2ZJS | pdb_00002zjs

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

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth L]	SCOP2B Superfamily	Immunoglobulin (Ig) domain-like	8091539	3000071	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)
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)
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)
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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	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)
A [auth Y]	1.10.3370.10	Mainly Alpha	Orthogonal Bundle	Preprotein translocase SecY subunit	SecY subunit domain	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
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 (202546-0)
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 (202546-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
D [auth L]	Light Chain	IGKV10	Kappa	preprotein translocase secy subunit	SAbDab (2025-11-28)
C [auth H]	Heavy Chain	IGHV1	-	preprotein translocase secy subunit	SAbDab (2025-11-28)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth L]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
D [auth L]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain		Domain
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
D [auth L]	Fab56 (light chain)	-	response to stimulus immune response immune system process adaptive immune response developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation response to stimulus immune response immune system process adaptive immune response developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation cell differentiation anatomical structure development cellular process leukocyte differentiation	protein-containing complex immunoglobulin complex cell periphery cellular anatomical structure plasma membrane membrane extracellular region
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	establishment of protein localization nitrogen compound transport transport protein transport by the Sec complex establishment of localization transmembrane transport localization protein transmembrane transport protein transport macromolecule localization cellular process intracellular protein localization protein targeting secretion establishment of protein localization nitrogen compound transport transport protein transport by the Sec complex establishment of localization transmembrane transport localization protein transmembrane transport protein transport macromolecule localization cellular process intracellular protein localization protein targeting secretion establishment of protein localization to extracellular region export from cell protein secretion protein localization to extracellular region secretion by cell cellular localization intracellular protein transmembrane transport intracellular transport establishment of localization in cell intracellular protein transport	cell periphery cellular anatomical structure plasma membrane membrane
A [auth Y]	Preprotein translocase SecY subunit	-	establishment of protein localization nitrogen compound transport transport protein transport by the Sec complex establishment of localization transmembrane transport localization protein transmembrane transport protein transport macromolecule localization cellular process intracellular protein localization protein targeting cellular localization establishment of protein localization nitrogen compound transport transport protein transport by the Sec complex establishment of localization transmembrane transport localization protein transmembrane transport protein transport macromolecule localization cellular process intracellular protein localization protein targeting cellular localization intracellular protein transmembrane transport intracellular transport establishment of localization in cell intracellular protein transport	cell periphery cellular anatomical structure plasma membrane membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
D [auth L]	IPR050150	Immunoglobulin Variable Light Chain	Family
D [auth L]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
D [auth L]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
D [auth L]	IPR013106	Immunoglobulin V-set domain	Domain
D [auth L]	IPR003599	Immunoglobulin domain subtype	Domain
D [auth L]	IPR007110	Immunoglobulin-like domain	Domain
D [auth L]	IPR003597	Immunoglobulin C1-set	Domain
D [auth L]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
D [auth L]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
D [auth L]	IPR007110	Immunoglobulin-like domain	Domain
D [auth L]	IPR050380	Immune Recognition and Response Modulators	Family
D [auth L]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site
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
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

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.