2ZJS

Crystal Structure of SecYE translocon from Thermus thermophilus with a Fab fragment

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
C [auth H]	d2zjsh1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth H]	d2zjsh2	Artifacts	Tags	Tags	Tags	N-terminal Tags	mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A [auth Y]	SecY	e2zjsY1	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)
C [auth H]	V-set_8	e2zjsH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
C [auth H]	C1-set_1	e2zjsH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_1	ECOD (1.6)
B [auth E]	SecE	e2zjsE1	A: extended segments	X: Preprotein translocase SecE subunit (From Topology)	H: Preprotein translocase SecE subunit (From Topology)	T: Preprotein translocase SecE subunit	F: SecE	ECOD (1.6)
D [auth L]	C1-set_4	e2zjsL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: C1-set_4	ECOD (1.6)
D [auth L]	V-set	e2zjsL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth Y]	1.10.3370.10	Mainly Alpha	Orthogonal Bundle	Preprotein translocase SecY subunit	SecY subunit domain	CATH (4.3.0)
C [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth E]	1.20.5.1030	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces	Preprotein translocase secy subunit	CATH (4.3.0)
D [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
C [auth H]	Fab 56	VH-CH1	Mus musculus (house mouse)	IGHV1-901, IGHJ201, IGHG1*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202448-0)
D [auth L]	Fab 56	L-KAPPA	Mus musculus (house mouse)	IGKV10-9601, IGKJ101, IGKJ102, IGKC01, IGKC*02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202448-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C [auth H]	Heavy Chain	IGHV1	-	preprotein translocase secy subunit	SAbDab (2024-12-06)
D [auth L]	Light Chain	IGKV10	Kappa	preprotein translocase secy subunit	SAbDab (2024-12-06)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth Y]	PF00344	SecY (SecY)	SecY	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth Y]	Preprotein translocase SecY subunit	macromolecule transmembrane transporter activity protein transporter activity protein transmembrane transporter activity transporter activity transmembrane transporter activity signal sequence binding binding peptide binding	protein localization establishment of protein localization cellular localization nitrogen compound transport transport protein transport by the Sec complex establishment of localization transmembrane transport localization protein transmembrane transport protein transport cellular macromolecule localization macromolecule localization cellular process protein localization establishment of protein localization cellular localization nitrogen compound transport transport protein transport by the Sec complex establishment of localization transmembrane transport localization protein transmembrane transport protein transport cellular macromolecule localization macromolecule localization cellular process protein targeting SRP-dependent cotranslational protein targeting to membrane establishment of localization in cell cotranslational protein targeting to membrane establishment of protein localization to endoplasmic reticulum protein localization to endoplasmic reticulum establishment of protein localization to membrane intracellular protein transmembrane transport intracellular transport localization within membrane protein localization to membrane protein targeting to membrane establishment of protein localization to organelle protein localization to organelle SRP-dependent cotranslational protein targeting to membrane, translocation intracellular protein transport protein targeting to ER	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex cell envelope Sec protein transport complex intracellular protein-containing complex
C [auth H]	Fab56 (heavy chain)	-	-	-
B [auth E]	Preprotein translocase SecE subunit	macromolecule transmembrane transporter activity protein transporter activity protein transmembrane transporter activity transporter activity transmembrane transporter activity	protein localization establishment of protein localization cellular localization nitrogen compound transport transport protein transport by the Sec complex establishment of localization transmembrane transport localization protein transmembrane transport protein transport cellular macromolecule localization macromolecule localization cellular process protein localization establishment of protein localization cellular localization nitrogen compound transport transport protein transport by the Sec complex establishment of localization transmembrane transport localization protein transmembrane transport protein transport cellular macromolecule localization macromolecule localization cellular process protein targeting secretion establishment of protein localization to extracellular region export from cell protein secretion protein localization to extracellular region secretion by cell intracellular protein transmembrane transport intracellular transport establishment of localization in cell intracellular protein transport	cell periphery cellular anatomical structure plasma membrane membrane
D [auth L]	Fab56 (light chain)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth Y]	IPR002208	SecY/SEC61-alpha family	Family
A [auth Y]	IPR030659	SecY conserved site	Conserved Site
A [auth Y]	IPR026593	Protein translocase subunit SecY	Family
A [auth Y]	IPR023201	SecY domain superfamily	Homologous Superfamily
B [auth E]	IPR005807	SecE subunit of protein translocation complex, bacterial-like	Family
B [auth E]	IPR001901	Protein translocase complex, SecE/Sec61-gamma subunit	Family
B [auth E]	IPR038379	SecE superfamily	Homologous Superfamily

Membrane Protein Annotation: OPM OPM Database Homepage

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

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A [auth Y], B [auth E]	PDBTM	Annotated as membrane protein by PDBTM

Membrane Protein Annotation: MemProtMD MemProtMD Database Homepage

Chains	External Link	Comment
A [auth Y], B [auth E]	MemProtMD	Annotated as membrane protein by MemProtMD

Membrane Protein Annotation: mpstruc mpstruc Database Homepage

Chains	Resource Link	Group	Subgroup	Protein
A [auth Y], B [auth E]	mpstruc	TRANSMEMBRANE PROTEINS: ALPHA-HELICAL	Sec, Translocase, and Insertase Proteins	SecYE translocon in complex with a Fab fragment

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.