2AKH | pdb_00002akh

Normal mode-based flexible fitted coordinates of a non-translocating SecYEG protein-conducting channel into the cryo-EM map of a SecYEG-nascent chain-70S ribosome complex from E. coli

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: PDBTM
Membrane Protein Annotation: MemProtMD

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth A]	SCOP2B Superfamily	Preprotein translocase subunit SecG-like	8053307	3002175	SCOP2B (2022-06-29)
A [auth X]	SCOP2B Superfamily	Preprotein translocase subunit SecG-like	8053307	3002175	SCOP2B (2022-06-29)
F [auth C]	SCOP2B Superfamily	Protein translocase subunit SecE-like	8053308	3002174	SCOP2B (2022-06-29)
C [auth Z]	SCOP2B Superfamily	Protein translocase subunit SecE-like	8053308	3002174	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 [auth A]	tRNA-synt_2d	e2akhA1	A: a/b three-layered sandwiches	X: SSHS domain	H: Class II aaRS and biotin synthetases	T: Class II aaRS and biotin synthetases	F: tRNA-synt_2d	ECOD (v294.1)
A [auth X]	Peptidase_U40	e2akhX1	A: a/b three-layered sandwiches	X: all-alpha NTP pyrophosphatases	H: all-alpha NTP pyrophosphatases	T: MazG-related	F: Peptidase_U40	ECOD (v294.1)
F [auth C]	MATH_2	e2akhC1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: MATH_2	ECOD (v294.1)
C [auth Z]	MATH_2	e2akhZ1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: MATH_2	ECOD (v294.1)
E [auth B]	MATH_2	e2akhB1	A: a/b three-layered sandwiches	X: HTH	H: Nudix	T: winged helix domain	F: MATH_2	ECOD (v294.1)
B [auth Y]	Thioredoxin	e2akhY1	A: a/b three-layered sandwiches	X: Globin-like	H: Globin-like	T: Globin-like	F: Thioredoxin	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth X], D [auth A]	PF03840	Preprotein translocase SecG subunit (SecG)	Preprotein translocase SecG subunit	-	Family
C [auth Z], F [auth C]	PF00584	SecE/Sec61-gamma subunits of protein translocation complex (SecE)	SecE/Sec61-gamma subunits of protein translocation complex	-	Family
B [auth Y], E [auth B]	PF00344	SecY (SecY)	SecY	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth X], D [auth A]	IPR004692	Preprotein translocase SecG subunit	Family
C [auth Z], F [auth C]	IPR005807	SecE subunit of protein translocation complex, bacterial-like	Family
C [auth Z], F [auth C]	IPR001901	Protein translocase complex, SecE/Sec61-gamma subunit	Family
C [auth Z], F [auth C]	IPR038379	SecE superfamily	Homologous Superfamily
B [auth Y], E [auth B]	IPR002208	SecY/SEC61-alpha family	Family
B [auth Y], E [auth B]	IPR030659	SecY conserved site	Conserved Site
B [auth Y], E [auth B]	IPR023201	SecY domain superfamily	Homologous Superfamily
B [auth Y], E [auth B]	IPR026593	Protein translocase subunit SecY	Family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

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

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

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

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.