3CFI | pdb_00003cfi

Nanobody-aided structure determination of the EPSI:EPSJ pseudopilin heterdimer from Vibrio Vulnificus

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

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
L	d3cfil1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
L	d3cfil2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
I	d3cfii1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
I	d3cfii2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
F	d3cfif1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
F	d3cfif2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
C	d3cfic1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
C	d3cfic2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
K	d3cfik_	Alpha and beta proteins (a+b)	Pili subunits	Pili subunits	EpsJ-like	Type II secretory pathway component EpsJ	(Vibrio vulnificus ) [TaxId: 672 ],	SCOPe (2.08)
H	d3cfih_	Alpha and beta proteins (a+b)	Pili subunits	Pili subunits	EpsJ-like	Type II secretory pathway component EpsJ	(Vibrio vulnificus ) [TaxId: 672 ],	SCOPe (2.08)
E	d3cfie_	Alpha and beta proteins (a+b)	Pili subunits	Pili subunits	EpsJ-like	Type II secretory pathway component EpsJ	(Vibrio vulnificus ) [TaxId: 672 ],	SCOPe (2.08)
B	d3cfib_	Alpha and beta proteins (a+b)	Pili subunits	Pili subunits	EpsJ-like	Type II secretory pathway component EpsJ	(Vibrio vulnificus ) [TaxId: 672 ],	SCOPe (2.08)
J	d3cfij_	Alpha and beta proteins (a+b)	Pili subunits	Pili subunits	GSPII I/J protein-like	Pseudopilin EpsI	(Vibrio vulnificus ) [TaxId: 672 ],	SCOPe (2.08)
G	d3cfig_	Alpha and beta proteins (a+b)	Pili subunits	Pili subunits	GSPII I/J protein-like	Pseudopilin EpsI	(Vibrio vulnificus ) [TaxId: 672 ],	SCOPe (2.08)
D	d3cfid_	Alpha and beta proteins (a+b)	Pili subunits	Pili subunits	GSPII I/J protein-like	Pseudopilin EpsI	(Vibrio vulnificus ) [TaxId: 672 ],	SCOPe (2.08)
A	d3cfia_	Alpha and beta proteins (a+b)	Pili subunits	Pili subunits	GSPII I/J protein-like	Pseudopilin EpsI	(Vibrio vulnificus ) [TaxId: 672 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
K	SCOP2B Superfamily	Pili subunits	8036885	3000097	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Pili subunits	8036885	3000097	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Pili subunits	8036885	3000097	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Pili subunits	8036885	3000097	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Pili subunits	8003827	3000097	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Pili subunits	8003827	3000097	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Pili subunits	8003827	3000097	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Pili subunits	8003827	3000097	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)
L	V-set_12	e3cfiL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
I	V-set_8	e3cfiI1	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)
F	V-set_12	e3cfiF1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
C	V-set_12	e3cfiC1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_12	ECOD (1.6)
K	T2SSJ	e3cfiK1	A: a+b two layers	X: Pili subunits (From Topology)	H: Pili subunits (From Topology)	T: Pili subunits	F: T2SSJ	ECOD (1.6)
H	T2SSJ	e3cfiH1	A: a+b two layers	X: Pili subunits (From Topology)	H: Pili subunits (From Topology)	T: Pili subunits	F: T2SSJ	ECOD (1.6)
E	T2SSJ	e3cfiE1	A: a+b two layers	X: Pili subunits (From Topology)	H: Pili subunits (From Topology)	T: Pili subunits	F: T2SSJ	ECOD (1.6)
B	T2SSJ	e3cfiB1	A: a+b two layers	X: Pili subunits (From Topology)	H: Pili subunits (From Topology)	T: Pili subunits	F: T2SSJ	ECOD (1.6)
J	T2SSI	e3cfiJ1	A: a+b two layers	X: Pili subunits (From Topology)	H: Pili subunits (From Topology)	T: Pili subunits	F: T2SSI	ECOD (1.6)
G	T2SSI	e3cfiG1	A: a+b two layers	X: Pili subunits (From Topology)	H: Pili subunits (From Topology)	T: Pili subunits	F: T2SSI	ECOD (1.6)
D	T2SSI	e3cfiD1	A: a+b two layers	X: Pili subunits (From Topology)	H: Pili subunits (From Topology)	T: Pili subunits	F: T2SSI	ECOD (1.6)
A	T2SSI	e3cfiA1	A: a+b two layers	X: Pili subunits (From Topology)	H: Pili subunits (From Topology)	T: Pili subunits	F: T2SSI	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
L	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
I	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
J	3.30.1300.30	Alpha Beta	2-Layer Sandwich	Pantoate--beta-alanine Ligase	Chain: A,domain 2	CATH (4.3.0)
G	3.30.1300.30	Alpha Beta	2-Layer Sandwich	Pantoate--beta-alanine Ligase	Chain: A,domain 2	CATH (4.3.0)
D	3.30.1300.30	Alpha Beta	2-Layer Sandwich	Pantoate--beta-alanine Ligase	Chain: A,domain 2	CATH (4.3.0)
A	3.30.1300.30	Alpha Beta	2-Layer Sandwich	Pantoate--beta-alanine Ligase	Chain: A,domain 2	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, F, I, L	Nanobody NBEPSIJ_11	VH	Lama glama (llama)	IGHV3S601, IGHJ401	V-DOMAIN VH	IG	(VH)	IMGT (202547-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C, F, I, L	Heavy Chain	IGHV3	-	type ii secretory pathway, pseudopilin epsj	SAbDab (2025-12-05)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, E, H, K	PF11612	Type II secretion system (T2SS), protein J (T2SSJ)	Type II secretion system (T2SS), protein J	-	Family
A, D, G, J	PF02501	Type II secretion system (T2SS), protein I (T2SSI)	Type II secretion system (T2SS), protein I	The Type II secretion system, also called Secretion-dependent pathway (SDP), is responsible for the transport of proteins across the outer membrane first exported to the periplasm by the Sec or Tat translocon in Gram-negative (diderm) bacteria. As me ...	The Type II secretion system, also called Secretion-dependent pathway (SDP), is responsible for the transport of proteins across the outer membrane first exported to the periplasm by the Sec or Tat translocon in Gram-negative (diderm) bacteria. As members of the T2SJ family, members of the T2SI family are pseudopilins containing prepilin signal sequences [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, F, I, L	Nanobody NBEPSIJ_11	-	-	-
B, E, H, K	Type II secretory pathway, PSEUDOPILIN EpsJ	-	protein transport across the cell outer membrane establishment of protein localization nitrogen compound transport transport secretion establishment of protein localization to extracellular region export from cell protein secretion by the type II secretion system protein secretion establishment of localization protein localization to extracellular region transmembrane transport localization secretion by cell protein transmembrane transport protein transport across the cell outer membrane establishment of protein localization nitrogen compound transport transport secretion establishment of protein localization to extracellular region export from cell protein secretion by the type II secretion system protein secretion establishment of localization protein localization to extracellular region transmembrane transport localization secretion by cell protein transmembrane transport protein transport macromolecule localization cellular process intracellular protein localization	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex type II protein secretion system complex
A, D, G, J	Type II secretory pathway, pseudopilin EpsI	-	protein transport across the cell outer membrane establishment of protein localization nitrogen compound transport transport secretion establishment of protein localization to extracellular region export from cell protein secretion by the type II secretion system protein secretion establishment of localization protein localization to extracellular region transmembrane transport localization secretion by cell protein transmembrane transport protein transport across the cell outer membrane establishment of protein localization nitrogen compound transport transport secretion establishment of protein localization to extracellular region export from cell protein secretion by the type II secretion system protein secretion establishment of localization protein localization to extracellular region transmembrane transport localization secretion by cell protein transmembrane transport protein transport macromolecule localization cellular process intracellular protein localization	cell periphery cellular anatomical structure plasma membrane membrane protein-containing complex type II protein secretion system complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, E, H, K	IPR010055	Type II secretion system protein GspJ	Family
B, E, H, K	IPR012902	Prokaryotic N-terminal methylation site	PTM
B, E, H, K	IPR051621	Type II secretion system protein J	Family
B, E, H, K	IPR045584	Pilin-like	Homologous Superfamily
A, D, G, J	IPR003413	Type II secretion system protein GspI, C-terminal	Domain
A, D, G, J	IPR012902	Prokaryotic N-terminal methylation site	PTM
A, D, G, J	IPR010052	Type II secretion system protein GspI	Family
A, D, G, J	IPR045584	Pilin-like	Homologous Superfamily

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.