3J9G | pdb_00003j9g

Atomic model of the VipA/VipB, the type six secretion system contractile sheath of Vibrio cholerae from cryo-EM

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
BA [auth b]		e3j9gb1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F:	ECOD (v294.1)
D	VipB_2	e3j9gD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: VipB_2	ECOD (v294.1)
D	Rv2632c-like	e3j9gD2	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: Rv2632c-like	ECOD (v294.1)
F	SLT	e3j9gF1	A: a/b three-layered sandwiches	X: Alpha-beta plaits	H: Protease propeptides/inhibitors	T: Protease propeptides/inhibitors	F: SLT	ECOD (v294.1)
H	SBP_bac_1	e3j9gH1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: SBP_bac_1	ECOD (v294.1)
HA [auth h]		e3j9gh1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F:	ECOD (v294.1)
HB [auth 8]		e3j9g81	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F:	ECOD (v294.1)
JA [auth j]		e3j9gj1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F:	ECOD (v294.1)
L		e3j9gL1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F:	ECOD (v294.1)
LA [auth l]		e3j9gl1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F:	ECOD (v294.1)
N		e3j9gN1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F:	ECOD (v294.1)
NA [auth n]		e3j9gn1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F:	ECOD (v294.1)
P		e3j9gP1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F:	ECOD (v294.1)
PA [auth p]		e3j9gp1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F:	ECOD (v294.1)
R		e3j9gR1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F:	ECOD (v294.1)
RA [auth r]		e3j9gr1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F:	ECOD (v294.1)
T		e3j9gT1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F:	ECOD (v294.1)
TA [auth t]		e3j9gt1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F:	ECOD (v294.1)
VA [auth v]		e3j9gv1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F:	ECOD (v294.1)
X		e3j9gX1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F:	ECOD (v294.1)
XA [auth x]		e3j9gx1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F:	ECOD (v294.1)
Z		e3j9gZ1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F:	ECOD (v294.1)
ZA [auth z]		e3j9gz1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F:	ECOD (v294.1)
V		e3j9gV1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F:	ECOD (v294.1)
J		e3j9gJ1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F:	ECOD (v294.1)
FB [auth 6]		e3j9g61	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F:	ECOD (v294.1)
FA [auth f]		e3j9gf1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F:	ECOD (v294.1)
DB [auth 4]		e3j9g41	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F:	ECOD (v294.1)
DA [auth d]		e3j9gd1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F:	ECOD (v294.1)
BB [auth 2]		e3j9g21	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F:	ECOD (v294.1)
B	VipB_2	e3j9gB1	A: a/b three-layered sandwiches	X: Aerolysin family of pore-forming toxins	H: Aerolysin family of pore-forming toxins	T: Aerolysin family of pore-forming toxins	F: VipB_2	ECOD (v294.1)
AB [auth 1]	N6_Mtase	e3j9g11	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.1)
C	WH2	e3j9gC1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Glycosyl hydrolase domain	T: Glycosyl hydrolase domain	F: WH2	ECOD (v294.1)
CA [auth c]	N6_Mtase	e3j9gc1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.1)
CB [auth 3]	N6_Mtase	e3j9g31	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.1)
EA [auth e]	N6_Mtase	e3j9ge1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.1)
EB [auth 5]	N6_Mtase	e3j9g51	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.1)
GA [auth g]	N6_Mtase	e3j9gg1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.1)
GB [auth 7]	N6_Mtase	e3j9g71	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.1)
I	N6_Mtase	e3j9gI1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.1)
K	N6_Mtase	e3j9gK1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.1)
KA [auth k]	N6_Mtase	e3j9gk1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.1)
MA [auth m]	N6_Mtase	e3j9gm1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.1)
O	N6_Mtase	e3j9gO1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.1)
OA [auth o]	N6_Mtase	e3j9go1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.1)
SA [auth s]	N6_Mtase	e3j9gs1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.1)
U	N6_Mtase	e3j9gU1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.1)
WA [auth w]	N6_Mtase	e3j9gw1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.1)
Y	N6_Mtase	e3j9gY1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.1)
YA [auth y]	N6_Mtase	e3j9gy1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.1)
W	N6_Mtase	e3j9gW1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.1)
UA [auth u]	N6_Mtase	e3j9gu1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.1)
S	N6_Mtase	e3j9gS1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.1)
QA [auth q]	N6_Mtase	e3j9gq1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.1)
Q	N6_Mtase	e3j9gQ1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.1)
M	N6_Mtase	e3j9gM1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.1)
IA [auth i]	N6_Mtase	e3j9gi1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.1)
G	N6_Mtase	e3j9gG1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.1)
E	N6_Mtase	e3j9gE1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.1)
AA [auth a]	N6_Mtase	e3j9ga1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: N6_Mtase	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, BA [auth b], BB [auth 2], D, DA [auth d], B, BA [auth b], BB [auth 2], D, DA [auth d], DB [auth 4], F, FA [auth f], FB [auth 6], H, HA [auth h], HB [auth 8], J, JA [auth j], L, LA [auth l], N, NA [auth n], P, PA [auth p], R, RA [auth r], T, TA [auth t], V, VA [auth v], X, XA [auth x], Z, ZA [auth z]	PF05943	EvpB/VC_A0108, tail sheath N-terminal domain (VipB)	EvpB/VC_A0108, tail sheath N-terminal domain	EvpB is a family of Gram-negative probable type VI secretion system components of the tail sheath. They have been known as COG:COG3517. These sheath-components, of which there are many copies in the sheath, are also variously referred to as VipA/VipB ...	EvpB is a family of Gram-negative probable type VI secretion system components of the tail sheath. They have been known as COG:COG3517. These sheath-components, of which there are many copies in the sheath, are also variously referred to as VipA/VipB and TssB/TssC. On contact with another bacterial cell the sheath contracts and pushes the puncturing device and tube through the cell envelope and punches the target bacterial cell [1].	Domain
B, BA [auth b], BB [auth 2], D, DA [auth d], B, BA [auth b], BB [auth 2], D, DA [auth d], DB [auth 4], F, FA [auth f], FB [auth 6], H, HA [auth h], HB [auth 8], J, JA [auth j], L, LA [auth l], N, NA [auth n], P, PA [auth p], R, RA [auth r], T, TA [auth t], V, VA [auth v], X, XA [auth x], Z, ZA [auth z]	PF18945	EvpB/VC_A0108, tail sheath gpW/gp25-like domain (VipB_2)	EvpB/VC_A0108, tail sheath gpW/gp25-like domain	EvpB is a family of Gram-negative probable type VI secretion system components of the tail sheath. They have been known as COG:COG3517. These sheath-components, of which there are many copies in the sheath, are also variously referred to as VipA/Vip ...	EvpB is a family of Gram-negative probable type VI secretion system components of the tail sheath. They have been known as COG:COG3517. These sheath-components, of which there are many copies in the sheath, are also variously referred to as VipA/VipB and TssB/TssC. On contact with another bacterial cell the sheath contracts and pushes the puncturing device and tube through the cell envelope and punches the target bacterial cell [1]. This entry represents the gpW/gp25-like domain.	Domain
A, AA [auth a], AB [auth 1], C, CA [auth c], A, AA [auth a], AB [auth 1], C, CA [auth c], CB [auth 3], E, EA [auth e], EB [auth 5], G, GA [auth g], GB [auth 7], I, IA [auth i], K, KA [auth k], M, MA [auth m], O, OA [auth o], Q, QA [auth q], S, SA [auth s], U, UA [auth u], W, WA [auth w], Y, YA [auth y]	PF05591	Type VI secretion system, VipA, VC_A0107 or Hcp2 (T6SS_VipA)	Type VI secretion system, VipA, VC_A0107 or Hcp2	-	Family

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, BA [auth b], BB [auth 2], D, DA [auth d], B, BA [auth b], BB [auth 2], D, DA [auth d], DB [auth 4], F, FA [auth f], FB [auth 6], H, HA [auth h], HB [auth 8], J, JA [auth j], L, LA [auth l], N, NA [auth n], P, PA [auth p], R, RA [auth r], T, TA [auth t], V, VA [auth v], X, XA [auth x], Z, ZA [auth z]	IPR010269	Type VI secretion system TssC-like	Family
B, BA [auth b], BB [auth 2], D, DA [auth d], B, BA [auth b], BB [auth 2], D, DA [auth d], DB [auth 4], F, FA [auth f], FB [auth 6], H, HA [auth h], HB [auth 8], J, JA [auth j], L, LA [auth l], N, NA [auth n], P, PA [auth p], R, RA [auth r], T, TA [auth t], V, VA [auth v], X, XA [auth x], Z, ZA [auth z]	IPR044032	TssC1, C-terminal	Domain
B, BA [auth b], BB [auth 2], D, DA [auth d], B, BA [auth b], BB [auth 2], D, DA [auth d], DB [auth 4], F, FA [auth f], FB [auth 6], H, HA [auth h], HB [auth 8], J, JA [auth j], L, LA [auth l], N, NA [auth n], P, PA [auth p], R, RA [auth r], T, TA [auth t], V, VA [auth v], X, XA [auth x], Z, ZA [auth z]	IPR044031	TssC1, N-terminal	Domain
A, AA [auth a], AB [auth 1], C, CA [auth c], A, AA [auth a], AB [auth 1], C, CA [auth c], CB [auth 3], E, EA [auth e], EB [auth 5], G, GA [auth g], GB [auth 7], I, IA [auth i], K, KA [auth k], M, MA [auth m], O, OA [auth o], Q, QA [auth q], S, SA [auth s], U, UA [auth u], W, WA [auth w], Y, YA [auth y]	IPR008312	Type VI secretion system sheath protein TssB1	Family