5URW | pdb_00005urw

Structure of the extended type VI secretion system sheath in Myxococcus xanthus

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 34]	T6SS_HCP	e5urw341	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: T6SS_HCP	ECOD (1.6)
YA [auth 33]	T6SS_HCP	e5urw331	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: T6SS_HCP	ECOD (1.6)
XA [auth 32]	T6SS_HCP	e5urw321	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: T6SS_HCP	ECOD (1.6)
WA [auth 31]	T6SS_HCP	e5urw311	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: T6SS_HCP	ECOD (1.6)
R [auth 16]	T6SS_HCP	e5urw161	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: T6SS_HCP	ECOD (1.6)
Q [auth 15]	T6SS_HCP	e5urw151	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: T6SS_HCP	ECOD (1.6)
P [auth 14]	T6SS_HCP	e5urw141	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: T6SS_HCP	ECOD (1.6)
O [auth 13]	T6SS_HCP	e5urw131	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: T6SS_HCP	ECOD (1.6)
N [auth 12]	T6SS_HCP	e5urw121	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: T6SS_HCP	ECOD (1.6)
M [auth 11]	T6SS_HCP	e5urw111	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: T6SS_HCP	ECOD (1.6)
JA [auth 26]	T6SS_HCP	e5urw261	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: T6SS_HCP	ECOD (1.6)
IA [auth 25]	T6SS_HCP	e5urw251	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: T6SS_HCP	ECOD (1.6)
HA [auth 24]	T6SS_HCP	e5urw241	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: T6SS_HCP	ECOD (1.6)
GA [auth 23]	T6SS_HCP	e5urw231	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: T6SS_HCP	ECOD (1.6)
FA [auth 22]	T6SS_HCP	e5urw221	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: T6SS_HCP	ECOD (1.6)
EA [auth 21]	T6SS_HCP	e5urw211	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: T6SS_HCP	ECOD (1.6)
BB [auth 36]	T6SS_HCP	e5urw361	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: T6SS_HCP	ECOD (1.6)
AB [auth 35]	T6SS_HCP	e5urw351	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: T6SS_HCP	ECOD (1.6)
Z [auth 2H]	VipB_C	e5urw2H2	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: VipB_C	ECOD (1.6)
Z [auth 2H]	VipB_N	e5urw2H1	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Domain III of tail sheath protein Gp18 (From Topology)	T: Domain III of tail sheath protein Gp18	F: VipB_N	ECOD (1.6)
X [auth 2F]	VipB_C	e5urw2F1	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: VipB_C	ECOD (1.6)
X [auth 2F]	VipB_N	e5urw2F2	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Domain III of tail sheath protein Gp18 (From Topology)	T: Domain III of tail sheath protein Gp18	F: VipB_N	ECOD (1.6)
VA [auth 3L]	VipB_C	e5urw3L1	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: VipB_C	ECOD (1.6)
VA [auth 3L]	VipB_N	e5urw3L2	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Domain III of tail sheath protein Gp18 (From Topology)	T: Domain III of tail sheath protein Gp18	F: VipB_N	ECOD (1.6)
V [auth 2D]	VipB_C	e5urw2D2	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: VipB_C	ECOD (1.6)
V [auth 2D]	VipB_N	e5urw2D1	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Domain III of tail sheath protein Gp18 (From Topology)	T: Domain III of tail sheath protein Gp18	F: VipB_N	ECOD (1.6)
TA [auth 3J]	VipB_C	e5urw3J1	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: VipB_C	ECOD (1.6)
TA [auth 3J]	VipB_N	e5urw3J2	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Domain III of tail sheath protein Gp18 (From Topology)	T: Domain III of tail sheath protein Gp18	F: VipB_N	ECOD (1.6)
T [auth 2B]	VipB_C	e5urw2B1	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: VipB_C	ECOD (1.6)
T [auth 2B]	VipB_N	e5urw2B2	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Domain III of tail sheath protein Gp18 (From Topology)	T: Domain III of tail sheath protein Gp18	F: VipB_N	ECOD (1.6)
RA [auth 3H]	VipB_C	e5urw3H2	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: VipB_C	ECOD (1.6)
RA [auth 3H]	VipB_N	e5urw3H1	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Domain III of tail sheath protein Gp18 (From Topology)	T: Domain III of tail sheath protein Gp18	F: VipB_N	ECOD (1.6)
PA [auth 3F]	VipB_C	e5urw3F2	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: VipB_C	ECOD (1.6)
PA [auth 3F]	VipB_N	e5urw3F1	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Domain III of tail sheath protein Gp18 (From Topology)	T: Domain III of tail sheath protein Gp18	F: VipB_N	ECOD (1.6)
NA [auth 3D]	VipB_C	e5urw3D1	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: VipB_C	ECOD (1.6)
NA [auth 3D]	VipB_N	e5urw3D2	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Domain III of tail sheath protein Gp18 (From Topology)	T: Domain III of tail sheath protein Gp18	F: VipB_N	ECOD (1.6)
LA [auth 3B]	VipB_C	e5urw3B2	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: VipB_C	ECOD (1.6)
LA [auth 3B]	VipB_N	e5urw3B1	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Domain III of tail sheath protein Gp18 (From Topology)	T: Domain III of tail sheath protein Gp18	F: VipB_N	ECOD (1.6)
L [auth 1L]	VipB_C	e5urw1L2	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: VipB_C	ECOD (1.6)
L [auth 1L]	VipB_N	e5urw1L1	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Domain III of tail sheath protein Gp18 (From Topology)	T: Domain III of tail sheath protein Gp18	F: VipB_N	ECOD (1.6)
J [auth 1J]	VipB_C	e5urw1J1	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: VipB_C	ECOD (1.6)
J [auth 1J]	VipB_N	e5urw1J2	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Domain III of tail sheath protein Gp18 (From Topology)	T: Domain III of tail sheath protein Gp18	F: VipB_N	ECOD (1.6)
H [auth 1H]	VipB_C	e5urw1H1	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: VipB_C	ECOD (1.6)
H [auth 1H]	VipB_N	e5urw1H2	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Domain III of tail sheath protein Gp18 (From Topology)	T: Domain III of tail sheath protein Gp18	F: VipB_N	ECOD (1.6)
F [auth 1F]	VipB_C	e5urw1F1	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: VipB_C	ECOD (1.6)
F [auth 1F]	VipB_N	e5urw1F2	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Domain III of tail sheath protein Gp18 (From Topology)	T: Domain III of tail sheath protein Gp18	F: VipB_N	ECOD (1.6)
DA [auth 2L]	VipB_C	e5urw2L1	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: VipB_C	ECOD (1.6)
DA [auth 2L]	VipB_N	e5urw2L2	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Domain III of tail sheath protein Gp18 (From Topology)	T: Domain III of tail sheath protein Gp18	F: VipB_N	ECOD (1.6)
D [auth 1D]	VipB_C	e5urw1D1	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: VipB_C	ECOD (1.6)
D [auth 1D]	VipB_N	e5urw1D2	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Domain III of tail sheath protein Gp18 (From Topology)	T: Domain III of tail sheath protein Gp18	F: VipB_N	ECOD (1.6)
BA [auth 2J]	VipB_C	e5urw2J1	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: VipB_C	ECOD (1.6)
BA [auth 2J]	VipB_N	e5urw2J2	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Domain III of tail sheath protein Gp18 (From Topology)	T: Domain III of tail sheath protein Gp18	F: VipB_N	ECOD (1.6)
B [auth 1B]	VipB_C	e5urw1B2	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: VipB_C	ECOD (1.6)
B [auth 1B]	VipB_N	e5urw1B1	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Domain III of tail sheath protein Gp18 (From Topology)	T: Domain III of tail sheath protein Gp18	F: VipB_N	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
AB [auth 35], BB [auth 36], EA [auth 21], FA [auth 22], GA [auth 23], AB [auth 35], BB [auth 36], EA [auth 21], FA [auth 22], GA [auth 23], HA [auth 24], IA [auth 25], JA [auth 26], M [auth 11], N [auth 12], O [auth 13], P [auth 14], Q [auth 15], R [auth 16], WA [auth 31], XA [auth 32], YA [auth 33], ZA [auth 34]	PF05638	Type VI secretion system effector, Hcp (T6SS_HCP)	Type VI secretion system effector, Hcp	HCP is a family of proteins which are expressed in up to 1000 copies in Gram-negative bacteria. Together these copies aggregate into a needle-like shaft or tube that will penetrate other bacteria via a puncturing protein attached to its head [1] bein ...	HCP is a family of proteins which are expressed in up to 1000 copies in Gram-negative bacteria. Together these copies aggregate into a needle-like shaft or tube that will penetrate other bacteria via a puncturing protein attached to its head [1] being part of the type VI secretion system [3,4]. Initially Hcp forms a hexameric structure with a central channel of 40 Angstroms. These hexamers pile up one on top of each other forming nanotubes resembling the gp19 tail phage tube [2].	Domain
B [auth 1B], BA [auth 2J], D [auth 1D], DA [auth 2L], F [auth 1F], B [auth 1B], BA [auth 2J], D [auth 1D], DA [auth 2L], F [auth 1F], H [auth 1H], J [auth 1J], L [auth 1L], LA [auth 3B], NA [auth 3D], PA [auth 3F], RA [auth 3H], T [auth 2B], TA [auth 3J], V [auth 2D], VA [auth 3L], X [auth 2F], Z [auth 2H]	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 [auth 1B], BA [auth 2J], D [auth 1D], DA [auth 2L], F [auth 1F], B [auth 1B], BA [auth 2J], D [auth 1D], DA [auth 2L], F [auth 1F], H [auth 1H], J [auth 1J], L [auth 1L], LA [auth 3B], NA [auth 3D], PA [auth 3F], RA [auth 3H], T [auth 2B], TA [auth 3J], V [auth 2D], VA [auth 3L], X [auth 2F], Z [auth 2H]	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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
AB [auth 35], BB [auth 36], EA [auth 21], FA [auth 22], GA [auth 23], AB [auth 35], BB [auth 36], EA [auth 21], FA [auth 22], GA [auth 23], HA [auth 24], IA [auth 25], JA [auth 26], M [auth 11], N [auth 12], O [auth 13], P [auth 14], Q [auth 15], R [auth 16], WA [auth 31], XA [auth 32], YA [auth 33], ZA [auth 34]	IPR036624	Hcp1-like superfamily	Homologous Superfamily
AB [auth 35], BB [auth 36], EA [auth 21], FA [auth 22], GA [auth 23], AB [auth 35], BB [auth 36], EA [auth 21], FA [auth 22], GA [auth 23], HA [auth 24], IA [auth 25], JA [auth 26], M [auth 11], N [auth 12], O [auth 13], P [auth 14], Q [auth 15], R [auth 16], WA [auth 31], XA [auth 32], YA [auth 33], ZA [auth 34]	IPR052947	Type VI secretion system Hcp1 domain-containing protein	Family
AB [auth 35], BB [auth 36], EA [auth 21], FA [auth 22], GA [auth 23], AB [auth 35], BB [auth 36], EA [auth 21], FA [auth 22], GA [auth 23], HA [auth 24], IA [auth 25], JA [auth 26], M [auth 11], N [auth 12], O [auth 13], P [auth 14], Q [auth 15], R [auth 16], WA [auth 31], XA [auth 32], YA [auth 33], ZA [auth 34]	IPR008514	Type VI secretion system effector Hcp	Family
B [auth 1B], BA [auth 2J], D [auth 1D], DA [auth 2L], F [auth 1F], B [auth 1B], BA [auth 2J], D [auth 1D], DA [auth 2L], F [auth 1F], H [auth 1H], J [auth 1J], L [auth 1L], LA [auth 3B], NA [auth 3D], PA [auth 3F], RA [auth 3H], T [auth 2B], TA [auth 3J], V [auth 2D], VA [auth 3L], X [auth 2F], Z [auth 2H]	IPR010269	Type VI secretion system TssC-like	Family
B [auth 1B], BA [auth 2J], D [auth 1D], DA [auth 2L], F [auth 1F], B [auth 1B], BA [auth 2J], D [auth 1D], DA [auth 2L], F [auth 1F], H [auth 1H], J [auth 1J], L [auth 1L], LA [auth 3B], NA [auth 3D], PA [auth 3F], RA [auth 3H], T [auth 2B], TA [auth 3J], V [auth 2D], VA [auth 3L], X [auth 2F], Z [auth 2H]	IPR044032	TssC1, C-terminal	Domain
B [auth 1B], BA [auth 2J], D [auth 1D], DA [auth 2L], F [auth 1F], B [auth 1B], BA [auth 2J], D [auth 1D], DA [auth 2L], F [auth 1F], H [auth 1H], J [auth 1J], L [auth 1L], LA [auth 3B], NA [auth 3D], PA [auth 3F], RA [auth 3H], T [auth 2B], TA [auth 3J], V [auth 2D], VA [auth 3L], X [auth 2F], Z [auth 2H]	IPR044031	TssC1, N-terminal	Domain
A [auth 1A], AA [auth 2I], C [auth 1C], CA [auth 2K], E [auth 1E], A [auth 1A], AA [auth 2I], C [auth 1C], CA [auth 2K], E [auth 1E], G [auth 1G], I [auth 1I], K [auth 1K], KA [auth 3A], MA [auth 3C], OA [auth 3E], QA [auth 3G], S [auth 2A], SA [auth 3I], U [auth 2C], UA [auth 3K], W [auth 2E], Y [auth 2G]	IPR008312	Type VI secretion system sheath protein TssB1	Family