Annotations: 8RTD

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

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
Z	CoV_Methyltr_2	e8rtdZ1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: CoV_Methyltr_2	ECOD (v295)
H [auth a]	CoV_Methyltr_2	e8rtda1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: CoV_Methyltr_2	ECOD (v295)
DA [auth e]	CoV_Methyltr_2	e8rtde1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: CoV_Methyltr_2	ECOD (v295)
Y	CoV_Methyltr_2	e8rtdY1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: CoV_Methyltr_2	ECOD (v295)
X	CoV_Methyltr_2	e8rtdX1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: CoV_Methyltr_2	ECOD (v295)
V [auth U]	CoV_Methyltr_2	e8rtdU1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: CoV_Methyltr_2	ECOD (v295)
T [auth S]	CoV_Methyltr_2	e8rtdS1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: CoV_Methyltr_2	ECOD (v295)
R [auth Q]	CoV_Methyltr_2	e8rtdQ1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: CoV_Methyltr_2	ECOD (v295)
HA [auth i]	CoV_Methyltr_2	e8rtdi1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: CoV_Methyltr_2	ECOD (v295)
F [auth G]	CoV_Methyltr_2	e8rtdG1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: CoV_Methyltr_2	ECOD (v295)
D [auth F]	CoV_Methyltr_2	e8rtdF1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: CoV_Methyltr_2	ECOD (v295)
CA [auth d]	CoV_Methyltr_2	e8rtdd1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: CoV_Methyltr_2	ECOD (v295)
BA [auth c]	CoV_Methyltr_2	e8rtdc1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: CoV_Methyltr_2	ECOD (v295)
B [auth D]	CoV_Methyltr_2	e8rtdD1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: CoV_Methyltr_2	ECOD (v295)
AA [auth b]	CoV_Methyltr_2	e8rtdb1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: CoV_Methyltr_2	ECOD (v295)
I [auth E]	CoV_Methyltr_2	e8rtdE1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: CoV_Methyltr_2	ECOD (v295)
G [auth K]	CoV_Methyltr_2	e8rtdK1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: CoV_Methyltr_2	ECOD (v295)
E [auth C]	CoV_Methyltr_2	e8rtdC1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: CoV_Methyltr_2	ECOD (v295)
C [auth B]	CoV_Methyltr_2	e8rtdB1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: CoV_Methyltr_2	ECOD (v295)
A	CoV_Methyltr_2	e8rtdA1	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: CoV_Methyltr_2	ECOD (v295)

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	-	cell periphery cellular anatomical structure plasma membrane membrane
EA [auth f], L [auth j], S [auth R]	TrwM protein	-	-	cell periphery cellular anatomical structure plasma membrane membrane
J [auth L], K [auth M], M [auth H], O [auth I], Q [auth J]	TrwI protein	-	establishment of protein localization 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 establishment of protein localization 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	cell periphery cellular anatomical structure plasma membrane membrane
DA [auth e], H [auth a], Z	TrwE protein	-	-	cell periphery cellular anatomical structure plasma membrane membrane cell outer membrane external encapsulating structure extracellular region cell envelope outer 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 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 establishment of protein localization 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	cell periphery cellular anatomical structure plasma membrane membrane
A, C [auth B], E [auth C], G [auth K], I [auth E]	TrwJ protein	-	-	cellular anatomical structure extracellular region periplasmic space pilus cell projection

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]	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]	IPR018145	Type IV secretion system ATPase VirB4/TrbE, middle 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	T4SS_component	Unknown
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	Type IV secretion system ATPase VirB4/TrbE	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]	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-like	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-like	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	VirB8/PtlE	Unknown
A, C [auth B], E [auth C], G [auth K], I [auth E]	IPR014158	Type IV secretion system protein VirB5-like	Family
A, C [auth B], E [auth C], G [auth K], I [auth E]	IPR023220	Type IV secretion system VirB5 superfamily	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], FA [auth g], G [auth K], GA [auth h], H [auth a], HA [auth i], I [auth E], J [auth L], K [auth M], L [auth j], M [auth H], N [auth O], O [auth I], P, Q [auth J], R [auth Q], S [auth R], T [auth S], U [auth T], V [auth U], W [auth V], X, Y, Z	PDBTM	Annotated as membrane protein by PDBTM

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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.

8RTD | pdb_00008rtd

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

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

Membrane Protein Annotation: PDBTM PDBTM Database Homepage