6ITC

Structure of a substrate engaged SecA-SecY protein translocation machine

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
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
Protein Modification Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth E]	SCOP2B Superfamily	Protein translocase subunit SecE-like	8053312	3002174	SCOP2B (2022-06-29)
F [auth G]	SCOP2B Superfamily	GFP-like	8096046	3000576	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Helical scaffold and wing domains of SecA	8040160	3001322	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8040165	3002019	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Pre-protein crosslinking domain of SecA	8040159	3001119	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8040163	3002019	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	RecA-like P-loop NTPases	8040163	3002019	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)
C [auth E]	SecE	e6itcE1	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)
F [auth G]	GFP	e6itcG1	A: beta barrels	X: GFP-like (From Topology)	H: GFP-like (From Topology)	T: GFP-like	F: GFP	ECOD (1.6)
A	SecA_PP_bind	e6itcA4	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	e6itcA1	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	e6itcA2	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	e6itcA3	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 Y]	SecY	e6itcY1	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)
D [auth V]	V-set_8	e6itcV1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
E [auth B]	PRK10954	e6itcB1	A: extended segments	X: NC100 (From Topology)	H: NC100 (From Topology)	T: NC100	F: PRK10954	ECOD (1.6)
G [auth C]	V-set_12	e6itcC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
D [auth V]	Heavy Chain	IGHV1	-	protein translocase subunit secy \| protein translocase subunit sece	SAbDab (2024-04-19)
G [auth C]	Heavy Chain	IGHV1	-	green fluorescent protein \| protein translocase subunit seca	SAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C [auth E]	PF00584	SecE/Sec61-gamma subunits of protein translocation complex (SecE)	SecE/Sec61-gamma subunits of protein translocation complex	-	Family
F [auth G]	PF01353	Green fluorescent protein (GFP)	Green fluorescent protein	-	Domain
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 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	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
B [auth Y]	PF00344	SecY (SecY)	SecY	-	Family
E [auth B]	PF01389	OmpA-like transmembrane domain (OmpA_membrane)	OmpA-like transmembrane domain	The structure of OmpA transmembrane domain shows that it consists of an eight stranded beta barrel [1]. This family includes some other distantly related outer membrane proteins with low scores.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth E]	Protein 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 organic substance transport protein transport by the Sec complex establishment of localization transmembrane transport localization protein transmembrane transport protein transport cellular macromolecule localization macromolecule localization protein localization establishment of protein localization cellular localization nitrogen compound transport transport organic substance 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 plasma membrane membrane cellular anatomical entity
F [auth G]	Green fluorescent protein	-	bioluminescence cellular metabolic process metabolic process cellular process generation of precursor metabolites and energy	-
A	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 cation binding metal ion binding	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	cell periphery plasma membrane membrane cellular anatomical entity membrane microdomain membrane raft protein-containing complex cell envelope Sec protein transport complex intracellular protein-containing complex intracellular anatomical structure cytoplasm
B [auth Y]	Protein translocase subunit SecY	-	protein localization establishment of protein localization cellular localization nitrogen compound transport transport organic substance transport protein transport by the Sec complex establishment of localization transmembrane transport localization protein transmembrane transport protein transport cellular macromolecule localization macromolecule localization protein localization establishment of protein localization cellular localization nitrogen compound transport transport organic substance 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 intracellular protein transmembrane transport intracellular transport establishment of localization in cell intracellular protein transport	cell periphery plasma membrane membrane cellular anatomical entity
D [auth V]	Nanobody	-	-	-
E [auth B]	Translocating peptide	wide pore channel activity passive transmembrane transporter activity channel activity porin activity transporter activity transmembrane transporter activity monoatomic ion transmembrane transporter activity identical protein binding protein binding binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process localization transport monoatomic ion transport establishment of localization biological process involved in interspecies interaction between organisms response to other organism detection of virus response to external stimulus cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process localization transport monoatomic ion transport establishment of localization biological process involved in interspecies interaction between organisms response to other organism detection of virus response to external stimulus response to external biotic stimulus response to virus response to biotic stimulus symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction	membrane cellular anatomical entity outer membrane protein-containing complex outer membrane protein complex membrane protein complex outer membrane-bounded periplasmic space cell envelope periplasmic space pore complex cell periphery cell outer membrane external encapsulating structure
G [auth C]	Nanobody	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth E]	IPR005807	SecE subunit of protein translocation complex, bacterial-like	Family
C [auth E]	IPR001901	Protein translocase complex, SecE/Sec61-gamma subunit	Family
C [auth E]	IPR038379	SecE superfamily	Homologous Superfamily
F [auth G]	IPR000786	Green fluorescent protein, GFP	Family
F [auth G]	IPR011584	Green fluorescent protein-related	Family
F [auth G]	IPR009017	Green fluorescent protein	Homologous Superfamily
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
B [auth Y]	IPR002208	SecY/SEC61-alpha family	Family
B [auth Y]	IPR030659	SecY conserved site	Conserved Site
B [auth Y]	IPR026593	Protein translocase subunit SecY	Family
B [auth Y]	IPR023201	SecY domain superfamily	Homologous Superfamily
E [auth B]	IPR006664	Outer membrane protein, bacterial	Domain
E [auth B]	IPR000498	Outer membrane protein OmpA-like, transmembrane domain	Domain
E [auth B]	IPR006690	Outer membrane protein, OmpA-like, conserved site	Conserved Site
E [auth B]	IPR036737	OmpA-like domain superfamily	Homologous Superfamily
E [auth B]	IPR011250	Outer membrane protein/outer membrane enzyme PagP, beta-barrel	Homologous Superfamily
E [auth B]	IPR006665	OmpA-like domain	Domain
E [auth B]	IPR002368	Outer membrane protein, OmpA	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B [auth Y], C [auth E], E [auth B]	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 Y], C [auth E], E [auth B]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

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

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B [auth Y], C [auth E], E [auth B]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Sec, Translocase, and Insertase Proteins	SecA-SecYE complex in nanodiscs, substrate-engaged

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
F [auth G]	GYS	Parent Component: SER, TYR, GLY RESID: AA0184 PSI-MOD : L-serine 5-imidazolinone glycine MOD:00192