Annotations: 2WWB

CRYO-EM STRUCTURE OF THE MAMMALIAN SEC61 COMPLEX BOUND TO THE ACTIVELY TRANSLATING WHEAT GERM 80S RIBOSOME

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	SCOP2 Family	SecY-like	8045133	4001751	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	SecY-like	8056967	3000333	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)
I	adh_short	e2wwbI1	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: adh_short	ECOD (v295.2)
H	adh_short	e2wwbH1	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: adh_short	ECOD (v295.2)
C	Trigger_C	e2wwbC1	A: alpha arrays	X: OB-fold	H: Nucleic acid-binding protein	T: Nucleic acid-binding protein	F: Trigger_C	ECOD (v295.2)
B	Penicil_amidase	e2wwbB1	A: alpha arrays	X: Ntn/PP2C	H: Ntn	T: Penicillin acylase, catalytic domain	F: Penicil_amidase	ECOD (v295.2)
O	adh_short	e2wwbO1	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: adh_short	ECOD (v295.2)
N	adh_short	e2wwbN1	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: adh_short	ECOD (v295.2)
M	adh_short	e2wwbM1	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: adh_short	ECOD (v295.2)
L	adh_short	e2wwbL1	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: adh_short	ECOD (v295.2)
K	adh_short	e2wwbK1	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: adh_short	ECOD (v295.2)
J	adh_short	e2wwbJ1	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: adh_short	ECOD (v295.2)
A	Spt4	e2wwbA1	A: alpha arrays	X: Cystatin-like	H: NTF2-like	T: NTF2-like	F: Spt4	ECOD (v295.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
I	PF00237	Ribosomal protein L22p/L17e (Ribosomal_L22)	Ribosomal protein L22p/L17e	This family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes.	Domain
H	PF00573	Ribosomal protein L4/L1 family (Ribosomal_L4)	Ribosomal protein L4/L1 family	-	Family
B	PF00584	SecE/Sec61-gamma subunits of protein translocation complex (SecE)	SecE/Sec61-gamma subunits of protein translocation complex	-	Family
O	PF00832	Ribosomal L39 protein (Ribosomal_L39)	Ribosomal L39 protein	-	Family
N	PF00831	Ribosomal L29 protein (Ribosomal_L29)	Ribosomal L29 protein	-	Family
L	PF16906	Ribosomal proteins L26 eukaryotic, L24P archaeal (Ribosomal_L26)	Ribosomal proteins L26 eukaryotic, L24P archaeal	-	Family
L	PF00467	KOW motif (KOW)	KOW motif	-	Family
K	PF00276	Ribosomal protein L23 (Ribosomal_L23)	Ribosomal protein L23	-	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
I	60S RIBOSOMAL PROTEIN L17-A	-	-	-
H	60S RIBOSOMAL PROTEIN L4-B	-	-	-
G	25S RRNA	-	-	-
F	25S RRNA	-	-	-
E	25S RRNA	-	-	-
D	5.8S RRNA	-	-	-
C	PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT BETA	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
B	PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT GAMMA	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
O	60S RIBOSOMAL PROTEIN L39	-	-	-
N	60S RIBOSOMAL PROTEIN L35	-	-	-
M	60S RIBOSOMAL PROTEIN L31-A	-	-	-
L	60S RIBOSOMAL PROTEIN L26-A	-	-	-
K	60S RIBOSOMAL PROTEIN L25	-	-	-
J	60S RIBOSOMAL PROTEIN L19	-	-	-
A	PROTEIN TRANSPORT PROTEIN SEC61 SUBUNIT ALPHA ISOFORM 1	macromolecule transmembrane transporter activity protein transporter activity transmembrane protein transporter activity transporter activity transmembrane transporter activity signal sequence receptor activity ribonucleoprotein complex binding protein-containing complex binding 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 animal gross anatomical part developmental process system development membrane organization establishment of protein 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 animal gross anatomical part developmental process 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C	IPR016482	Protein transport protein SecG/Sec61-beta/Sbh	Family
C	IPR030671	Protein transport Sec61-beta/Sbh	Family
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
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	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