1TF5 | pdb_00001tf5

Crystal structure of SecA in an open conformation from Bacillus Subtilis

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1tf5a1	All alpha proteins	Pre-protein crosslinking domain of SecA	Pre-protein crosslinking domain of SecA	Pre-protein crosslinking domain of SecA	Pre-protein crosslinking domain of SecA	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d1tf5a2	All alpha proteins	Helical scaffold and wing domains of SecA	Helical scaffold and wing domains of SecA	Helical scaffold and wing domains of SecA	Helical scaffold and wing domains of SecA	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d1tf5a4	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	Translocation ATPase SecA, nucleotide-binding domains, C-terminal domain	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d1tf5a3	Alpha and beta proteins (a/b)	P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	Tandem AAA-ATPase domain	Translocation ATPase SecA, nucleotide-binding domains, N-terminal domain	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)
A	d1tf5a5	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Bacillus subtilis ) [TaxId: 1423 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Pre-protein crosslinking domain of SecA	8027780	4002337	SCOP2 (2022-06-29)
A	SCOP2 Family	Helical scaffold and wing domains of SecA	8027781	4002486	SCOP2 (2022-06-29)
A	SCOP2 Family	Tandem AAA-ATPase domain	8027784	4000282	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Pre-protein crosslinking domain of SecA	8040159	3001119	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Helical scaffold and wing domains of SecA	8040160	3001322	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RecA-like P-loop NTPases	8040163	3002019	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	RecA-like P-loop NTPases	8040165	3002019	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)
A	SecA_PP_bind	e1tf5A1	A: alpha arrays	X: Pre-protein crosslinking domain of SecA (From Topology)	H: Pre-protein crosslinking domain of SecA (From Topology)	T: Pre-protein crosslinking domain of SecA	F: SecA_PP_bind	ECOD (1.6)
A	SecA_SW	e1tf5A2	A: alpha complex topology	X: Helical scaffold and wing domains of SecA (From Topology)	H: Helical scaffold and wing domains of SecA (From Topology)	T: Helical scaffold and wing domains of SecA	F: SecA_SW	ECOD (1.6)
A	SecA_DEAD	e1tf5A3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: SecA_DEAD	ECOD (1.6)
A	Helicase_C_10	e1tf5A4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: Helicase_C_10	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
A	3.90.1440.10	Alpha Beta	Alpha-Beta Complex	Pre-protein croslinking domain of SecA	SecA, preprotein cross-linking domain	CATH (4.3.0)
A	1.10.3060.10	Mainly Alpha	Orthogonal Bundle	Helical scaffold and wing domains of SecA	Helical scaffold and wing domains of SecA	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01043	SecA preprotein cross-linking domain (SecA_PP_bind)	SecA preprotein cross-linking domain	The SecA ATPase is involved in the insertion and retraction of preproteins through the plasma membrane. This domain has been found to cross-link to preproteins, thought to indicate a role in preprotein binding. The pre-protein cross-linking domai ...	The SecA ATPase is involved in the insertion and retraction of preproteins through the plasma membrane. This domain has been found to cross-link to preproteins, thought to indicate a role in preprotein binding. The pre-protein cross-linking domain is comprised of two sub domains that are inserted within the ATPase domain [1].	Domain
A	PF07517	SecA DEAD-like domain (SecA_DEAD)	SecA DEAD-like domain	SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane. SecA protein achieves this translocation, in association with SecY protein, in an ATP dependent manner [1,2]. This dom ...	SecA protein binds to the plasma membrane where it interacts with proOmpA to support translocation of proOmpA through the membrane. SecA protein achieves this translocation, in association with SecY protein, in an ATP dependent manner [1,2]. This domain represents the N-terminal ATP-dependent helicase domain, which is related to the Pfam:PF00270 [3].	Domain
A	PF07516	SecA Wing and Scaffold domain (SecA_SW)	SecA Wing and Scaffold domain	-	Family
A	PF21090	SecA P-loop domain (P-loop_SecA)	SecA P-loop domain	SecA is the preprotein translocase ATPase subunit and a superfamily 2 (SF2) RNA helicase [4]. This entry corresponds to the second P-loop domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Preprotein translocase secA subunit	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding protein transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity protein transmembrane transporter activity protein-transporting ATPase activity protein-exporting ATPase activity ATP-dependent activity macromolecule transmembrane transporter activity active transmembrane transporter activity transporter activity transmembrane transporter activity cation binding metal ion binding	protein localization protein import establishment of protein localization cellular localization nitrogen compound transport transport establishment of localization localization protein transport cellular macromolecule localization macromolecule localization cellular process protein targeting intracellular protein transmembrane transport protein localization protein import establishment of protein localization cellular localization nitrogen compound transport transport establishment of localization localization protein transport cellular macromolecule localization macromolecule localization cellular process protein targeting intracellular protein transmembrane transport intracellular transport transmembrane transport protein transmembrane transport establishment of localization in cell intracellular protein transport protein transport by the Sec complex	cell periphery cellular anatomical structure plasma membrane membrane membrane microdomain membrane raft protein-containing complex cell envelope Sec protein transport complex intracellular protein-containing complex intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR011130	SecA, preprotein cross-linking domain	Domain
A	IPR011116	SecA Wing/Scaffold	Domain
A	IPR036266	SecA, Wing/Scaffold superfamily	Homologous Superfamily
A	IPR001650	Helicase, C-terminal domain-like	Domain
A	IPR000185	Protein translocase subunit SecA	Family
A	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A	IPR004027	SEC-C motif	Conserved Site
A	IPR014018	SecA motor DEAD	Domain
A	IPR020937	SecA conserved site	Conserved Site
A	IPR011115	SecA DEAD-like, N-terminal	Domain
A	IPR044722	SecA, C-terminal helicase domain	Domain
A	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A	IPR036670	SecA, preprotein cross-linking domain superfamily	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A	OPM	Monotopic/peripheral	Alpha/Beta monotopic/peripheral	P-loop containing nucleoside triphosphate hydrolases	Tandem RecA ATPase-like

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.