5MXN

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


Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
G [auth 3]PF05638e5mxn31 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: FMN-binding split barrelF: PF05638ECOD (1.6)
J [auth 4]PF05638e5mxn41 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: FMN-binding split barrelF: PF05638ECOD (1.6)
M [auth 5]PF05638e5mxn51 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: FMN-binding split barrelF: PF05638ECOD (1.6)
P [auth 6]PF05638e5mxn61 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: FMN-binding split barrelF: PF05638ECOD (1.6)
A [auth 1]PF05638e5mxn11 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: FMN-binding split barrelF: PF05638ECOD (1.6)
D [auth 2]PF05638e5mxn21 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: FMN-binding split barrelF: PF05638ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

ChainDomainClassArchitectureTopologyHomologyProvenance Source (Version)
G [auth 3]2.30.110.20 Mainly Beta Roll Pnp Oxidase Chain ACATH (4.3.0)
J [auth 4]2.30.110.20 Mainly Beta Roll Pnp Oxidase Chain ACATH (4.3.0)
M [auth 5]2.30.110.20 Mainly Beta Roll Pnp Oxidase Chain ACATH (4.3.0)
P [auth 6]2.30.110.20 Mainly Beta Roll Pnp Oxidase Chain ACATH (4.3.0)
A [auth 1]2.30.110.20 Mainly Beta Roll Pnp Oxidase Chain ACATH (4.3.0)
D [auth 2]2.30.110.20 Mainly Beta Roll Pnp Oxidase Chain ACATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF05638Type VI secretion system effector, Hcp (T6SS_HCP)Type VI secretion system effector, HcpHCP 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]. In ...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]. 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
PF05943EvpB/VC_A0108, tail sheath N-terminal domain (VipB)EvpB/VC_A0108, tail sheath N-terminal domainEvpB 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
PF18945EvpB/VC_A0108, tail sheath gpW/gp25-like domain (VipB_2)EvpB/VC_A0108, tail sheath gpW/gp25-like domainEvpB 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
PF05591Type VI secretion system, VipA, VC_A0107 or Hcp2 (T6SS_VipA)Type VI secretion system, VipA, VC_A0107 or Hcp2- Family