1RH5 | pdb_00001rh5

The structure of a protein conducting channel

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
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	d1rh5a_	Membrane and cell surface proteins and peptides	Preprotein translocase SecY subunit	Preprotein translocase SecY subunit	Preprotein translocase SecY subunit	Preprotein translocase SecY subunit	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
B	d1rh5b_	Membrane and cell surface proteins and peptides	Single transmembrane helix	Preprotein translocase SecE subunit	Preprotein translocase SecE subunit	Preprotein translocase SecE subunit	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)
C	d1rh5c_	Membrane and cell surface proteins and peptides	Transmembrane helix hairpin	Sec-beta or SecG subunit of protein translocation channel	Sec-beta subunit	Sec-beta subunit	(Methanocaldococcus jannaschii ) [TaxId: 2190 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	SecY-like	8028250	4001751	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	SecY-like	8040629	3000333	SCOP2 (2022-06-29)
B	SCOP2 Family	Protein translocase subunit SecE-like	8028251	4005885	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	Protein translocase subunit SecE-like	8040630	3002174	SCOP2 (2022-06-29)
C	SCOP2 Family	Sec-beta subunit	8028253	4001714	SCOP2 (2022-06-29)
C	SCOP2 Superfamily	Sec-beta subunit	8040632	3000289	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	e1rh5A1	A: Preprotein translocase SecY subunit	X: Preprotein translocase SecY subunit	H: Preprotein translocase SecY subunit	T: SecY,Plug_translocon	F:	ECOD (20:10:01)
B	e1rh5B1	A: Preprotein translocase SecE subunit	X: Preprotein translocase SecE subunit	H: Preprotein translocase SecE subunit	T: SecE	F:	ECOD (20:10:01)
C	e1rh5C1	A: Sec-beta subunit	X: Sec-beta subunit	H: Sec-beta subunit	T: Sec61_beta	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.3370.10	Mainly Alpha	Orthogonal Bundle	Preprotein translocase SecY subunit	SecY subunit domain	CATH (4.3.0)
B	1.20.5.820	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Preprotein translocase SecE subunit	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF10559	Plug domain of Sec61p (Plug_translocon)	Plug domain of Sec61p	The Sec61/SecY translocon mediates translocation of proteins across the membrane and integration of membrane proteins into the lipid bilayer. The structure of the translocon revealed a plug domain blocking the pore on the lumenal side.The plug is unl ...	The Sec61/SecY translocon mediates translocation of proteins across the membrane and integration of membrane proteins into the lipid bilayer. The structure of the translocon revealed a plug domain blocking the pore on the lumenal side.The plug is unlikely to be important for sealing the translocation pore in yeast but it plays a role in stabilising Sec61p during translocon formation. The domain runs from residues 52-74 [1].	Domain
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Preprotein translocase secY subunit	macromolecule transmembrane transporter activity protein transporter activity protein transmembrane transporter activity transporter activity transmembrane transporter activity signal sequence binding binding peptide binding	establishment of protein localization cellular localization transport protein targeting localization SRP-dependent cotranslational protein targeting to membrane protein transmembrane transport establishment of localization in cell cotranslational protein targeting to membrane intracellular protein localization establishment of protein localization to endoplasmic reticulum establishment of protein localization to membrane intracellular protein transmembrane transport intracellular transport establishment of protein localization cellular localization transport protein targeting localization SRP-dependent cotranslational protein targeting to membrane protein transmembrane transport establishment of localization in cell cotranslational protein targeting to membrane intracellular protein localization establishment of protein localization to endoplasmic reticulum establishment of protein localization to membrane intracellular protein transmembrane transport intracellular transport localization within membrane establishment of localization protein targeting to membrane transmembrane transport establishment of protein localization to organelle protein transport macromolecule localization SRP-dependent cotranslational protein targeting to membrane, translocation cellular process intracellular protein transport protein targeting to ER	cell periphery cellular anatomical structure plasma membrane membrane
B	Preprotein translocase secE subunit	macromolecule transmembrane transporter activity protein transporter activity protein transmembrane transporter activity transporter activity transmembrane transporter activity	localization establishment of protein localization protein targeting establishment of localization transport secretion establishment of protein localization to extracellular region export from cell protein secretion protein localization to extracellular region secretion by cell protein transport macromolecule localization cellular process localization establishment of protein localization protein targeting establishment of localization transport secretion establishment of protein localization to extracellular region export from cell protein secretion protein localization to extracellular region secretion by cell protein transport macromolecule localization cellular process intracellular protein localization cellular localization intracellular protein transmembrane transport intracellular transport transmembrane transport protein transmembrane transport establishment of localization in cell intracellular protein transport	cell periphery cellular anatomical structure plasma membrane membrane
C	SecBeta	-	localization establishment of protein localization protein transport transport macromolecule localization intracellular protein localization establishment of localization	cell periphery cellular anatomical structure plasma membrane membrane

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	IPR026593	Protein translocase subunit SecY	Family
A	IPR019561	Translocon Sec61/SecY, plug domain	Domain
A	IPR023201	SecY domain superfamily	Homologous Superfamily
B	IPR008158	Protein translocase SEC61 complex, gamma subunit	Family
B	IPR001901	Protein translocase complex, SecE/Sec61-gamma subunit	Family
B	IPR023391	Protein translocase SecE domain superfamily	Homologous Superfamily
C	IPR016482	Protein transport protein SecG/Sec61-beta/Sbh	Family
C	IPR023531	Preprotein translocase subunit SecG	Family

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C	OPM	Transmembrane	Alpha-helical polytopic	General secretory pathway (Sec)	Protein translocase

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, B, C	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Sec, Translocase, and Insertase Proteins	SecYEβ translocon

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.

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