7AFT | pdb_00007aft

Cryo-EM structure of the signal sequence-engaged post-translational Sec translocon

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: mpstruc

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	Protein translocase subunit SecE-like	8053310	3002174	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	SecY-like	8080650	3000333	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)
G	TrkA_C	e7aftG01	A: a/b three-layered sandwiches	X: Rossmann-like	H: all-alpha NTP pyrophosphatases	T: Hypothetical protein AF_0060	F: TrkA_C	ECOD (v294.1)
F	FAD_binding_3, Pyr_redox_3	e7aftF1	A: a/b three-layered sandwiches	X: CNF1/YfiH-like putative cysteine hydrolases	H: RIFT-related	T: FMN-binding split barrel 2	F: FAD_binding_3, Pyr_redox_3	ECOD (v294.1)
C	RNA_pol_Rpb2_1,RNA_pol_Rpb2_3	e7aftC1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: RNA_pol_Rpb2_1,RNA_pol_Rpb2_3	ECOD (v294.1)
B	RNA_pol_Rpb2_1,RNA_pol_Rpb2_3	e7aftB1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: RNA_pol_Rpb2_1,RNA_pol_Rpb2_3	ECOD (v294.1)
A	RNA_pol_Rpb2_1,RNA_pol_Rpb2_3	e7aftA1	A: a/b three-layered sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: RNA_pol_Rpb2_1,RNA_pol_Rpb2_3	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
C	PF00584	SecE/Sec61-gamma subunits of protein translocation complex (SecE)	SecE/Sec61-gamma subunits of protein translocation complex	-	Family
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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
H	Mating factor alpha-1,Mating factor alpha-1	cation binding cupric ion binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding pheromone activity molecular function activator activity mating pheromone activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity cation binding cupric ion binding transition metal ion binding copper ion binding ion binding binding metal ion binding small molecule binding pheromone activity molecular function activator activity mating pheromone activity molecular function regulator activity signaling receptor regulator activity receptor ligand activity signaling receptor activator activity	sexual reproduction reproductive process mating multi-organism reproductive process cellular response to stimulus regulation of cellular process response to stimulus signaling regulation of reproductive process positive regulation of biological process regulation of conjugation with cellular fusion response to pheromone cellular response to pheromone cell communication sexual reproduction reproductive process mating multi-organism reproductive process cellular response to stimulus regulation of cellular process response to stimulus signaling regulation of reproductive process positive regulation of biological process regulation of conjugation with cellular fusion response to pheromone cellular response to pheromone cell communication positive regulation of conjugation with cellular fusion signal transduction positive regulation of reproductive process pheromone-dependent signal transduction involved in conjugation with cellular fusion regulation of biological process signal transduction involved in positive regulation of conjugation with cellular fusion biological regulation conjugation with cellular fusion response to pheromone triggering conjugation with cellular fusion cellular response to chemical stimulus response to chemical cellular process	cellular anatomical structure extracellular region
G	Translocation protein SEC62,Translocation protein SEC62	macromolecule transmembrane transporter activity protein transporter activity transmembrane protein transporter activity transporter activity transmembrane transporter activity	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	membrane-bounded organelle protein-containing complex intracellular anatomical structure organelle subcompartment membrane membrane protein complex intracellular membrane-bounded organelle endomembrane system rough endoplasmic reticulum endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure bounding membrane of organelle translocon complex membrane-bounded organelle protein-containing complex intracellular anatomical structure organelle subcompartment membrane membrane protein complex intracellular membrane-bounded organelle endomembrane system rough endoplasmic reticulum endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure bounding membrane of organelle translocon complex rough endoplasmic reticulum membrane organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cytoplasm organelle membrane endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane Sec62/Sec63 complex endoplasmic reticulum Sec complex
F	Translocation protein SEC72	macromolecule transmembrane transporter activity protein transporter activity transmembrane protein transporter activity transporter activity transmembrane transporter activity	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	membrane-bounded organelle protein-containing complex intracellular anatomical structure organelle subcompartment membrane membrane protein complex intracellular membrane-bounded organelle endomembrane system rough endoplasmic reticulum endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure bounding membrane of organelle translocon complex membrane-bounded organelle protein-containing complex intracellular anatomical structure organelle subcompartment membrane membrane protein complex intracellular membrane-bounded organelle endomembrane system rough endoplasmic reticulum endoplasmic reticulum subcompartment intracellular organelle cellular anatomical structure bounding membrane of organelle translocon complex rough endoplasmic reticulum membrane organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cytoplasm organelle membrane endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane Sec62/Sec63 complex endoplasmic reticulum Sec complex
E	Translocation protein SEC66	-	growth filamentous growth 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 growth filamentous growth 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	cell periphery cellular anatomical structure membrane-bounded organelle protein-containing complex intracellular anatomical structure organelle subcompartment membrane membrane protein complex intracellular membrane-bounded organelle endomembrane system rough endoplasmic reticulum endoplasmic reticulum subcompartment intracellular organelle bounding membrane of organelle cell periphery cellular anatomical structure membrane-bounded organelle protein-containing complex intracellular anatomical structure organelle subcompartment membrane membrane protein complex intracellular membrane-bounded organelle endomembrane system rough endoplasmic reticulum endoplasmic reticulum subcompartment intracellular organelle bounding membrane of organelle translocon complex rough endoplasmic reticulum membrane organelle nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum cytoplasm organelle membrane endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane Sec62/Sec63 complex endoplasmic reticulum Sec complex
D	Protein translocation protein SEC63	macromolecule transmembrane transporter activity protein transporter activity transmembrane protein transporter activity transporter activity transmembrane transporter activity	establishment of protein localization cellular localization establishment of protein localization to membrane protein targeting localization within membrane establishment of localization protein targeting to membrane localization SRP-dependent cotranslational protein targeting to membrane establishment of protein localization to organelle cotranslational protein targeting to membrane cellular process establishment of protein localization to endoplasmic reticulum protein targeting to ER establishment of protein localization cellular localization establishment of protein localization to membrane protein targeting localization within membrane establishment of localization protein targeting to membrane localization SRP-dependent cotranslational protein targeting to membrane establishment of protein localization to organelle cotranslational protein targeting to membrane cellular process establishment of protein localization to endoplasmic reticulum protein targeting to ER post-translational protein targeting to endoplasmic reticulum membrane transmembrane transport intercellular transport transport establishment of localization in cell intracellular transport cytosol to endoplasmic reticulum transport protein transmembrane transport post-translational protein targeting to membrane, translocation intracellular protein localization intracellular protein transmembrane transport protein transport macromolecule localization intracellular protein transport	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle organelle inner membrane nuclear membrane membrane nucleus endomembrane system organelle envelope membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle organelle inner membrane nuclear membrane membrane nucleus endomembrane system organelle envelope nuclear inner membrane nuclear envelope organelle membrane protein-containing complex organelle subcompartment membrane protein complex rough endoplasmic reticulum endoplasmic reticulum subcompartment bounding membrane of organelle translocon complex rough endoplasmic reticulum membrane nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum protein-containing complex endoplasmic reticulum membrane Sec62/Sec63 complex endoplasmic reticulum Sec complex
C	Protein transport protein SSS1	macromolecule transmembrane transporter activity protein transporter activity transmembrane protein transporter activity transporter activity transmembrane transporter activity structural molecule activity	establishment of protein localization cellular localization establishment of protein localization to membrane protein targeting localization within membrane establishment of localization protein targeting to membrane localization SRP-dependent cotranslational protein targeting to membrane establishment of protein localization to organelle cotranslational protein targeting to membrane cellular process establishment of protein localization to endoplasmic reticulum protein targeting to ER establishment of protein localization cellular localization establishment of protein localization to membrane protein targeting localization within membrane establishment of localization protein targeting to membrane localization SRP-dependent cotranslational protein targeting to membrane establishment of protein localization to organelle cotranslational protein targeting to membrane cellular process establishment of protein localization to endoplasmic reticulum protein targeting to ER transport protein transmembrane transport establishment of localization in cell post-translational protein targeting to membrane, translocation intracellular protein localization intracellular protein transmembrane transport intracellular transport post-translational protein targeting to endoplasmic reticulum membrane transmembrane transport protein transport macromolecule localization intracellular protein transport 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 organelle inner membrane nuclear membrane nucleus organelle envelope nuclear inner membrane nuclear envelope Ssh1 translocon complex
B	Protein transport protein SBH1	macromolecule transmembrane transporter activity protein transporter activity transmembrane protein transporter activity transporter activity transmembrane transporter activity GTPase regulator activity enzyme regulator activity guanyl-nucleotide exchange factor activity nucleoside-triphosphatase regulator activity molecular function regulator activity	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 cytosol
A	Protein transport protein SEC61	peptide transmembrane transporter activity transporter activity transmembrane transporter activity macromolecule transmembrane transporter activity protein transporter activity transmembrane protein transporter activity signal sequence binding binding peptide binding ribonucleoprotein complex binding protein-containing complex binding ribosome binding active transmembrane transporter activity primary active transmembrane transporter activity peptide transmembrane transporter activity transporter activity transmembrane transporter activity macromolecule transmembrane transporter activity protein transporter activity transmembrane protein transporter activity signal sequence binding binding peptide binding ribonucleoprotein complex binding protein-containing complex binding ribosome binding 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 misfolded protein transport intracellular transport establishment of localization localization protein transport establishment of localization in cell macromolecule localization cellular process intracellular protein localization intracellular protein transport cellular response to stimulus cellular localization establishment of protein localization transport misfolded protein transport intracellular transport establishment of localization localization protein transport establishment of localization in cell macromolecule localization cellular process intracellular protein localization intracellular protein transport cellular response to stimulus catabolic process response to stimulus proteasomal protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process ERAD pathway cellular response to stress response to chemical response to stress metabolic process protein metabolic process macromolecule metabolic process response to endoplasmic reticulum stress protein targeting protein transmembrane transport post-translational protein targeting to membrane, translocation establishment of protein localization to endoplasmic reticulum establishment of protein localization to membrane intracellular protein transmembrane transport post-translational protein targeting to endoplasmic reticulum membrane localization within membrane protein targeting to membrane transmembrane transport establishment of protein localization to organelle protein targeting to ER protein exit from endoplasmic reticulum intercellular transport endoplasmic reticulum to cytosol transport retrograde protein transport, ER to cytosol 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
H	IPR006742	Mating factor alpha, C-terminal repeat	Repeat
H	IPR008675	Mating factor alpha precursor, N-terminal	Domain
G	IPR011553	Translocation protein Sec62, ascomycota	Family
G	IPR004728	Translocation protein Sec62	Family
F	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
F	IPR019734	Tetratricopeptide repeat	Repeat
E	IPR018624	Translocation protein Sec66	Family
D	IPR018253	DnaJ domain, conserved site	Conserved Site
D	IPR036869	Chaperone J-domain superfamily	Homologous Superfamily
D	IPR004179	Sec63 domain	Domain
D	IPR001623	DnaJ domain	Domain
D	IPR014756	Immunoglobulin E-set	Homologous Superfamily
C	IPR008158	Protein translocase SEC61 complex, gamma subunit	Family
C	IPR001901	Protein translocase complex, SecE/Sec61-gamma subunit	Family
C	IPR023391	Protein translocase SecE domain superfamily	Homologous Superfamily
B	IPR030671	Protein transport Sec61-beta/Sbh	Family
B	IPR016482	Protein transport protein SecG/Sec61-beta/Sbh	Family
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

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C, D, E A, B, C, D, E, G, H	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, D, E A, B, C, D, E, G, H	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D, E A, B, C, D, E, G, H	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Sec, Translocase, and Insertase Proteins	Sec protein-translocation channel complex (Sec61-Sec63-Sec71-Sec72) post-translational complex