7KB5 | pdb_00007kb5

Cryo-EM structure of the Sec complex from yeast, Sec63 FN3 and residues 210-216 mutated

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	SCOP2B Superfamily	SecY-like	8080650	3000333	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Protein translocase subunit SecE-like	8053310	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	SecY	e7kb5A1	A: alpha complex topology	X: Preprotein translocase SecY subunit (From Topology)	H: Preprotein translocase SecY subunit (From Topology)	T: Preprotein translocase SecY subunit	F: SecY	ECOD (1.6)
B	Sec61_beta	e7kb5B1	A: extended segments	X: Sec-beta subunit (From Topology)	H: Sec-beta subunit (From Topology)	T: Sec-beta subunit	F: Sec61_beta	ECOD (1.6)
C	SecE_1	e7kb5C1	A: extended segments	X: Preprotein translocase SecE subunit (From Topology)	H: Preprotein translocase SecE subunit (From Topology)	T: Preprotein translocase SecE subunit	F: SecE_1	ECOD (1.6)
F	TPR_11_2	e7kb5F1	A: alpha superhelices	X: Repetitive alpha hairpins	H: ARM repeat (From Topology)	T: ARM repeat	F: TPR_11_2	ECOD (1.6)

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 (utative)

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
C	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	Protein transport protein SEC61	peptide transmembrane transporter activity transporter activity transmembrane transporter activity macromolecule transmembrane transporter activity protein transporter activity protein transmembrane 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 protein transmembrane 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 nitrogen compound transport 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 localization establishment of protein localization nitrogen compound transport 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 proteolysis involved in protein catabolic process response to nitrogen compound 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 proteolysis 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 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
B	Protein transport protein SBH1	macromolecule transmembrane transporter activity protein transporter activity protein transmembrane 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 nitrogen compound transport 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 establishment of protein localization cellular localization nitrogen compound transport 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
C	Protein transport protein SSS1	macromolecule transmembrane transporter activity protein transporter activity protein transmembrane 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 nitrogen compound transport 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
D	Protein translocation protein SEC63	macromolecule transmembrane transporter activity protein transporter activity protein transmembrane 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 transport establishment of localization in cell intracellular transport cytosol to endoplasmic reticulum transport nitrogen compound 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
E	Translocation protein SEC66	-	growth filamentous growth establishment of protein localization cellular localization nitrogen compound transport 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 growth filamentous growth establishment of protein localization cellular localization nitrogen compound transport 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
F	Translocation protein SEC72	macromolecule transmembrane transporter activity protein transporter activity protein transmembrane transporter activity transporter activity transmembrane transporter activity	establishment of protein localization cellular localization nitrogen compound transport 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 establishment of protein localization cellular localization nitrogen compound transport 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

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	IPR030671	Protein transport Sec61-beta/Sbh	Family
B	IPR016482	Protein transport protein SecG/Sec61-beta/Sbh	Family
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
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
E	IPR018624	Translocation protein Sec66	Family
F	IPR011990	Tetratricopeptide-like helical domain superfamily	Homologous Superfamily
F	IPR019734	Tetratricopeptide repeat	Repeat

Membrane Protein Annotation: OPM OPM Database Homepage

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

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

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

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A, B, C, D, E	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Sec, Translocase, and Insertase Proteins	Sec protein-translocation channel complexes. Wild-type Sec61 without Sec62

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.