6U5B

CryoEM Structure of Pyocin R2 - precontracted - baseplate

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
AB [auth L]	SCOP2B Superfamily	T6SS-like	8101743	3000580	SCOP2B (2022-06-29)
BA [auth T]	SCOP2B Superfamily	T6SS-like	8101743	3000580	SCOP2B (2022-06-29)
BB [auth I]	SCOP2B Superfamily	T6SS-like	8101743	3000580	SCOP2B (2022-06-29)
C [auth S]	SCOP2B Superfamily	T6SS-like	8101743	3000580	SCOP2B (2022-06-29)
CA [auth W]	SCOP2B Superfamily	T6SS-like	8101743	3000580	SCOP2B (2022-06-29)
CB [auth J]	SCOP2B Superfamily	T6SS-like	8101743	3000580	SCOP2B (2022-06-29)
DA [auth X]	SCOP2B Superfamily	T6SS-like	8101743	3000580	SCOP2B (2022-06-29)
EA [auth U]	SCOP2B Superfamily	T6SS-like	8101743	3000580	SCOP2B (2022-06-29)
FA [auth V]	SCOP2B Superfamily	T6SS-like	8101743	3000580	SCOP2B (2022-06-29)
SA [auth G]	SCOP2B Superfamily	T6SS-like	8101743	3000580	SCOP2B (2022-06-29)
YA [auth H]	SCOP2B Superfamily	T6SS-like	8101743	3000580	SCOP2B (2022-06-29)
ZA [auth K]	SCOP2B Superfamily	T6SS-like	8101743	3000580	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B [auth M]	Phage_sheath_1C	e6u5bM2	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: Phage_sheath_1C	ECOD (1.6)
B [auth M]	Phage_sheath_1	e6u5bM1	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: Phage_sheath_1	ECOD (1.6)
GA [auth N]	Phage_sheath_1C	e6u5bN2	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: Phage_sheath_1C	ECOD (1.6)
GA [auth N]	Phage_sheath_1	e6u5bN1	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: Phage_sheath_1	ECOD (1.6)
HA [auth Q]	Phage_sheath_1C	e6u5bQ1	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: Phage_sheath_1C	ECOD (1.6)
HA [auth Q]	Phage_sheath_1	e6u5bQ2	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: Phage_sheath_1	ECOD (1.6)
IA [auth R]	Phage_sheath_1C	e6u5bR1	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: Phage_sheath_1C	ECOD (1.6)
IA [auth R]	Phage_sheath_1	e6u5bR2	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: Phage_sheath_1	ECOD (1.6)
JA [auth O]	Phage_sheath_1C	e6u5bO1	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: Phage_sheath_1C	ECOD (1.6)
JA [auth O]	Phage_sheath_1	e6u5bO2	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: Phage_sheath_1	ECOD (1.6)
KA [auth P]	Phage_sheath_1C	e6u5bP1	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: Phage_sheath_1C	ECOD (1.6)
KA [auth P]	Phage_sheath_1	e6u5bP2	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: Phage_sheath_1	ECOD (1.6)
RA [auth A]	Phage_sheath_1C	e6u5bA1	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: Phage_sheath_1C	ECOD (1.6)
RA [auth A]	Phage_sheath_1	e6u5bA2	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: Phage_sheath_1	ECOD (1.6)
TA [auth B]	Phage_sheath_1C	e6u5bB1	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: Phage_sheath_1C	ECOD (1.6)
TA [auth B]	Phage_sheath_1	e6u5bB2	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: Phage_sheath_1	ECOD (1.6)
UA [auth E]	Phage_sheath_1C	e6u5bE1	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: Phage_sheath_1C	ECOD (1.6)
UA [auth E]	Phage_sheath_1	e6u5bE2	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: Phage_sheath_1	ECOD (1.6)
VA [auth F]	Phage_sheath_1C	e6u5bF1	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: Phage_sheath_1C	ECOD (1.6)
VA [auth F]	Phage_sheath_1	e6u5bF2	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: Phage_sheath_1	ECOD (1.6)
WA [auth C]	Phage_sheath_1C	e6u5bC1	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: Phage_sheath_1C	ECOD (1.6)
WA [auth C]	Phage_sheath_1	e6u5bC2	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: Phage_sheath_1	ECOD (1.6)
XA [auth D]	Phage_sheath_1C	e6u5bD2	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: Phage_sheath_1C	ECOD (1.6)
XA [auth D]	Phage_sheath_1	e6u5bD1	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: Phage_sheath_1	ECOD (1.6)
AB [auth L]	Phage_tube	e6u5bL1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Phage tail proteins	F: Phage_tube	ECOD (1.6)
BA [auth T]	Phage_tube	e6u5bT1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Phage tail proteins	F: Phage_tube	ECOD (1.6)
BB [auth I]	Phage_tube	e6u5bI1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Phage tail proteins	F: Phage_tube	ECOD (1.6)
C [auth S]	Phage_tube	e6u5bS1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Phage tail proteins	F: Phage_tube	ECOD (1.6)
CA [auth W]	Phage_tube	e6u5bW1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Phage tail proteins	F: Phage_tube	ECOD (1.6)
CB [auth J]	Phage_tube	e6u5bJ1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Phage tail proteins	F: Phage_tube	ECOD (1.6)
DA [auth X]	Phage_tube	e6u5bX1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Phage tail proteins	F: Phage_tube	ECOD (1.6)
EA [auth U]	Phage_tube	e6u5bU1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Phage tail proteins	F: Phage_tube	ECOD (1.6)
FA [auth V]	Phage_tube	e6u5bV1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Phage tail proteins	F: Phage_tube	ECOD (1.6)
SA [auth G]	Phage_tube	e6u5bG1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Phage tail proteins	F: Phage_tube	ECOD (1.6)
YA [auth H]	Phage_tube	e6u5bH1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Phage tail proteins	F: Phage_tube	ECOD (1.6)
ZA [auth K]	Phage_tube	e6u5bK1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: Phage tail proteins	F: Phage_tube	ECOD (1.6)
E [auth a]	GPW_gp25	e6u5ba1	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: GPW_gp25	ECOD (1.6)
H [auth b]	GPW_gp25	e6u5bb1	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: GPW_gp25	ECOD (1.6)
I [auth e]	GPW_gp25	e6u5be1	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: GPW_gp25	ECOD (1.6)
J [auth f]	GPW_gp25	e6u5bf1	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: GPW_gp25	ECOD (1.6)
K [auth c]	GPW_gp25	e6u5bc1	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: GPW_gp25	ECOD (1.6)
L [auth d]	GPW_gp25	e6u5bd1	A: a+b duplicates or obligate multimers	X: Creatinase/aminopeptidase-like	H: gpW/gp25-like (From Topology)	T: gpW/gp25-like	F: GPW_gp25	ECOD (1.6)
F [auth 6]	Phage_tail_X	e6u5b61	A: alpha arrays	X: HTH	H: LysM domain (From Topology)	T: LysM domain	F: Phage_tail_X	ECOD (1.6)
M [auth 7]	Phage_tail_X	e6u5b71	A: alpha arrays	X: HTH	H: LysM domain (From Topology)	T: LysM domain	F: Phage_tail_X	ECOD (1.6)
N [auth Y]	Phage_tail_X	e6u5bY1	A: alpha arrays	X: HTH	H: LysM domain (From Topology)	T: LysM domain	F: Phage_tail_X	ECOD (1.6)
O [auth Z]	Phage_tail_X	e6u5bZ1	A: alpha arrays	X: HTH	H: LysM domain (From Topology)	T: LysM domain	F: Phage_tail_X	ECOD (1.6)
P [auth 8]	Phage_tail_X	e6u5b81	A: alpha arrays	X: HTH	H: LysM domain (From Topology)	T: LysM domain	F: Phage_tail_X	ECOD (1.6)
Q [auth 9]	Phage_tail_X	e6u5b91	A: alpha arrays	X: HTH	H: LysM domain (From Topology)	T: LysM domain	F: Phage_tail_X	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth M], GA [auth N], HA [auth Q], IA [auth R], JA [auth O], B [auth M], GA [auth N], HA [auth Q], IA [auth R], JA [auth O], KA [auth P], RA [auth A], TA [auth B], UA [auth E], VA [auth F], WA [auth C], XA [auth D]	PF17482	Phage tail sheath C-terminal domain (Phage_sheath_1C)	Phage tail sheath C-terminal domain	This entry represents the C-terminal domain in a variety of phage tail sheath proteins [4].	Domain
B [auth M], GA [auth N], HA [auth Q], IA [auth R], JA [auth O], B [auth M], GA [auth N], HA [auth Q], IA [auth R], JA [auth O], KA [auth P], RA [auth A], TA [auth B], UA [auth E], VA [auth F], WA [auth C], XA [auth D]	PF22671	Tail sheath protein Gp18 domain III N-terminal region (Gp18_domIII_N)	Tail sheath protein Gp18 domain III N-terminal region	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 ...	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
B [auth M], GA [auth N], HA [auth Q], IA [auth R], JA [auth O], B [auth M], GA [auth N], HA [auth Q], IA [auth R], JA [auth O], KA [auth P], RA [auth A], TA [auth B], UA [auth E], VA [auth F], WA [auth C], XA [auth D]	PF04984	Phage tail sheath protein subtilisin-like domain (Phage_sheath_1)	Phage tail sheath protein subtilisin-like domain	This entry represents the second domain in a variety of phage tail sheath proteins. According to ECOD this domain has a subtilisin-like structure.	Domain
B [auth M], GA [auth N], HA [auth Q], IA [auth R], JA [auth O], B [auth M], GA [auth N], HA [auth Q], IA [auth R], JA [auth O], KA [auth P], RA [auth A], TA [auth B], UA [auth E], VA [auth F], WA [auth C], XA [auth D]	PF04965	Baseplate wedge protein gp25 (GPW_gp25)	Baseplate wedge protein gp25	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 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
B [auth M], GA [auth N], HA [auth Q], IA [auth R], JA [auth O], B [auth M], GA [auth N], HA [auth Q], IA [auth R], JA [auth O], KA [auth P], RA [auth A], TA [auth B], UA [auth E], VA [auth F], WA [auth C], XA [auth D]	PF04865	Baseplate J-like protein (Baseplate_J)	Baseplate J-like protein	-	Family
AB [auth L], BA [auth T], BB [auth I], C [auth S], CA [auth W], AB [auth L], BA [auth T], BB [auth I], C [auth S], CA [auth W], CB [auth J], DA [auth X], EA [auth U], FA [auth V], SA [auth G], YA [auth H], ZA [auth K]	PF06995	Phage P2 GpU (Phage_P2_GpU)	Phage P2 GpU	-	Family
AB [auth L], BA [auth T], BB [auth I], C [auth S], CA [auth W], AB [auth L], BA [auth T], BB [auth I], C [auth S], CA [auth W], CB [auth J], DA [auth X], EA [auth U], FA [auth V], SA [auth G], YA [auth H], ZA [auth K]	PF04985	Phage tail tube protein FII (Phage_tube)	Phage tail tube protein FII	-	Family
AB [auth L], BA [auth T], BB [auth I], C [auth S], CA [auth W], AB [auth L], BA [auth T], BB [auth I], C [auth S], CA [auth W], CB [auth J], DA [auth X], EA [auth U], FA [auth V], SA [auth G], YA [auth H], ZA [auth K]	PF04865	Baseplate J-like protein (Baseplate_J)	Baseplate J-like protein	-	Family
AA [auth 3], D [auth 0], W [auth 1], X [auth 4], Y [auth 5], AA [auth 3], D [auth 0], W [auth 1], X [auth 4], Y [auth 5], Z [auth 2]	PF09684	Phage tail protein (Tail_P2_I) (Tail_P2_I)	Phage tail protein (Tail_P2_I)	-	Family
F [auth 6], M [auth 7], N [auth Y], O [auth Z], P [auth 8], F [auth 6], M [auth 7], N [auth Y], O [auth Z], P [auth 8], Q [auth 9]	PF05489	Phage Tail Protein X (Phage_tail_X)	Phage Tail Protein X	This 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

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth m], DB [auth t], EB [auth w], FB [auth x], GB [auth u], A [auth m], DB [auth t], EB [auth w], FB [auth x], GB [auth u], HB [auth v], QA [auth s], R [auth n], S [auth q], T [auth r], U [auth o], V [auth p]	IPR014507	Baseplate assembly protein J, predicted	Family
A [auth m], DB [auth t], EB [auth w], FB [auth x], GB [auth u], A [auth m], DB [auth t], EB [auth w], FB [auth x], GB [auth u], HB [auth v], QA [auth s], R [auth n], S [auth q], T [auth r], U [auth o], V [auth p]	IPR006949	Baseplate protein J-like	Domain
A [auth m], DB [auth t], EB [auth w], FB [auth x], GB [auth u], A [auth m], DB [auth t], EB [auth w], FB [auth x], GB [auth u], HB [auth v], QA [auth s], R [auth n], S [auth q], T [auth r], U [auth o], V [auth p]	IPR052726	Bacteriophage Baseplate Hub	Family
B [auth M], GA [auth N], HA [auth Q], IA [auth R], JA [auth O], B [auth M], GA [auth N], HA [auth Q], IA [auth R], JA [auth O], KA [auth P], RA [auth A], TA [auth B], UA [auth E], VA [auth F], WA [auth C], XA [auth D]	IPR020287	Tail sheath protein, C-terminal domain	Domain
B [auth M], GA [auth N], HA [auth Q], IA [auth R], JA [auth O], B [auth M], GA [auth N], HA [auth Q], IA [auth R], JA [auth O], KA [auth P], RA [auth A], TA [auth B], UA [auth E], VA [auth F], WA [auth C], XA [auth D]	IPR054564	Tail sheath protein Gp18-like, domain III N-terminal region	Domain
B [auth M], GA [auth N], HA [auth Q], IA [auth R], JA [auth O], B [auth M], GA [auth N], HA [auth Q], IA [auth R], JA [auth O], KA [auth P], RA [auth A], TA [auth B], UA [auth E], VA [auth F], WA [auth C], XA [auth D]	IPR035089	Tail sheath protein, subtilisin-like domain	Domain
B [auth M], GA [auth N], HA [auth Q], IA [auth R], JA [auth O], B [auth M], GA [auth N], HA [auth Q], IA [auth R], JA [auth O], KA [auth P], RA [auth A], TA [auth B], UA [auth E], VA [auth F], WA [auth C], XA [auth D]	IPR052042	Bacteriophage Tail Sheath Structural Protein	Family
AB [auth L], BA [auth T], BB [auth I], C [auth S], CA [auth W], AB [auth L], BA [auth T], BB [auth I], C [auth S], CA [auth W], CB [auth J], DA [auth X], EA [auth U], FA [auth V], SA [auth G], YA [auth H], ZA [auth K]	IPR006498	Tail tube protein	Family
AB [auth L], BA [auth T], BB [auth I], C [auth S], CA [auth W], AB [auth L], BA [auth T], BB [auth I], C [auth S], CA [auth W], CB [auth J], DA [auth X], EA [auth U], FA [auth V], SA [auth G], YA [auth H], ZA [auth K]	IPR052042	Bacteriophage Tail Sheath Structural Protein	Family
AA [auth 3], D [auth 0], W [auth 1], X [auth 4], Y [auth 5], AA [auth 3], D [auth 0], W [auth 1], X [auth 4], Y [auth 5], Z [auth 2]	IPR006521	Tail protein I	Family
E [auth a], H [auth b], I [auth e], J [auth f], K [auth c], E [auth a], H [auth b], I [auth e], J [auth f], K [auth c], L [auth d]	IPR007048	IraD/Gp25-like	Domain
F [auth 6], M [auth 7], N [auth Y], O [auth Z], P [auth 8], F [auth 6], M [auth 7], N [auth Y], O [auth Z], P [auth 8], Q [auth 9]	IPR008861	Phage Tail Protein X-like	Family
G [auth h], LA [auth g], MA [auth l], NA [auth k], OA [auth j], G [auth h], LA [auth g], MA [auth l], NA [auth k], OA [auth j], PA [auth i]	IPR009734	Myoviridae, GpU	Family
G [auth h], LA [auth g], MA [auth l], NA [auth k], OA [auth j], G [auth h], LA [auth g], MA [auth l], NA [auth k], OA [auth j], PA [auth i]	IPR014458	Uncharacterised protein family, phage P2-GpU-fusion	Family