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

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

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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.