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]	APG6	e5urw341	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
YA [auth 33]	APG6	e5urw331	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
XA [auth 32]	APG6	e5urw321	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
WA [auth 31]	APG6	e5urw311	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
R [auth 16]	APG6	e5urw161	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
Q [auth 15]	APG6	e5urw151	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
P [auth 14]	APG6	e5urw141	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
O [auth 13]	APG6	e5urw131	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
N [auth 12]	APG6	e5urw121	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
M [auth 11]	APG6	e5urw111	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
JA [auth 26]	APG6	e5urw261	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
IA [auth 25]	APG6	e5urw251	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
HA [auth 24]	APG6	e5urw241	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
GA [auth 23]	APG6	e5urw231	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
FA [auth 22]	APG6	e5urw221	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
EA [auth 21]	APG6	e5urw211	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
BB [auth 36]	APG6	e5urw361	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
AB [auth 35]	APG6	e5urw351	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
Z [auth 2H]	APG6	e5urw2H1	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
X [auth 2F]	APG6	e5urw2F1	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
VA [auth 3L]	APG6	e5urw3L1	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
V [auth 2D]	APG6	e5urw2D1	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
TA [auth 3J]	APG6	e5urw3J1	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
T [auth 2B]	APG6	e5urw2B1	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
RA [auth 3H]	APG6	e5urw3H1	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
PA [auth 3F]	APG6	e5urw3F1	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
NA [auth 3D]	APG6	e5urw3D1	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
LA [auth 3B]	APG6	e5urw3B1	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
L [auth 1L]	APG6	e5urw1L1	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
J [auth 1J]	APG6	e5urw1J1	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
H [auth 1H]	APG6	e5urw1H1	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
F [auth 1F]	APG6	e5urw1F1	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
DA [auth 2L]	APG6	e5urw2L1	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
D [auth 1D]	APG6	e5urw1D1	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
BA [auth 2J]	APG6	e5urw2J1	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
B [auth 1B]	APG6	e5urw1B1	A: beta barrels	X: HAD domain-like	H: Class I glutamine amidotransferase-like	T: CheY-like	F: APG6	ECOD (v294.2)
A [auth 1A]	MCM	e5urw1A01	A: beta barrels	X: Voltage-gated ion channels	H: Voltage-gated ion channels	T: ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	F: MCM	ECOD (v294.2)

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	T6SS_Hcp1_domain	Unknown
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	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]	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

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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.