembrane domain-like	Cation efflux protein transmembrane domain-like	Cation efflux protein transmembrane domain-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d3h90b2	Alpha and beta proteins (a+b)	Alpha-lytic protease prodomain-like	Cation efflux protein cytoplasmic domain-like	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d3h90b1	Membrane and cell surface proteins and peptides	Cation efflux protein transmembrane domain-like	Cation efflux protein transmembrane domain-like	Cation efflux protein transmembrane domain-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d3h90a2	Alpha and beta proteins (a+b)	Alpha-lytic protease prodomain-like	Cation efflux protein cytoplasmic domain-like	automated matches	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d3h90a1	Membrane and cell surface proteins and peptides	Cation efflux protein transmembrane domain-like	Cation efflux protein transmembrane domain-like	Cation efflux protein transmembrane domain-like	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	Cation efflux protein transmembrane domain-like	8035909	3001720	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Cation efflux protein cytoplasmic domain-like	8035908	3000470	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cation efflux protein cytoplasmic domain-like	8035908	3000470	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cation efflux protein transmembrane domain-like	8035909	3001720	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cation efflux protein cytoplasmic domain-like	8035908	3000470	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cation efflux protein transmembrane domain-like	8035909	3001720	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cation efflux protein cytoplasmic domain-like	8035908	3000470	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cation efflux protein transmembrane domain-like	8035909	3001720	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)
D	Cation_efflux	e3h90D1	A: alpha bundles	X: Cation efflux protein transmembrane domain-like (From Topology)	H: Cation efflux protein transmembrane domain-like (From Topology)	T: Cation efflux protein transmembrane domain-like	F: Cation_efflux	ECOD (1.6)
D	ZT_dimer	e3h90D2	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: Cation efflux protein cytoplasmic domain-like (From Topology)	T: Cation efflux protein cytoplasmic domain-like	F: ZT_dimer	ECOD (1.6)
C	Cation_efflux	e3h90C1	A: alpha bundles	X: Cation efflux protein transmembrane domain-like (From Topology)	H: Cation efflux protein transmembrane domain-like (From Topology)	T: Cation efflux protein transmembrane domain-like	F: Cation_efflux	ECOD (1.6)
C	ZT_dimer	e3h90C2	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: Cation efflux protein cytoplasmic domain-like (From Topology)	T: Cation efflux protein cytoplasmic domain-like	F: ZT_dimer	ECOD (1.6)
B	Cation_efflux	e3h90B1	A: alpha bundles	X: Cation efflux protein transmembrane domain-like (From Topology)	H: Cation efflux protein transmembrane domain-like (From Topology)	T: Cation efflux protein transmembrane domain-like	F: Cation_efflux	ECOD (1.6)
B	ZT_dimer	e3h90B2	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: Cation efflux protein cytoplasmic domain-like (From Topology)	T: Cation efflux protein cytoplasmic domain-like	F: ZT_dimer	ECOD (1.6)
A	Cation_efflux	e3h90A1	A: alpha bundles	X: Cation efflux protein transmembrane domain-like (From Topology)	H: Cation efflux protein transmembrane domain-like (From Topology)	T: Cation efflux protein transmembrane domain-like	F: Cation_efflux	ECOD (1.6)
A	ZT_dimer	e3h90A2	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: Cation efflux protein cytoplasmic domain-like (From Topology)	T: Cation efflux protein cytoplasmic domain-like	F: ZT_dimer	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.20.1510.10	Mainly Alpha	Up-down Bundle	Alpha-lytic protease prodomain-like	Cation efflux protein transmembrane domain	CATH (4.3.0)
D	3.30.70.1350	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Cation efflux protein, cytoplasmic domain	CATH (4.3.0)
C	1.20.1510.10	Mainly Alpha	Up-down Bundle	Alpha-lytic protease prodomain-like	Cation efflux protein transmembrane domain	CATH (4.3.0)
C	3.30.70.1350	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Cation efflux protein, cytoplasmic domain	CATH (4.3.0)
B	1.20.1510.10	Mainly Alpha	Up-down Bundle	Alpha-lytic protease prodomain-like	Cation efflux protein transmembrane domain	CATH (4.3.0)
B	3.30.70.1350	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Cation efflux protein, cytoplasmic domain	CATH (4.3.0)
A	1.20.1510.10	Mainly Alpha	Up-down Bundle	Alpha-lytic protease prodomain-like	Cation efflux protein transmembrane domain	CATH (4.3.0)
A	3.30.70.1350	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Cation efflux protein, cytoplasmic domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF16916	Cation efflux protein, cytoplasmic domain (ZT_dimer)	Cation efflux protein, cytoplasmic domain	This entry represents the cytoplasmic domain in Cation Diffusion Facilitator (CDD) transporter proteins including zinc transporters. These proteins are involved in the transport of divalent metal cations across cellular membranes. They facilitate the ...	This entry represents the cytoplasmic domain in Cation Diffusion Facilitator (CDD) transporter proteins including zinc transporters. These proteins are involved in the transport of divalent metal cations across cellular membranes. They facilitate the efflux or sequestration of metals such as zinc, cadmium, iron, manganese, and cobalt, contributing to metal homeostasis and detoxification. These proteins often function as antiporters, coupling the transport of metal ions with protons or other ions. They play crucial roles in various biological processes, including maintaining cellular metal ion balance, protecting cells from metal toxicity, and regulating metal ion concentrations in specific cellular compartments. These proteins include subfamilies like SCL30A, which are involved in zinc transport, and FieF, which is associated with metal detoxification. This domain is the dimerisation region of the whole molecule of zinc transporters since the full-length members form a homodimer during activity. The domain lies within the cytoplasm and exhibits an overall structural similarity with the copper metallochaperone Hah1 Swissprot:O00244, exhibiting an open alpha-beta domain with two alpha helices (H1 and H2) aligned on one side and a three-stranded mixed beta-sheet (S1 to S3) on the other side. The N-terminal domain is represented by Pfam:PF01545 [1].	Domain
A, B, C, D	PF01545	Cation efflux transmembrane domain (Cation_efflux)	Cation efflux transmembrane domain	This entry represents the transmembrane domain at the N-terminal in Cation Diffusion Facilitator (CDF) transporter proteins. These proteins are involved in the transport of divalent metal cations across cellular membranes. They facilitate the efflux ...	This entry represents the transmembrane domain at the N-terminal in Cation Diffusion Facilitator (CDF) transporter proteins. These proteins are involved in the transport of divalent metal cations across cellular membranes. They facilitate the efflux or sequestration of metals such as zinc, cadmium, iron, manganese, and cobalt, contributing to metal homeostasis and detoxification. These proteins often function as antiporters, coupling the transport of metal ions with protons or other ions. They play crucial roles in various biological processes, including maintaining cellular metal ion balance, protecting cells from metal toxicity, and regulating metal ion concentrations in specific cellular compartments. These proteins include subfamilies like SLC30A, which are involved in zinc transport, and FieF, which is associated with metal detoxification. [1-2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Ferrous-iron efflux pump fieF	monoatomic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transition metal ion transmembrane transporter activity metal ion transmembrane transporter activity cadmium ion transmembrane transporter activity transmembrane transporter activity iron ion transmembrane transporter activity ferrous iron transmembrane transporter activity zinc ion transmembrane transporter activity metal cation:monoatomic cation antiporter activity proton transmembrane transporter activity zinc efflux antiporter activity secondary active transmembrane transporter activity monoatomic cation transmembrane transporter activity monoatomic ion transmembrane transporter activity transporter activity transition metal ion transmembrane transporter activity metal ion transmembrane transporter activity cadmium ion transmembrane transporter activity transmembrane transporter activity iron ion transmembrane transporter activity ferrous iron transmembrane transporter activity zinc ion transmembrane transporter activity metal cation:monoatomic cation antiporter activity proton transmembrane transporter activity zinc efflux antiporter activity secondary active transmembrane transporter activity antiporter activity zinc:proton antiporter activity metal cation:proton antiporter activity active transmembrane transporter activity cation binding ion binding binding metal ion binding small molecule binding identical protein binding protein binding	intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis transport monoatomic ion transmembrane transport iron ion transport iron ion transmembrane transport intracellular iron ion homeostasis inorganic ion homeostasis cellular homeostasis chemical homeostasis homeostatic process intracellular monoatomic cation homeostasis monoatomic ion homeostasis intracellular chemical homeostasis monoatomic cation homeostasis intracellular monoatomic ion homeostasis transport monoatomic ion transmembrane transport iron ion transport iron ion transmembrane transport establishment of localization metal ion transport monoatomic cation transmembrane transport transmembrane transport localization transition metal ion transport monoatomic ion transport cellular process monoatomic cation transport zinc ion transport zinc ion transmembrane transport cadmium ion transport cadmium ion transmembrane transport intracellular zinc ion homeostasis	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR050291	Cation-efflux pump FieF-like	Family
A, B, C, D	IPR027470	Cation efflux protein, cytoplasmic domain	Domain
A, B, C, D	IPR023783	Cation efflux pump FieF	Family
A, B, C, D	IPR036837	Cation efflux protein, cytoplasmic domain superfamily	Homologous Superfamily
A, B, C, D	IPR002524	Cation efflux	Family
A, B, C, D	IPR027469	Cation efflux transmembrane domain superfamily	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D	OPM	Transmembrane	Alpha-helical polytopic	Cation diffusion facilitator	Bacterial zinc transporters

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C, D	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C, D	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Cation Diffusion Facilitator (CDF) Family	YiiP Zinc Transporter

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.