Annotations: 5NBG

Structure of the cytoplasmic domain I of OutF in the D. dadantii type II secretion system

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2 Family	T2SS protein F-like	8081357	4005829	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	T2SS protein F-like	8081358	3002176	SCOP2 (2022-06-29)
A	SCOP2B Superfamily	T2SS protein F-like	8081358	3002176	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)
B	V-set	e5nbgB1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: V-set	ECOD (v294.1)
A	Ig_2	e5nbgA1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: Ig_2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.20.81.30	Mainly Alpha	Up-down Bundle	Receptor-associated Protein	Type II secretion system (T2SS), domain F	CATH (4.3.0)
A	1.20.81.30	Mainly Alpha	Up-down Bundle	Receptor-associated Protein	Type II secretion system (T2SS), domain F	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00482	Type II secretion system (T2SS), protein F (T2SSF)	Type II secretion system (T2SS), protein F	The original family covered both the regions found by the current model. The splitting of the family has allowed the related FlaJ_arch (archaeal FlaJ family) to be merged with it. Proteins with this domain in form a platform for the machiney of the T ...	The original family covered both the regions found by the current model. The splitting of the family has allowed the related FlaJ_arch (archaeal FlaJ family) to be merged with it. Proteins with this domain in form a platform for the machiney of the Type II secretion system, as well as the Type 4 pili and the archaeal flagella [1]. This domain seems to show some similarity to PF00664 but this may just be due to similarities in the TM helices (personal obs: C Yeats).	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	General secretion pathway protein F	cation binding ion binding binding metal ion binding small molecule binding	protein transport across the cell outer membrane establishment of protein localization 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 protein transport across the cell outer membrane establishment of protein localization 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 primary metabolic process gene expression macromolecule biosynthetic process protein maturation biosynthetic process proteolysis protein processing metabolic process protein metabolic process macromolecule metabolic process	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
A, B	IPR042094	Type II secretion system GspF domain superfamily	Homologous Superfamily
A, B	IPR018076	Type II secretion system protein GspF domain	Domain
A, B	IPR003004	GspF/PilC family	Family
A, B	IPR001992	T2SS_GspF/T4SS_PilC conserved site	Conserved Site
A, B	IPR011850	Type II secretion system protein GspF	Family

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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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.