3DIN

Crystal structure of the protein-translocation complex formed by the SecY channel and the SecA ATPase

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
A	d3dina1	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	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
A	d3dina2	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	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
A	d3dina3	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	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
A	d3dina4	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	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
E [auth B]	d3dinb1	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	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
E [auth B]	d3dinb2	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	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
E [auth B]	d3dinb3	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	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
E [auth B]	d3dinb4	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	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
B [auth C]	d3dinc_	Membrane and cell surface proteins and peptides	Preprotein translocase SecY subunit	Preprotein translocase SecY subunit	Preprotein translocase SecY subunit	Preprotein translocase SecY subunit	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
F	d3dinf_	Membrane and cell surface proteins and peptides	Preprotein translocase SecY subunit	Preprotein translocase SecY subunit	Preprotein translocase SecY subunit	Preprotein translocase SecY subunit	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
C [auth D]	d3dind_	Membrane and cell surface proteins and peptides	Single transmembrane helix	Preprotein translocase SecE subunit	Preprotein translocase SecE subunit	Preprotein translocase SecE subunit	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
G	d3ding_	Membrane and cell surface proteins and peptides	Single transmembrane helix	Preprotein translocase SecE subunit	Preprotein translocase SecE subunit	Preprotein translocase SecE subunit	(Thermotoga maritima MSB8 ) [TaxId: 243274 ],	SCOPe (2.08)
D [auth E]	d3dine_	Membrane and cell surface proteins and peptides	Transmembrane helix hairpin	Sec-beta or SecG subunit of protein translocation channel	SecG subunit	SecG	(Thermotoga sp. RQ2 ) [TaxId: 126740 ],	SCOPe (2.08)
H	d3dinh_	Membrane and cell surface proteins and peptides	Transmembrane helix hairpin	Sec-beta or SecG subunit of protein translocation channel	SecG subunit	SecG	(Thermotoga sp. RQ2 ) [TaxId: 126740 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth D]	SCOP2B Superfamily	Protein translocase subunit SecE-like	8053306	3002174	SCOP2B (2022-06-29)
G	SCOP2 Family	Protein translocase subunit SecE-like	8047941	4005885	SCOP2 (2022-06-29)
G	SCOP2 Superfamily	Protein translocase subunit SecE-like	8053306	3002174	SCOP2 (2022-06-29)
D [auth E]	SCOP2B Superfamily	Preprotein translocase subunit SecG-like	8053305	3002175	SCOP2B (2022-06-29)
H	SCOP2 Family	Preprotein translocase, SecG subunit -like	8044986	4004237	SCOP2 (2022-06-29)
H	SCOP2 Superfamily	Preprotein translocase subunit SecG-like	8053305	3002175	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	e3dinA8	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	e3dinA4	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	e3dinA7	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	e3dinA1	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)
E [auth B]	SecA_PP_bind	e3dinB8	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)
E [auth B]	SecA_SW	e3dinB2	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)
E [auth B]	SecA_DEAD	e3dinB7	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)
E [auth B]	Helicase_C_10	e3dinB4	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)
B [auth C]	SecY	e3dinC2	A: alpha complex topology	X: Preprotein translocase SecY subunit (From Topology)	H: Preprotein translocase SecY subunit (From Topology)	T: Preprotein translocase SecY subunit	F: SecY	ECOD (1.6)
F	SecY	e3dinF2	A: alpha complex topology	X: Preprotein translocase SecY subunit (From Topology)	H: Preprotein translocase SecY subunit (From Topology)	T: Preprotein translocase SecY subunit	F: SecY	ECOD (1.6)
C [auth D]	SecE	e3dinD1	A: extended segments	X: Preprotein translocase SecE subunit (From Topology)	H: Preprotein translocase SecE subunit (From Topology)	T: Preprotein translocase SecE subunit	F: SecE	ECOD (1.6)
G	SecE	e3dinG1	A: extended segments	X: Preprotein translocase SecE subunit (From Topology)	H: Preprotein translocase SecE subunit (From Topology)	T: Preprotein translocase SecE subunit	F: SecE	ECOD (1.6)
D [auth E]	SecG	e3dinE1	A: alpha bundles	X: Protein-export membrane protein secG (From Topology)	H: Protein-export membrane protein secG (From Topology)	T: Protein-export membrane protein secG	F: SecG	ECOD (1.6)
H	SecG	e3dinH1	A: alpha bundles	X: Protein-export membrane protein secG (From Topology)	H: Protein-export membrane protein secG (From Topology)	T: Protein-export membrane protein secG	F: SecG	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, E [auth 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, E [auth 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, E [auth B]	PF07516	SecA Wing and Scaffold domain (SecA_SW)	SecA Wing and Scaffold domain	-	Family
A, E [auth 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
B [auth C], F	PF00344	SecY (SecY)	SecY	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, E [auth B]	Protein translocase subunit secA	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	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 protein-containing complex cell envelope Sec protein transport complex intracellular protein-containing complex intracellular anatomical structure cytoplasm
B [auth C], F	Preprotein translocase subunit SecY	macromolecule transmembrane transporter activity protein transporter activity protein transmembrane transporter activity transporter activity transmembrane transporter activity signal sequence binding binding peptide binding	protein localization establishment of protein localization cellular localization nitrogen compound transport transport protein transport by the Sec complex establishment of localization transmembrane transport localization protein transmembrane transport protein transport cellular macromolecule localization macromolecule localization cellular process protein localization establishment of protein localization cellular localization nitrogen compound transport transport protein transport by the Sec complex establishment of localization transmembrane transport localization protein transmembrane transport protein transport cellular macromolecule localization macromolecule localization cellular process protein targeting SRP-dependent cotranslational protein targeting to membrane establishment of localization in cell cotranslational protein targeting to membrane establishment of protein localization to endoplasmic reticulum protein localization to endoplasmic reticulum establishment of protein localization to membrane intracellular protein transmembrane transport intracellular transport localization within membrane protein localization to membrane protein targeting to membrane establishment of protein localization to organelle protein localization to organelle SRP-dependent cotranslational protein targeting to membrane, translocation intracellular protein transport protein targeting to ER	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex cell envelope Sec protein transport complex intracellular protein-containing complex
C [auth D], G	Preprotein translocase subunit secE	macromolecule transmembrane transporter activity protein transporter activity protein transmembrane transporter activity transporter activity transmembrane transporter activity	protein localization establishment of protein localization cellular localization nitrogen compound transport transport protein transport by the Sec complex establishment of localization transmembrane transport localization protein transmembrane transport protein transport cellular macromolecule localization macromolecule localization cellular process protein localization establishment of protein localization cellular localization nitrogen compound transport transport protein transport by the Sec complex establishment of localization transmembrane transport localization protein transmembrane transport protein transport cellular macromolecule localization macromolecule localization cellular process protein targeting secretion establishment of protein localization to extracellular region export from cell protein secretion protein localization to extracellular region secretion by cell intracellular protein transmembrane transport intracellular transport establishment of localization in cell intracellular protein transport	cell periphery cellular anatomical structure plasma membrane membrane
D [auth E], H	Preprotein translocase subunit SecG	macromolecule transmembrane transporter activity active transmembrane transporter activity protein transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity protein transmembrane transporter activity protein-transporting ATPase activity transporter activity transmembrane transporter activity ATP-dependent activity	protein localization establishment of protein localization cellular localization nitrogen compound transport transport protein transport by the Sec complex establishment of localization transmembrane transport localization protein transmembrane transport protein transport cellular macromolecule localization macromolecule localization cellular process protein localization establishment of protein localization cellular localization nitrogen compound transport transport protein transport by the Sec complex establishment of localization transmembrane transport localization protein transmembrane transport protein transport cellular macromolecule localization macromolecule localization cellular process secretion establishment of protein localization to extracellular region export from cell protein secretion protein localization to extracellular region secretion by cell intracellular protein transmembrane transport intracellular transport establishment of localization in cell intracellular protein transport	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, E [auth B]	IPR011130	SecA, preprotein cross-linking domain	Domain
A, E [auth B]	IPR011116	SecA Wing/Scaffold	Domain
A, E [auth B]	IPR036266	SecA, Wing/Scaffold superfamily	Homologous Superfamily
A, E [auth B]	IPR001650	Helicase, C-terminal domain-like	Domain
A, E [auth B]	IPR000185	Protein translocase subunit SecA	Family
A, E [auth B]	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A, E [auth B]	IPR014018	SecA motor DEAD	Domain
A, E [auth B]	IPR020937	SecA conserved site	Conserved Site
A, E [auth B]	IPR011115	SecA DEAD-like, N-terminal	Domain
A, E [auth B]	IPR044722	SecA, C-terminal helicase domain	Domain
A, E [auth B]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, E [auth B]	IPR036670	SecA, preprotein cross-linking domain superfamily	Homologous Superfamily
B [auth C], F	IPR002208	SecY/SEC61-alpha family	Family
B [auth C], F	IPR030659	SecY conserved site	Conserved Site
B [auth C], F	IPR026593	Protein translocase subunit SecY	Family
B [auth C], F	IPR023201	SecY domain superfamily	Homologous Superfamily
C [auth D], G	IPR005807	SecE subunit of protein translocation complex, bacterial-like	Family
C [auth D], G	IPR001901	Protein translocase complex, SecE/Sec61-gamma subunit	Family
C [auth D], G	IPR038379	SecE superfamily	Homologous Superfamily
D [auth E], H	IPR004692	Preprotein translocase SecG subunit	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B [auth C], C [auth D], D [auth E], E [auth B] A, B [auth C], C [auth D], D [auth E], E [auth B], F, G, H	OPM	Transmembrane	Alpha-helical polytopic	General secretory pathway (Sec)	Protein translocase

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B [auth C], C [auth D], D [auth E], E [auth B] A, B [auth C], C [auth D], D [auth E], E [auth B], F, G, H	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B [auth C], C [auth D], D [auth E], E [auth B] A, B [auth C], C [auth D], D [auth E], E [auth B], F, G, H	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B [auth C], C [auth D], D [auth E], E [auth B] A, B [auth C], C [auth D], D [auth E], E [auth B], F, G, H	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Sec, Translocase, and Insertase Proteins	SecYEG translocon in complex with SecA