5ABB

Visualization of a polytopic membrane protein during SecY-mediated membrane insertion

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	Protein translocase subunit SecE-like	8047944	4005885	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Protein translocase subunit SecE-like	8053311	3002174	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	PF00344	e5abbA1	A: alpha complex topology	X: Preprotein translocase SecY subunit (From Topology)	H: Preprotein translocase SecY subunit (From Topology)	T: Preprotein translocase SecY subunit	F: PF00344	ECOD (1.6)
B	PF00584	e5abbB1	A: extended segments	X: Preprotein translocase SecE subunit (From Topology)	H: Preprotein translocase SecE subunit (From Topology)	T: Preprotein translocase SecE subunit	F: PF00584	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF00344	SecY (SecY)	SecY	-	Family
B	PF00584	SecE/Sec61-gamma subunits of protein translocation complex (SecE)	SecE/Sec61-gamma subunits of protein translocation complex	-	Family
C [auth Z]	PF01036	Bacteriorhodopsin-like protein (Bac_rhodopsin)	Bacteriorhodopsin-like protein	The bacterial opsins are retinal-binding proteins that provide light- dependent ion transport and sensory functions to a family of halophilic bacteria [2,3]. They are integral membrane proteins believed to contain seven transmembrane (TM) domains, th ...	The bacterial opsins are retinal-binding proteins that provide light- dependent ion transport and sensory functions to a family of halophilic bacteria [2,3]. They are integral membrane proteins believed to contain seven transmembrane (TM) domains, the last of which contains the attachment point for retinal (a conserved lysine). This family also includes distantly related proteins that do not contain the retinal binding lysine and so cannot function as opsins. Some fungal examples are: Swiss:O74870, Swiss:P25619, Swiss:P38079, Swiss:Q12117.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	PROTEIN 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 cellular localization establishment of protein localization nitrogen compound transport transport organic substance transport intracellular transport establishment of localization localization protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization cellular process protein localization cellular localization establishment of protein localization nitrogen compound transport transport organic substance transport intracellular transport establishment of localization localization protein transport establishment of localization in cell cellular macromolecule localization macromolecule localization cellular process intracellular protein transport membrane organization establishment of protein localization to membrane localization within membrane protein localization to membrane cellular component organization protein insertion into membrane from inner side cellular component organization or biogenesis protein insertion into membrane 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 protein localization to endoplasmic reticulum protein targeting to membrane establishment of protein localization to organelle protein localization to organelle SRP-dependent cotranslational protein targeting to membrane, translocation protein targeting to ER	membrane cellular anatomical entity cell periphery plasma membrane protein-containing complex cell envelope Sec protein transport complex intracellular protein-containing complex
B	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
C [auth Z]	GREEN-LIGHT ABSORBING PROTEORHODOPSIN	passive transmembrane transporter activity monoatomic ion channel activity channel activity monoatomic ion transmembrane transporter activity transporter activity light-activated monoatomic ion channel activity transmembrane transporter activity molecular transducer activity photoreceptor activity signaling receptor activity	transport proton transmembrane transport monoatomic ion transmembrane transport inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport transmembrane transport monoatomic cation transmembrane transport localization monoatomic ion transport cellular process monoatomic cation transport phototransduction cellular response to stimulus transport proton transmembrane transport monoatomic ion transmembrane transport inorganic ion transmembrane transport establishment of localization inorganic cation transmembrane transport transmembrane transport monoatomic cation transmembrane transport localization monoatomic ion transport cellular process monoatomic cation transport phototransduction cellular response to stimulus detection of light stimulus response to light stimulus detection of external stimulus regulation of biological process regulation of cellular process response to stimulus signaling biological regulation response to external stimulus detection of abiotic stimulus cell communication detection of stimulus response to abiotic stimulus response to radiation signal transduction	cell periphery plasma membrane membrane cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR002208	SecY/SEC61-alpha family	Family
A	IPR030659	SecY conserved site	Conserved Site
A	IPR023201	SecY domain superfamily	Homologous Superfamily
A	IPR026593	Protein translocase subunit SecY	Family
B	IPR005807	SecE subunit of protein translocation complex, bacterial-like	Family
B	IPR001901	Protein translocase complex, SecE/Sec61-gamma subunit	Family
B	IPR038379	SecE superfamily	Homologous Superfamily
C [auth Z]	IPR017402	Proteorhodopsin	Family
C [auth Z]	IPR018229	Rhodopsin, retinal binding site	Binding Site
C [auth Z]	IPR001425	Archaeal/bacterial/fungal rhodopsins	Family

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C [auth Z]	PDBTM	Annotated as membrane protein by PDBTM

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.