1NL3

CRYSTAL STRUCTURE OF THE SECA PROTEIN TRANSLOCATION ATPASE FROM MYCOBACTERIUM TUBERCULOSIS in APO FORM

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)
B	d1nl3b1	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	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
B	d1nl3b2	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	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
B	d1nl3b4	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	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
B	d1nl3b3	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	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
B	d1nl3b5	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
A	d1nl3a1	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	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
A	d1nl3a2	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	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
A	d1nl3a4	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	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
A	d1nl3a3	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	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)
A	d1nl3a5	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Mycobacterium tuberculosis ) [TaxId: 1773 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8033411	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8033410	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RecA-like P-loop NTPases	8033410	3002019	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Pre-protein crosslinking domain of SecA	8033408	3001119	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Helical scaffold and wing domains of SecA	8033409	3001322	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Helical scaffold and wing domains of SecA	8033409	3001322	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8033411	3002019	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8033410	3002019	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8033410	3002019	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Pre-protein crosslinking domain of SecA	8033408	3001119	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)
B	SecA_PP_bind	e1nl3B4	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)
B	SecA_SW	e1nl3B1	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)
B	SecA_DEAD	e1nl3B2	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)
B	Helicase_C_10	e1nl3B3	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)
A	SecA_PP_bind	e1nl3A4	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	e1nl3A1	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	e1nl3A2	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	e1nl3A3	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)
B	3.40.50.300	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	P-loop containing nucleotide triphosphate hydrolases	CATH (4.3.0)
B	3.90.1440.10	Alpha Beta	Alpha-Beta Complex	Pre-protein croslinking domain of SecA	SecA, preprotein cross-linking domain	CATH (4.3.0)
B	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)
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, B	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, B	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 do ...	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, B	PF07516	SecA Wing and Scaffold domain (SecA_SW)	SecA Wing and Scaffold domain	-	Family
A, B	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, B	PREPROTEIN TRANSLOCASE SECA 1 SUBUNIT	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 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 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 catalytic activity	protein localization protein import establishment of protein localization cellular localization nitrogen compound transport transport organic substance transport establishment of localization localization protein transport cellular macromolecule localization macromolecule localization cellular process protein targeting protein localization protein import establishment of protein localization cellular localization nitrogen compound transport transport organic substance 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	extracellular region cellular anatomical entity intracellular anatomical structure cytoplasm cytosol cell periphery plasma membrane membrane protein-containing complex cell envelope Sec protein transport complex intracellular protein-containing complex external encapsulating structure cell wall peptidoglycan-based cell wall

InterPro: Protein Family Classification InterPro Database Homepage

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

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.