3EZJ

Crystal structure of the N-terminal domain of the secretin GspD from ETEC determined with the assistance of a nanobody

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)
E [auth B]	d3ezjb1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
E [auth B]	d3ezjb2	Artifacts	Tags	Tags	Tags	C-terminal Tags	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
E [auth B]	d3ezjb3	Artifacts	Tags	Tags	Tags	N-terminal Tags	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
F [auth D]	d3ezjd1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
F [auth D]	d3ezjd2	Artifacts	Tags	Tags	Tags	C-terminal Tags	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
F [auth D]	d3ezjd3	Artifacts	Tags	Tags	Tags	N-terminal Tags	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
G [auth F]	d3ezjf1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
G [auth F]	d3ezjf2	Artifacts	Tags	Tags	Tags	C-terminal Tags	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
G [auth F]	d3ezjf3	Artifacts	Tags	Tags	Tags	N-terminal Tags	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
H	d3ezjh1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
H	d3ezjh2	Artifacts	Tags	Tags	Tags	C-terminal Tags	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
H	d3ezjh3	Artifacts	Tags	Tags	Tags	N-terminal Tags	llama (Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	Secretin repeat domain-like	8045241	4004368	SCOP2 (2022-06-29)
A	SCOP2 Family	Secretin repeat domain-like	8057188	4004368	SCOP2 (2022-06-29)
A	SCOP2 Family	STN domain-like	8057193	4006665	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Secretin repeat domain-like	8057190	3002387	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Secretin repeat domain-like	8057191	3002387	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	STN domain-like	8057195	3002388	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)
A	Secretin_N	e3ezjA3	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: Ring-building motif II in type III secretion system (From Topology)	T: Ring-building motif II in type III secretion system	F: Secretin_N	ECOD (1.6)
A	type_II_gspD_1	e3ezjA2	A: a+b complex topology	X: N0 domain in phage tail proteins and secretins-like	H: N0 domain in phage tail proteins and secretins (From Topology)	T: N0 domain in phage tail proteins and secretins	F: type_II_gspD_1	ECOD (1.6)
B [auth C]	Secretin_N	e3ezjC2	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: Ring-building motif II in type III secretion system (From Topology)	T: Ring-building motif II in type III secretion system	F: Secretin_N	ECOD (1.6)
B [auth C]	type_II_gspD_1	e3ezjC1	A: a+b complex topology	X: N0 domain in phage tail proteins and secretins-like	H: N0 domain in phage tail proteins and secretins (From Topology)	T: N0 domain in phage tail proteins and secretins	F: type_II_gspD_1	ECOD (1.6)
C [auth E]	Secretin_N	e3ezjE4	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: Ring-building motif II in type III secretion system (From Topology)	T: Ring-building motif II in type III secretion system	F: Secretin_N	ECOD (1.6)
C [auth E]	type_II_gspD_1	e3ezjE2	A: a+b complex topology	X: N0 domain in phage tail proteins and secretins-like	H: N0 domain in phage tail proteins and secretins (From Topology)	T: N0 domain in phage tail proteins and secretins	F: type_II_gspD_1	ECOD (1.6)
D [auth G]	Secretin_N	e3ezjG1	A: a+b two layers	X: Alpha-lytic protease prodomain-like	H: Ring-building motif II in type III secretion system (From Topology)	T: Ring-building motif II in type III secretion system	F: Secretin_N	ECOD (1.6)
D [auth G]	type_II_gspD_1	e3ezjG3	A: a+b complex topology	X: N0 domain in phage tail proteins and secretins-like	H: N0 domain in phage tail proteins and secretins (From Topology)	T: N0 domain in phage tail proteins and secretins	F: type_II_gspD_1	ECOD (1.6)
E [auth B]	V-set_8	e3ezjB1	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 [auth D]	V-set_8	e3ezjD1	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)
G [auth F]	V-set_8	e3ezjF1	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)
H	V-set_8	e3ezjH1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.55.50.30	Alpha Beta	3-Layer(bab) Sandwich	Phage tail protein beta-alpha-beta fold		CATH (4.3.0)
A	3.30.1370.120	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
B [auth C]	3.55.50.30	Alpha Beta	3-Layer(bab) Sandwich	Phage tail protein beta-alpha-beta fold		CATH (4.3.0)
B [auth C]	3.30.1370.120	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
C [auth E]	3.55.50.30	Alpha Beta	3-Layer(bab) Sandwich	Phage tail protein beta-alpha-beta fold		CATH (4.3.0)
C [auth E]	3.30.1370.120	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
D [auth G]	3.55.50.30	Alpha Beta	3-Layer(bab) Sandwich	Phage tail protein beta-alpha-beta fold		CATH (4.3.0)
D [auth G]	3.30.1370.120	Alpha Beta	2-Layer Sandwich	Ribosomal Protein S8	Chain: A, domain 1	CATH (4.3.0)
E [auth B]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth D]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G [auth F]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
H	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
E [auth B], F [auth D], G [auth F], H	Nanobody NBGSPD_7	VH	Lama glama (llama)	IGHV3S301, IGHJ401	V-DOMAIN VH	IG	(VH)	IMGT (202415-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
E [auth B], F [auth D], G [auth F], H	Heavy Chain	IGHV1	-	general secretion pathway protein gspd	SAbDab (2024-04-19)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth C], C [auth E], D [auth G]	PF03958	Bacterial type II/III secretion system short domain (Secretin_N)	Bacterial type II/III secretion system short domain	This is a short, often repeated, domain found in bacterial type II/III secretory system proteins. All previous NolW-like domains fall into this family.	Domain
A, B [auth C], C [auth E], D [auth G]	PF21305	GspD-like, N0 domain (type_II_gspD_N0)	GspD-like, N0 domain	GspD is a type II general secretion pathway protein involved in protein export. This is the N0 domain found at the N-terminal of GspD type II secretins and its close homologues [1-5]. These proteins form a dodecameric ring, in which the N0 domain med ...	GspD is a type II general secretion pathway protein involved in protein export. This is the N0 domain found at the N-terminal of GspD type II secretins and its close homologues [1-5]. These proteins form a dodecameric ring, in which the N0 domain mediate extensive contacts suggesting that dodecameric N0 ring is an important feature of T2SS secretins [4]. This domain is also found in virion export proteins, proteins thought to form a channel across the host outer membrane for the purposes of extruding the bacteriophage.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth C], C [auth E], D [auth G]	General secretion pathway protein GspD	-	protein localization protein transport across the cell outer membrane establishment of protein localization cellular localization nitrogen compound transport transport secretion organic substance transport 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 protein localization protein transport across the cell outer membrane establishment of protein localization cellular localization nitrogen compound transport transport secretion organic substance transport 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 cellular macromolecule localization macromolecule localization cellular process	protein-containing complex type II protein secretion system complex cell periphery cell outer membrane external encapsulating structure membrane cell envelope outer membrane cellular anatomical entity
E [auth B], F [auth D], G [auth F], H	NANOBODY NBGSPD_7	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth C], C [auth E], D [auth G]	IPR005644	NolW-like	Domain
A, B [auth C], C [auth E], D [auth G]	IPR004846	Type II/III secretion system, secretin-like domain	Domain
A, B [auth C], C [auth E], D [auth G]	IPR038591	NolW-like superfamily	Homologous Superfamily
A, B [auth C], C [auth E], D [auth G]	IPR049371	GspD-like, N0 domain	Domain
A, B [auth C], C [auth E], D [auth G]	IPR001775	GspD/PilQ family	Family
A, B [auth C], C [auth E], D [auth G]	IPR013356	Type II secretion system protein GspD	Family

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.