6GYB

Cryo-EM structure of the bacteria-killing type IV secretion system core complex from Xanthomonas citri

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
GA [auth L]	SCOP2 Family	TrbI-like	8100211	4004140	SCOP2 (2022-06-29)
GA [auth L]	SCOP2 Superfamily	TrbI-like	8100212	3002141	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 [auth a]	PF10671	e6gyba1	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: PF10671	ECOD (1.6)
BA [auth G]	PF10671	e6gybG1	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: PF10671	ECOD (1.6)
D [auth d]	PF10671	e6gybd1	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: PF10671	ECOD (1.6)
EA [auth J]	PF10671	e6gybJ1	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: PF10671	ECOD (1.6)
J [auth j]	PF10671	e6gybj1	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: PF10671	ECOD (1.6)
KA [auth P]	PF10671	e6gybP1	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: PF10671	ECOD (1.6)
M [auth m]	PF10671	e6gybm1	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: PF10671	ECOD (1.6)
P [auth p]	PF10671	e6gybp1	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: PF10671	ECOD (1.6)
S [auth s]	PF10671	e6gybs1	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: PF10671	ECOD (1.6)
V [auth A]	PF10671	e6gybA1	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: PF10671	ECOD (1.6)
Y [auth D]	PF10671	e6gybD1	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: PF10671	ECOD (1.6)
G [auth g]	PF10671	e6gybg1	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: PF10671	ECOD (1.6)
HA [auth M]	PF10671	e6gybM1	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: PF10671	ECOD (1.6)
NA [auth S]	PF10671	e6gybS1	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: PF10671	ECOD (1.6)
B [auth b]	PF03524	e6gybb1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF03524	ECOD (1.6)
B [auth b]	PF03524	e6gybb2	A: beta sandwiches	X: TraO N-terminal domain (From Topology)	H: TraO N-terminal domain (From Topology)	T: TraO N-terminal domain	F: PF03524	ECOD (1.6)
CA [auth H]	PF03524	e6gybH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF03524	ECOD (1.6)
CA [auth H]	PF03524	e6gybH2	A: beta sandwiches	X: TraO N-terminal domain (From Topology)	H: TraO N-terminal domain (From Topology)	T: TraO N-terminal domain	F: PF03524	ECOD (1.6)
E [auth e]	PF03524	e6gybe1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF03524	ECOD (1.6)
E [auth e]	PF03524	e6gybe2	A: beta sandwiches	X: TraO N-terminal domain (From Topology)	H: TraO N-terminal domain (From Topology)	T: TraO N-terminal domain	F: PF03524	ECOD (1.6)
FA [auth K]	PF03524	e6gybK1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF03524	ECOD (1.6)
FA [auth K]	PF03524	e6gybK2	A: beta sandwiches	X: TraO N-terminal domain (From Topology)	H: TraO N-terminal domain (From Topology)	T: TraO N-terminal domain	F: PF03524	ECOD (1.6)
H [auth h]	PF03524	e6gybh1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF03524	ECOD (1.6)
H [auth h]	PF03524	e6gybh2	A: beta sandwiches	X: TraO N-terminal domain (From Topology)	H: TraO N-terminal domain (From Topology)	T: TraO N-terminal domain	F: PF03524	ECOD (1.6)
IA [auth N]	PF03524	e6gybN2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF03524	ECOD (1.6)
IA [auth N]	PF03524	e6gybN1	A: beta sandwiches	X: TraO N-terminal domain (From Topology)	H: TraO N-terminal domain (From Topology)	T: TraO N-terminal domain	F: PF03524	ECOD (1.6)
K [auth k]	PF03524	e6gybk1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF03524	ECOD (1.6)
K [auth k]	PF03524	e6gybk2	A: beta sandwiches	X: TraO N-terminal domain (From Topology)	H: TraO N-terminal domain (From Topology)	T: TraO N-terminal domain	F: PF03524	ECOD (1.6)
LA [auth Q]	PF03524	e6gybQ1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF03524	ECOD (1.6)
LA [auth Q]	PF03524	e6gybQ2	A: beta sandwiches	X: TraO N-terminal domain (From Topology)	H: TraO N-terminal domain (From Topology)	T: TraO N-terminal domain	F: PF03524	ECOD (1.6)
N [auth n]	PF03524	e6gybn1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF03524	ECOD (1.6)
N [auth n]	PF03524	e6gybn2	A: beta sandwiches	X: TraO N-terminal domain (From Topology)	H: TraO N-terminal domain (From Topology)	T: TraO N-terminal domain	F: PF03524	ECOD (1.6)
OA [auth T]	PF03524	e6gybT1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF03524	ECOD (1.6)
OA [auth T]	PF03524	e6gybT2	A: beta sandwiches	X: TraO N-terminal domain (From Topology)	H: TraO N-terminal domain (From Topology)	T: TraO N-terminal domain	F: PF03524	ECOD (1.6)
T [auth t]	PF03524	e6gybt2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF03524	ECOD (1.6)
T [auth t]	PF03524	e6gybt1	A: beta sandwiches	X: TraO N-terminal domain (From Topology)	H: TraO N-terminal domain (From Topology)	T: TraO N-terminal domain	F: PF03524	ECOD (1.6)
W [auth B]	PF03524	e6gybB1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF03524	ECOD (1.6)
W [auth B]	PF03524	e6gybB2	A: beta sandwiches	X: TraO N-terminal domain (From Topology)	H: TraO N-terminal domain (From Topology)	T: TraO N-terminal domain	F: PF03524	ECOD (1.6)
Z [auth E]	PF03524	e6gybE2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF03524	ECOD (1.6)
Z [auth E]	PF03524	e6gybE1	A: beta sandwiches	X: TraO N-terminal domain (From Topology)	H: TraO N-terminal domain (From Topology)	T: TraO N-terminal domain	F: PF03524	ECOD (1.6)
Q [auth q]	PF03524	e6gybq1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF03524	ECOD (1.6)
Q [auth q]	PF03524	e6gybq2	A: beta sandwiches	X: TraO N-terminal domain (From Topology)	H: TraO N-terminal domain (From Topology)	T: TraO N-terminal domain	F: PF03524	ECOD (1.6)
C [auth c]	PF03743	e6gybc1	A: beta barrels	X: CBF-like	H: TraF (From Topology)	T: TraF	F: PF03743	ECOD (1.6)
DA [auth I]	PF03743	e6gybI1	A: beta barrels	X: CBF-like	H: TraF (From Topology)	T: TraF	F: PF03743	ECOD (1.6)
F [auth f]	PF03743	e6gybf1	A: beta barrels	X: CBF-like	H: TraF (From Topology)	T: TraF	F: PF03743	ECOD (1.6)
GA [auth L]	PF03743	e6gybL1	A: beta barrels	X: CBF-like	H: TraF (From Topology)	T: TraF	F: PF03743	ECOD (1.6)
I [auth i]	PF03743	e6gybi1	A: beta barrels	X: CBF-like	H: TraF (From Topology)	T: TraF	F: PF03743	ECOD (1.6)
JA [auth O]	PF03743	e6gybO1	A: beta barrels	X: CBF-like	H: TraF (From Topology)	T: TraF	F: PF03743	ECOD (1.6)
L [auth l]	PF03743	e6gybl1	A: beta barrels	X: CBF-like	H: TraF (From Topology)	T: TraF	F: PF03743	ECOD (1.6)
MA [auth R]	PF03743	e6gybR1	A: beta barrels	X: CBF-like	H: TraF (From Topology)	T: TraF	F: PF03743	ECOD (1.6)
O [auth o]	PF03743	e6gybo1	A: beta barrels	X: CBF-like	H: TraF (From Topology)	T: TraF	F: PF03743	ECOD (1.6)
PA [auth U]	PF03743	e6gybU1	A: beta barrels	X: CBF-like	H: TraF (From Topology)	T: TraF	F: PF03743	ECOD (1.6)
R [auth r]	PF03743	e6gybr1	A: beta barrels	X: CBF-like	H: TraF (From Topology)	T: TraF	F: PF03743	ECOD (1.6)
X [auth C]	PF03743	e6gybC1	A: beta barrels	X: CBF-like	H: TraF (From Topology)	T: TraF	F: PF03743	ECOD (1.6)
AA [auth F]	PF03743	e6gybF1	A: beta barrels	X: CBF-like	H: TraF (From Topology)	T: TraF	F: PF03743	ECOD (1.6)
U [auth u]	PF03743	e6gybu1	A: beta barrels	X: CBF-like	H: TraF (From Topology)	T: TraF	F: PF03743	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth a], BA [auth G], D [auth d], EA [auth J], G [auth g], A [auth a], BA [auth G], D [auth d], EA [auth J], G [auth g], HA [auth M], J [auth j], KA [auth P], M [auth m], NA [auth S], P [auth p], S [auth s], V [auth A], Y [auth D]	PF10671	Toxin co-regulated pilus biosynthesis protein Q (TcpQ)	Toxin co-regulated pilus biosynthesis protein Q	-	Family
B [auth b], CA [auth H], E [auth e], FA [auth K], H [auth h], B [auth b], CA [auth H], E [auth e], FA [auth K], H [auth h], IA [auth N], K [auth k], LA [auth Q], N [auth n], OA [auth T], Q [auth q], T [auth t], W [auth B], Z [auth E]	PF03524	Conjugal transfer protein (CagX)	Conjugal transfer protein	-	Family
AA [auth F], C [auth c], DA [auth I], F [auth f], GA [auth L], AA [auth F], C [auth c], DA [auth I], F [auth f], GA [auth L], I [auth i], JA [auth O], L [auth l], MA [auth R], O [auth o], PA [auth U], R [auth r], U [auth u], X [auth C]	PF03743	Bacterial conjugation TrbI-like protein (TrbI)	Bacterial conjugation TrbI-like protein	-	Family

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 R01GM133198.

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6GYB

Cryo-EM structure of the bacteria-killing type IV secretion system core complex from Xanthomonas citri

External Resource: Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Domain Annotation: ECOD Classification ECOD Database Homepage

Protein Family Annotation Pfam Database Homepage