6U5B | pdb_00006u5b

CryoEM Structure of Pyocin R2 - precontracted - baseplate


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
ZA [auth K]SCOP2B SuperfamilyT6SS-like 8101743 3000580 SCOP2B (2022-06-29)
YA [auth H]SCOP2B SuperfamilyT6SS-like 8101743 3000580 SCOP2B (2022-06-29)
SA [auth G]SCOP2B SuperfamilyT6SS-like 8101743 3000580 SCOP2B (2022-06-29)
FA [auth V]SCOP2B SuperfamilyT6SS-like 8101743 3000580 SCOP2B (2022-06-29)
EA [auth U]SCOP2B SuperfamilyT6SS-like 8101743 3000580 SCOP2B (2022-06-29)
DA [auth X]SCOP2B SuperfamilyT6SS-like 8101743 3000580 SCOP2B (2022-06-29)
CB [auth J]SCOP2B SuperfamilyT6SS-like 8101743 3000580 SCOP2B (2022-06-29)
CA [auth W]SCOP2B SuperfamilyT6SS-like 8101743 3000580 SCOP2B (2022-06-29)
C [auth S]SCOP2B SuperfamilyT6SS-like 8101743 3000580 SCOP2B (2022-06-29)
BB [auth I]SCOP2B SuperfamilyT6SS-like 8101743 3000580 SCOP2B (2022-06-29)
BA [auth T]SCOP2B SuperfamilyT6SS-like 8101743 3000580 SCOP2B (2022-06-29)
AB [auth L]SCOP2B SuperfamilyT6SS-like 8101743 3000580 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
Q [auth 9]G-alphae6u5b91 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
P [auth 8]G-alphae6u5b81 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
O [auth Z]G-alphae6u5bZ1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
N [auth Y]G-alphae6u5bY1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
M [auth 7]G-alphae6u5b71 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
F [auth 6]Ribosomal_L4e6u5b61 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: Ribosomal_L4ECOD (develop294)
L [auth d]G-alphae6u5bd1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
K [auth c]G-alphae6u5bc1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
J [auth f]G-alphae6u5bf1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
I [auth e]G-alphae6u5be1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
H [auth b]G-alphae6u5bb1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
E [auth a]Ribosomal_L4e6u5ba1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: Ribosomal_L4ECOD (develop294)
ZA [auth K]G-alphae6u5bK1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
YA [auth H]G-alphae6u5bH1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
SA [auth G]G-alphae6u5bG1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
FA [auth V]G-alphae6u5bV1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
EA [auth U]G-alphae6u5bU1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
DA [auth X]G-alphae6u5bX1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
CB [auth J]G-alphae6u5bJ1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
CA [auth W]G-alphae6u5bW1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
C [auth S]G-alphae6u5bS1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
BB [auth I]G-alphae6u5bI1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
BA [auth T]G-alphae6u5bT1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
AB [auth L]G-alphae6u5bL1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
XA [auth D]G-alphae6u5bD1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
WA [auth C]G-alphae6u5bC1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
VA [auth F]G-alphae6u5bF1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
UA [auth E]G-alphae6u5bE1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
TA [auth B]G-alphae6u5bB1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
RA [auth A]G-alphae6u5bA1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
KA [auth P]G-alphae6u5bP1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
JA [auth O]G-alphae6u5bO1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
IA [auth R]G-alphae6u5bR1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
HA [auth Q]G-alphae6u5bQ1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
GA [auth N]G-alphae6u5bN1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)
B [auth M]G-alphae6u5bM1 A: alpha bundlesX: Immunoglobulin-like beta-sandwichH: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesT: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetasesF: G-alphaECOD (develop294)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
PF05489Phage Tail Protein X (Phage_tail_X)Phage Tail Protein XThis domain is found in a family of phage tail proteins. Visual analysis suggests that it is related to Pfam:PF01476 (personal obs: C Yeats). The functional annotation of family members further confirms this hypothesis. Domain
PF09684Phage tail protein (Tail_P2_I) (Tail_P2_I)Phage tail protein (Tail_P2_I)- Family
PF26078Baseplate J-like central domain (Baseplate_J_M)Baseplate J-like central domainThe P2 bacteriophage J protein lies at the edge of the baseplate. This family also includes a number of bacterial homologues, which are thought to have been horizontally transferred. This entry represents a domain found in baseplate J-like proteins. ...The P2 bacteriophage J protein lies at the edge of the baseplate. This family also includes a number of bacterial homologues, which are thought to have been horizontally transferred. This entry represents a domain found in baseplate J-like proteins.
Domain
PF06995Phage P2 GpU (Phage_P2_GpU)Phage P2 GpU- Family
PF04985Phage tail tube protein FII (Phage_tube)Phage tail tube protein FII- Family
PF17482Phage tail sheath C-terminal domain (Phage_sheath_1C)Phage tail sheath C-terminal domainThis entry represents the C-terminal domain in a variety of phage tail sheath proteins [4]. Domain
PF22671Tail sheath protein Gp18 domain III N-terminal region (Gp18_domIII_N)Tail sheath protein Gp18 domain III N-terminal regionThis entry represents the N-terminal segment of domain III from the phage tail sheath protein Gp18 y similar sequences [1-5]. Domain III is completed by Pfam:PF04984 with an overall structure consisting of a beta-sheet with five parallel and one anti ...This entry represents the N-terminal segment of domain III from the phage tail sheath protein Gp18 y similar sequences [1-5]. Domain III is completed by Pfam:PF04984 with an overall structure consisting of a beta-sheet with five parallel and one anti-parallel beta-strands plus six alpha-helices, which surround the beta-sheet.
Domain
PF26079Baseplate J-like protein C-terminal domain (Baseplate_J_C)Baseplate J-like protein C-terminal domainThe P2 bacteriophage J protein lies at the edge of the baseplate. This family also includes a number of bacterial homologues, which are thought to have been horizontally transferred. This entry represents a C-terminal domain found in these protein. Domain
PF26078Baseplate J-like central domain (Baseplate_J_M)Baseplate J-like central domainThe P2 bacteriophage J protein lies at the edge of the baseplate. This family also includes a number of bacterial homologues, which are thought to have been horizontally transferred. This entry represents a domain found in baseplate J-like proteins. ...The P2 bacteriophage J protein lies at the edge of the baseplate. This family also includes a number of bacterial homologues, which are thought to have been horizontally transferred. This entry represents a domain found in baseplate J-like proteins.
Domain
PF04984Phage tail sheath protein subtilisin-like domain (Phage_sheath_1)Phage tail sheath protein subtilisin-like domainThis entry represents the second domain in a variety of phage tail sheath proteins. According to ECOD this domain has a subtilisin-like structure. Domain
PF04965Baseplate wedge protein gp25 (GPW_gp25)Baseplate wedge protein gp25This family represents T4 phage gp25 protein and gp25-like proteins, found in several systems, including contractile tail bacteriophages, the type VI secretion system (T6SS) and R-type pyocins, which constitute a multiprotein tubular apparatus to att ...This family represents T4 phage gp25 protein and gp25-like proteins, found in several systems, including contractile tail bacteriophages, the type VI secretion system (T6SS) and R-type pyocins, which constitute a multiprotein tubular apparatus to attach to and penetrate host cell membranes. Gp25 is a component of the conserved wedge in the inner part of the baseplate and serves as a nucleus for sheath polymerisation, playing a critical role in sheath assembly and contraction [1,2]. The EPR motif (Glu-Pro-Arg, residues 85-87 of gp25) is conserved across all members of the family including orthologues from the RpoS-mediated general stress response system (called IraD) [3,4]. This motif interacts with the 'core bundle' composed of orthologues of T4 gp6 and gp7 proteins in contractile injection systems.
Domain

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
IPR009734Myoviridae, GpUFamily
IPR014458Uncharacterised protein family, phage P2-GpU-fusionFamily
IPR008861Phage Tail Protein X-likeFamily
IPR007048IraD/Gp25-likeDomain
IPR006521Tail protein IFamily
IPR052042Tail sheath structural proteinFamily
IPR006498Tail tube proteinFamily
IPR052042Tail sheath structural proteinFamily
IPR020287Tail sheath protein, C-terminal domainDomain
IPR054564Tail sheath protein Gp18-like, domain III N-terminal regionDomain
IPR035089Tail sheath protein, subtilisin-like domainDomain
IPR058530Baseplate J-like, C-terminal domainDomain
IPR014507Baseplate assembly protein J, predictedFamily
IPR058531Baseplate J-like, central domainDomain
IPR052726Bacteriophage Baseplate HubFamily