5A6U | pdb_00005a6u

Native mammalian ribosome-bound Sec61 protein-conducting channel in the 'non-inserting' state

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: OPM
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)
A	SCOP2B Superfamily	SecY-like	8056967	3000333	SCOP2B (2022-06-29)
C [auth G]	SCOP2B Superfamily	Protein translocase subunit SecE-like	8053309	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)
A	IF-2B	e5a6uA1	A: a/b three-layered sandwiches	X: Hsp90 co-chaperone CDC37 middle domain	H: Lysozyme-like	T: Lysozyme-like	F: IF-2B	ECOD (v294.1)
B	IF-2B	e5a6uB1	A: a/b three-layered sandwiches	X: Hsp90 co-chaperone CDC37 middle domain	H: Lysozyme-like	T: Lysozyme-like	F: IF-2B	ECOD (v294.1)
C [auth G]	IF-2B	e5a6uG1	A: a/b three-layered sandwiches	X: Hsp90 co-chaperone CDC37 middle domain	H: Lysozyme-like	T: Lysozyme-like	F: IF-2B	ECOD (v294.1)

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	PF03911	Sec61beta family (Sec61_beta)	Sec61beta family	-	Family
C [auth G]	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	SEC61A	macromolecule transmembrane transporter activity protein transporter activity transmembrane protein 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 membrane organization establishment of protein localization 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 membrane organization establishment of protein localization cellular localization establishment of protein localization to membrane localization within membrane endoplasmic reticulum organization establishment of localization cellular component organization localization organelle organization protein localization to organelle macromolecule localization cellular process intracellular protein localization cellular component organization or biogenesis protein insertion into membrane protein insertion into ER membrane endomembrane system organization protein targeting cotranslational protein targeting to membrane protein targeting to membrane transport protein transmembrane transport establishment of localization in cell post-translational protein targeting to membrane, translocation establishment of protein localization to endoplasmic reticulum intracellular protein transmembrane 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 cellular anatomical structure bounding membrane of organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane 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 cellular anatomical structure bounding membrane of organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane organelle subcompartment membrane intracellular membrane-bounded organelle translocon complex rough endoplasmic reticulum membrane organelle endoplasmic reticulum cytoplasm organelle membrane
B	SEC61B	macromolecule transmembrane transporter activity active transmembrane transporter activity protein transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity protein-transporting ATPase activity transmembrane protein transporter activity transporter activity transmembrane transporter activity ATP-dependent activity GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity macromolecule transmembrane transporter activity active transmembrane transporter activity protein transporter activity primary active transmembrane transporter activity ATPase-coupled transmembrane transporter activity protein-transporting ATPase activity transmembrane protein transporter activity transporter activity transmembrane transporter activity ATP-dependent activity GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity ribonucleoprotein complex binding protein-containing complex binding binding ribosome binding	establishment of protein localization cellular localization transport protein targeting localization protein transmembrane transport establishment of localization in cell post-translational protein targeting to membrane, translocation intracellular protein localization establishment of protein localization to endoplasmic reticulum establishment of protein localization to membrane intracellular protein transmembrane transport intracellular transport post-translational protein targeting to endoplasmic reticulum membrane establishment of protein localization cellular localization transport protein targeting localization protein transmembrane transport establishment of localization in cell post-translational protein targeting to membrane, translocation intracellular protein localization establishment of protein localization to endoplasmic reticulum establishment of protein localization to membrane intracellular protein transmembrane transport intracellular transport post-translational protein targeting to endoplasmic reticulum membrane localization within membrane establishment of localization protein targeting to membrane transmembrane transport establishment of protein localization to organelle protein transport macromolecule localization cellular process intracellular protein transport protein targeting to ER SRP-dependent cotranslational protein targeting to membrane 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 cellular anatomical structure bounding membrane of organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane 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 cellular anatomical structure bounding membrane of organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane organelle subcompartment membrane intracellular membrane-bounded organelle translocon complex rough endoplasmic reticulum membrane organelle endoplasmic reticulum cytoplasm organelle membrane endoplasmic reticulum Sec complex
C [auth G]	SEC61G	macromolecule transmembrane transporter activity protein transporter activity transmembrane protein 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 establishment of protein localization cellular localization transport protein targeting localization protein transmembrane transport establishment of localization in cell post-translational protein targeting to membrane, translocation intracellular protein localization establishment of protein localization to endoplasmic reticulum establishment of protein localization to membrane intracellular protein transmembrane transport cellular process membrane docking establishment of protein localization cellular localization transport protein targeting localization protein transmembrane transport establishment of localization in cell post-translational protein targeting to membrane, translocation intracellular protein localization establishment of protein localization to endoplasmic reticulum establishment of protein localization to membrane intracellular protein transmembrane transport intracellular transport post-translational protein targeting to endoplasmic reticulum membrane localization within membrane establishment of localization protein targeting to membrane transmembrane transport establishment of protein localization to organelle protein transport macromolecule localization 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 cellular anatomical structure bounding membrane of organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane Ssh1 translocon complex membrane-bounded organelle protein-containing complex intracellular anatomical structure membrane protein complex endomembrane system rough endoplasmic reticulum endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure 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 intracellular membrane-bounded organelle translocon complex rough endoplasmic reticulum membrane organelle endoplasmic reticulum cytoplasm organelle 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	IPR023201	SecY domain superfamily	Homologous Superfamily
A	IPR019561	Translocon Sec61/SecY, plug domain	Domain
B	IPR016482	Protein transport protein SecG/Sec61-beta/Sbh	Family
B	IPR030671	Protein transport Sec61-beta/Sbh	Family
C [auth G]	IPR008158	Protein translocase SEC61 complex, gamma subunit	Family
C [auth G]	IPR001901	Protein translocase complex, SecE/Sec61-gamma subunit	Family
C [auth G]	IPR023391	Protein translocase SecE domain superfamily	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

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

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A, B, C [auth G]	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.

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