3JC2

The structure of the mammalian Sec61 channel opened by a signal sequence

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth 1]	SCOP2B Superfamily	SecY-like	8056967	3000333	SCOP2B (2022-06-29)
B [auth 2]	SCOP2 Family	Protein translocase subunit SecE-like	8047940	4005885	SCOP2 (2022-06-29)
B [auth 2]	SCOP2 Superfamily	Protein translocase subunit SecE-like	8053309	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 [auth 1]	PF00344	e3jc211	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 [auth 2]	PF00584	e3jc221	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth 2]	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 [auth 1]	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 [auth 1]	PF00344	SecY (SecY)	SecY	-	Family
C [auth w]	PF00103	Somatotropin hormone family (Hormone_1)	Somatotropin hormone family	-	Domain
B [auth 2]	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 [auth 1]	Protein transport protein Sec61 subunit alpha isoform 1	macromolecule transmembrane transporter activity protein transporter activity protein transmembrane transporter activity transporter activity transmembrane transporter activity signal sequence binding binding peptide binding ribonucleoprotein complex binding protein-containing complex binding ribosome binding	developmental process multicellular organismal process pronephric nephron development animal organ development renal system development multicellular organism development pronephros development anatomical structure development nephron development kidney development system development protein localization membrane organization cellular localization developmental process multicellular organismal process pronephric nephron development animal organ development renal system development multicellular organism development pronephros development anatomical structure development nephron development kidney development system development protein localization membrane organization cellular localization establishment of protein localization establishment of protein localization to membrane localization within membrane protein localization to membrane endoplasmic reticulum organization establishment of localization cellular component organization localization organelle organization protein localization to organelle cellular macromolecule localization macromolecule localization cellular process cellular component organization or biogenesis protein insertion into membrane protein insertion into ER membrane endomembrane system organization protein targeting protein targeting to membrane cotranslational protein targeting to membrane nitrogen compound transport transport protein transmembrane transport establishment of localization in cell post-translational protein targeting to membrane, translocation establishment of protein localization to endoplasmic reticulum protein localization to endoplasmic reticulum intracellular protein transmembrane transport organic substance transport intracellular transport post-translational protein targeting to endoplasmic reticulum membrane transmembrane transport establishment of protein localization to organelle protein transport intracellular protein transport protein targeting to ER SRP-dependent cotranslational protein targeting to membrane SRP-dependent cotranslational protein targeting to membrane, translocation	membrane-bounded organelle protein-containing complex intracellular anatomical structure Sec61 translocon complex membrane protein complex endomembrane system rough endoplasmic reticulum endoplasmic reticulum subcompartment intracellular organelle bounding membrane of organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane organelle subcompartment membrane-bounded organelle protein-containing complex intracellular anatomical structure Sec61 translocon complex membrane protein complex endomembrane system rough endoplasmic reticulum endoplasmic reticulum subcompartment intracellular organelle bounding membrane of organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane organelle subcompartment membrane cellular anatomical entity intracellular membrane-bounded organelle translocon complex rough endoplasmic reticulum membrane organelle endoplasmic reticulum cytoplasm organelle membrane
C [auth w]	Prolactin	protein binding binding signaling receptor binding cytokine receptor binding prolactin receptor binding hormone activity molecular function activator activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity	regulation of biosynthetic process regulation of nitric oxide biosynthetic process regulation of biological process biological regulation positive regulation of biological process reactive nitrogen species metabolic process positive regulation of nitric oxide metabolic process nitric oxide metabolic process positive regulation of metabolic process nitric oxide biosynthetic process biosynthetic process positive regulation of biosynthetic process metabolic process regulation of nitric oxide metabolic process regulation of biosynthetic process regulation of nitric oxide biosynthetic process regulation of biological process biological regulation positive regulation of biological process reactive nitrogen species metabolic process positive regulation of nitric oxide metabolic process nitric oxide metabolic process positive regulation of metabolic process nitric oxide biosynthetic process biosynthetic process positive regulation of biosynthetic process metabolic process regulation of nitric oxide metabolic process positive regulation of nitric oxide biosynthetic process regulation of metabolic process developmental process multicellular organismal process chordate embryonic development embryo development in utero embryonic development multicellular organism development anatomical structure morphogenesis blastocyst formation embryo development ending in birth or egg hatching anatomical structure development anatomical structure formation involved in morphogenesis blastocyst development cellular response to stimulus positive regulation of cell communication regulation of cellular process positive regulation of signal transduction positive regulation of canonical NF-kappaB signal transduction response to stimulus signaling regulation of signal transduction intracellular signal transduction cell communication positive regulation of response to stimulus regulation of intracellular signal transduction intracellular signaling cassette signal transduction positive regulation of cellular process regulation of signaling positive regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of response to stimulus regulation of cell communication regulation of canonical NF-kappaB signal transduction cellular process positive regulation of signaling multi-multicellular organism process reproductive process female pregnancy multi-organism reproductive process nitric oxide mediated signal transduction regulation of nitric oxide mediated signal transduction positive regulation of nitric oxide mediated signal transduction negative regulation of programmed cell death regulation of apoptotic process negative regulation of biological process regulation of programmed cell death cell death negative regulation of apoptotic process negative regulation of cellular process apoptotic process programmed cell death cellular biosynthetic process positive regulation of cellular metabolic process positive regulation of macromolecule biosynthetic process organic substance metabolic process organic substance biosynthetic process positive regulation of macromolecule metabolic process cellular metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression positive regulation of gene expression regulation of macromolecule biosynthetic process macromolecule metabolic process positive regulation of cellular biosynthetic process response to external stimulus response to external biotic stimulus response to biotic stimulus oxoacid metabolic process regulation of lipid metabolic process organic acid biosynthetic process organic acid metabolic process carboxylic acid biosynthetic process regulation of primary metabolic process cellular ketone metabolic process regulation of small molecule metabolic process positive regulation of lipid metabolic process small molecule metabolic process regulation of cellular ketone metabolic process primary metabolic process cellular lipid metabolic process regulation of fatty acid metabolic process regulation of fatty acid biosynthetic process monocarboxylic acid metabolic process lipid biosynthetic process positive regulation of fatty acid biosynthetic process positive regulation of fatty acid metabolic process fatty acid metabolic process monocarboxylic acid biosynthetic process small molecule biosynthetic process carboxylic acid metabolic process fatty acid biosynthetic process positive regulation of lipid biosynthetic process regulation of lipid biosynthetic process positive regulation of small molecule metabolic process lipid metabolic process regulation of localization import into cell positive regulation of cellular component organization regulation of cellular component organization transport vesicle-mediated transport cellular component organization localization positive regulation of endocytosis phagocytosis cellular component organization or biogenesis regulation of endocytosis regulation of transport regulation of phagocytosis regulation of vesicle-mediated transport establishment of localization positive regulation of phagocytosis positive regulation of transport endocytosis mammary gland development gland development animal organ development nitrogen compound transport hormone secretion peptide secretion secretion by cell amide transport signal release regulation of biological quality secretion regulation of hormone levels organic substance transport cell-cell signaling export from cell peptide transport peptide hormone secretion hormone transport cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation response to mechanical stimulus response to abiotic stimulus cell surface receptor signaling pathway response to light stimulus photoperiodism response to radiation long-day photoperiodism negative regulation of signaling negative regulation of intracellular signal transduction negative regulation of cell communication negative regulation of response to stimulus negative regulation of signal transduction negative regulation of nitric oxide mediated signal transduction cell surface receptor signaling pathway via STAT positive regulation of receptor signaling pathway via STAT positive regulation of receptor signaling pathway via JAK-STAT regulation of receptor signaling pathway via JAK-STAT regulation of receptor signaling pathway via STAT cell surface receptor signaling pathway via JAK-STAT regulation of body fluid levels body fluid secretion lactation regulation of non-canonical NF-kappaB signal transduction non-canonical NF-kappaB signal transduction positive regulation of non-canonical NF-kappaB signal transduction meiotic cell cycle process involved in oocyte maturation sexual reproduction cellular developmental process regulation of reproductive process cell development cellular process involved in reproduction in multicellular organism developmental process involved in reproduction female gamete generation meiotic cell cycle process gamete generation oocyte development cell differentiation cell maturation cell cycle regulation of cell cycle cell cycle process regulation of cell cycle process meiotic cell cycle multicellular organismal reproductive process oogenesis regulation of meiotic cell cycle process involved in oocyte maturation developmental maturation anatomical structure maturation germ cell development oocyte maturation oocyte differentiation response to nutrient levels negative regulation of cellular metabolic process negative regulation of macromolecule metabolic process negative regulation of metabolic process negative regulation of cellular biosynthetic process negative regulation of gene expression negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process response to acid chemical response to organic substance response to chemical response to organonitrogen compound response to L-arginine response to oxygen-containing compound response to nitrogen compound response to amino acid response to food regulation of developmental process positive regulation of developmental process positive regulation of secretion regulation of multicellular organismal process regulation of multicellular organismal development regulation of secretion positive regulation of lactation regulation of lactation positive regulation of multicellular organismal process	intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle organelle subcompartment membrane intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum intracellular anatomical structure cytoplasm cellular anatomical entity cytosol membrane-bounded organelle organelle subcompartment membrane intracellular membrane-bounded organelle endomembrane system endoplasmic reticulum subcompartment intracellular organelle organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum organelle membrane endoplasmic reticulum membrane membrane-enclosed lumen intracellular organelle lumen endoplasmic reticulum lumen organelle lumen extracellular region extracellular space
B [auth 2]	Protein transport protein Sec61 subunit gamma	macromolecule transmembrane transporter activity protein transporter activity protein transmembrane transporter activity transporter activity transmembrane transporter activity binding phospholipid binding lipid binding ribonucleoprotein complex binding protein-containing complex binding ribosome binding	cellular process membrane docking protein localization establishment of protein localization cellular localization nitrogen compound transport transport protein targeting localization protein transmembrane transport cellular macromolecule localization establishment of localization in cell post-translational protein targeting to membrane, translocation establishment of protein localization to endoplasmic reticulum cellular process membrane docking protein localization establishment of protein localization cellular localization nitrogen compound transport transport protein targeting localization protein transmembrane transport cellular macromolecule localization establishment of localization in cell post-translational protein targeting to membrane, translocation establishment of protein localization to endoplasmic reticulum protein localization to endoplasmic reticulum establishment of protein localization to membrane intracellular protein transmembrane transport organic substance transport intracellular transport post-translational protein targeting to endoplasmic reticulum membrane localization within membrane protein localization to membrane establishment of localization protein targeting to membrane transmembrane transport establishment of protein localization to organelle protein transport macromolecule localization protein localization to organelle intracellular protein transport protein targeting to ER	membrane-bounded organelle protein-containing complex intracellular anatomical structure membrane protein complex endomembrane system rough endoplasmic reticulum endoplasmic reticulum subcompartment intracellular organelle bounding membrane of organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane Ssh1 translocon complex organelle subcompartment membrane-bounded organelle protein-containing complex intracellular anatomical structure membrane protein complex endomembrane system rough endoplasmic reticulum endoplasmic reticulum subcompartment intracellular organelle bounding membrane of organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane Ssh1 translocon complex organelle subcompartment membrane cellular anatomical entity intracellular membrane-bounded organelle translocon complex rough endoplasmic reticulum membrane organelle endoplasmic reticulum cytoplasm organelle membrane
D [auth 3]	Protein transport protein Sec61 subunit beta	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth 1]	IPR002208	SecY/SEC61-alpha family	Family
A [auth 1]	IPR030659	SecY conserved site	Conserved Site
A [auth 1]	IPR023201	SecY domain superfamily	Homologous Superfamily
A [auth 1]	IPR019561	Translocon Sec61/SecY, plug domain	Domain
C [auth w]	IPR001400	Somatotropin/prolactin	Family
C [auth w]	IPR018116	Somatotropin hormone, conserved site	Conserved Site
C [auth w]	IPR009079	Four-helical cytokine-like, core	Homologous Superfamily
B [auth 2]	IPR008158	Protein translocase SEC61 complex, gamma subunit	Family
B [auth 2]	IPR001901	Protein translocase complex, SecE/Sec61-gamma subunit	Family
B [auth 2]	IPR023391	Protein translocase SecE domain superfamily	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A [auth 1], B [auth 2], C [auth w]	OPM	Transmembrane	Alpha-helical polytopic	General secretory pathway (Sec)	Protein translocase

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A [auth 1], B [auth 2], C [auth w]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A [auth 1], B [auth 2], C [auth w]	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth 1], B [auth 2], C [auth w]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Sec, Translocase, and Insertase Proteins	Sec61 translocase opened by a signal sequence

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 R01GM133198.