8RTD | pdb_00008rtd

Stalk-Arches-IMC structure from the fully-assembled R388 type IV secretion system determined by cryo-EM.

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: PDBTM

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
FA [auth g], GA [auth h], N [auth O], P, U [auth T], FA [auth g], GA [auth h], N [auth O], P, U [auth T], W [auth V]	PF03135	CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)	CagE, TrbE, VirB family, component of type IV transporter system	-	Family
EA [auth f], L [auth j], S [auth R]	PF05101	Type IV secretory pathway, VirB3-like protein (VirB3)	Type IV secretory pathway, VirB3-like protein	-	Family
J [auth L], K [auth M], M [auth H], O [auth I], Q [auth J]	PF05101	Type IV secretory pathway, VirB3-like protein (VirB3)	Type IV secretory pathway, VirB3-like protein	-	Family
J [auth L], K [auth M], M [auth H], O [auth I], Q [auth J]	PF03135	CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)	CagE, TrbE, VirB family, component of type IV transporter system	-	Family
J [auth L], K [auth M], M [auth H], O [auth I], Q [auth J]	PF04335	VirB8 protein (VirB8)	VirB8 protein	VirB8 is a bacterial virulence protein with cytoplasmic, transmembrane, and periplasmic regions. It is thought that it is a primary constituent of a DNA transporter. The periplasmic region interacts with VirB9, VirB10, and itself [1]. This family als ...	VirB8 is a bacterial virulence protein with cytoplasmic, transmembrane, and periplasmic regions. It is thought that it is a primary constituent of a DNA transporter. The periplasmic region interacts with VirB9, VirB10, and itself [1]. This family also includes the conjugal transfer protein family TrbF, a family of proteins known to be involved in conjugal transfer. The TrbF protein is thought to compose part of the pilus required for transfer [2]. This domain has a similar fold to the NTF2 protein.	Domain
J [auth L], K [auth M], M [auth H], O [auth I], Q [auth J]	PF04610	TrbL/VirB6 plasmid conjugal transfer protein (TrbL)	TrbL/VirB6 plasmid conjugal transfer protein	-	Family
AA [auth b], B [auth D], BA [auth c], CA [auth d], D [auth F], AA [auth b], B [auth D], BA [auth c], CA [auth d], D [auth F], F [auth G], HA [auth i], R [auth Q], T [auth S], V [auth U], X, Y	PF05101	Type IV secretory pathway, VirB3-like protein (VirB3)	Type IV secretory pathway, VirB3-like protein	-	Family
AA [auth b], B [auth D], BA [auth c], CA [auth d], D [auth F], AA [auth b], B [auth D], BA [auth c], CA [auth d], D [auth F], F [auth G], HA [auth i], R [auth Q], T [auth S], V [auth U], X, Y	PF03135	CagE, TrbE, VirB family, component of type IV transporter system (CagE_TrbE_VirB)	CagE, TrbE, VirB family, component of type IV transporter system	-	Family
AA [auth b], B [auth D], BA [auth c], CA [auth d], D [auth F], AA [auth b], B [auth D], BA [auth c], CA [auth d], D [auth F], F [auth G], HA [auth i], R [auth Q], T [auth S], V [auth U], X, Y	PF04335	VirB8 protein (VirB8)	VirB8 protein	VirB8 is a bacterial virulence protein with cytoplasmic, transmembrane, and periplasmic regions. It is thought that it is a primary constituent of a DNA transporter. The periplasmic region interacts with VirB9, VirB10, and itself [1]. This family als ...	VirB8 is a bacterial virulence protein with cytoplasmic, transmembrane, and periplasmic regions. It is thought that it is a primary constituent of a DNA transporter. The periplasmic region interacts with VirB9, VirB10, and itself [1]. This family also includes the conjugal transfer protein family TrbF, a family of proteins known to be involved in conjugal transfer. The TrbF protein is thought to compose part of the pilus required for transfer [2]. This domain has a similar fold to the NTF2 protein.	Domain
A, C [auth B], E [auth C], G [auth K], I [auth E]	PF04335	VirB8 protein (VirB8)	VirB8 protein	VirB8 is a bacterial virulence protein with cytoplasmic, transmembrane, and periplasmic regions. It is thought that it is a primary constituent of a DNA transporter. The periplasmic region interacts with VirB9, VirB10, and itself [1]. This family als ...	VirB8 is a bacterial virulence protein with cytoplasmic, transmembrane, and periplasmic regions. It is thought that it is a primary constituent of a DNA transporter. The periplasmic region interacts with VirB9, VirB10, and itself [1]. This family also includes the conjugal transfer protein family TrbF, a family of proteins known to be involved in conjugal transfer. The TrbF protein is thought to compose part of the pilus required for transfer [2]. This domain has a similar fold to the NTF2 protein.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
FA [auth g], GA [auth h], N [auth O], P, U [auth T], FA [auth g], GA [auth h], N [auth O], P, U [auth T], W [auth V]	Type IV secretion system protein virB4	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity	-	-
EA [auth f], L [auth j], S [auth R]	TrwM protein	-	-	cellular anatomical structure membrane
J [auth L], K [auth M], M [auth H], O [auth I], Q [auth J]	TrwI protein	-	establishment of protein localization nitrogen compound transport transport secretion establishment of protein localization to extracellular region export from cell protein secretion establishment of localization protein localization to extracellular region transmembrane transport localization secretion by cell protein transmembrane transport protein transport protein secretion by the type IV secretion system establishment of protein localization nitrogen compound transport transport secretion establishment of protein localization to extracellular region export from cell protein secretion establishment of localization protein localization to extracellular region transmembrane transport localization secretion by cell protein transmembrane transport protein transport protein secretion by the type IV secretion system macromolecule localization cellular process secretion by the type IV secretion system intracellular protein localization	cellular anatomical structure membrane
DA [auth e], H [auth a], Z	TrwE protein	-	-	cell periphery cellular anatomical structure plasma membrane membrane
AA [auth b], B [auth D], BA [auth c], CA [auth d], D [auth F], AA [auth b], B [auth D], BA [auth c], CA [auth d], D [auth F], F [auth G], HA [auth i], R [auth Q], T [auth S], V [auth U], X, Y	TrwG protein	-	establishment of protein localization nitrogen compound transport transport secretion establishment of protein localization to extracellular region export from cell protein secretion establishment of localization protein localization to extracellular region transmembrane transport localization secretion by cell protein transmembrane transport protein transport protein secretion by the type IV secretion system establishment of protein localization nitrogen compound transport transport secretion establishment of protein localization to extracellular region export from cell protein secretion establishment of localization protein localization to extracellular region transmembrane transport localization secretion by cell protein transmembrane transport protein transport protein secretion by the type IV secretion system macromolecule localization cellular process secretion by the type IV secretion system intracellular protein localization	cellular anatomical structure membrane
A, C [auth B], E [auth C], G [auth K], I [auth E]	TrwJ protein	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
FA [auth g], GA [auth h], N [auth O], P, U [auth T], FA [auth g], GA [auth h], N [auth O], P, U [auth T], W [auth V]	IPR004346	CagE, TrbE, VirB component of type IV transporter system	Family
FA [auth g], GA [auth h], N [auth O], P, U [auth T], FA [auth g], GA [auth h], N [auth O], P, U [auth T], W [auth V]	IPR018145	CagE, TrbE, VirB component of type IV transporter system, central domain	Domain
FA [auth g], GA [auth h], N [auth O], P, U [auth T], FA [auth g], GA [auth h], N [auth O], P, U [auth T], W [auth V]	IPR051162	Type IV secretion system component	Family
FA [auth g], GA [auth h], N [auth O], P, U [auth T], FA [auth g], GA [auth h], N [auth O], P, U [auth T], W [auth V]	IPR043964	TraG, P-loop domain	Domain
FA [auth g], GA [auth h], N [auth O], P, U [auth T], FA [auth g], GA [auth h], N [auth O], P, U [auth T], W [auth V]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
EA [auth f], L [auth j], S [auth R]	IPR007792	Type IV secretion system, VirB3 / TrbD / AvhB	Family
J [auth L], K [auth M], M [auth H], O [auth I], Q [auth J]	IPR007688	Plasmid conjugal transfer TrbL/VirB6	Family
DA [auth e], H [auth a], Z	IPR047695	Type IV secretion system, VirB10/PtlG	Family
DA [auth e], H [auth a], Z	IPR042217	Type IV secretion system, VirB10/TrbI	Homologous Superfamily
DA [auth e], H [auth a], Z	IPR005498	Type IV secretion system, VirB10/TraB/TrbI	Family
AA [auth b], B [auth D], BA [auth c], CA [auth d], D [auth F], AA [auth b], B [auth D], BA [auth c], CA [auth d], D [auth F], F [auth G], HA [auth i], R [auth Q], T [auth S], V [auth U], X, Y	IPR032710	NTF2-like domain superfamily	Homologous Superfamily
AA [auth b], B [auth D], BA [auth c], CA [auth d], D [auth F], AA [auth b], B [auth D], BA [auth c], CA [auth d], D [auth F], F [auth G], HA [auth i], R [auth Q], T [auth S], V [auth U], X, Y	IPR007430	Bacterial virulence protein VirB8	Domain
AA [auth b], B [auth D], BA [auth c], CA [auth d], D [auth F], AA [auth b], B [auth D], BA [auth c], CA [auth d], D [auth F], F [auth G], HA [auth i], R [auth Q], T [auth S], V [auth U], X, Y	IPR026264	Type IV secretion system protein VirB8/PtlE	Family
A, C [auth B], E [auth C], G [auth K], I [auth E]	IPR014158	Type IV secretion system, VirB5	Family
A, C [auth B], E [auth C], G [auth K], I [auth E]	IPR023220	Type IV secretion system, VirB5-domain	Homologous Superfamily

Membrane Protein Annotation: PDBTM PDBTM Database Homepage

Chains	External Link	Comment
A, AA [auth b], B [auth D], BA [auth c], C [auth B] A, AA [auth b], B [auth D], BA [auth c], C [auth B], CA [auth d], D [auth F], DA [auth e], E [auth C], EA [auth f], F [auth G], G [auth K], H [auth a], HA [auth i], I [auth E], J [auth L], K [auth M], L [auth j], M [auth H], O [auth I], Q [auth J], R [auth Q], S [auth R], T [auth S], V [auth U], X, Y, Z	PDBTM	Annotated as membrane protein by PDBTM

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.