7AEF | pdb_00007aef

Cryo-EM structure of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis, the baseplate complex in extended state applied 3-fold symmetry.

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product 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)
PA [auth p]	F_UNCLASSIFIED	e7aefp1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: F_UNCLASSIFIED	ECOD (1.6)
OA [auth o]	F_UNCLASSIFIED	e7aefo1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: F_UNCLASSIFIED	ECOD (1.6)
NA [auth n]	F_UNCLASSIFIED	e7aefn1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: F_UNCLASSIFIED	ECOD (1.6)
MA [auth m]	F_UNCLASSIFIED	e7aefm1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: F_UNCLASSIFIED	ECOD (1.6)
LA [auth l]	F_UNCLASSIFIED	e7aefl1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: F_UNCLASSIFIED	ECOD (1.6)
KA [auth k]	F_UNCLASSIFIED	e7aefk1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: F_UNCLASSIFIED	ECOD (1.6)
Z	F_UNCLASSIFIED	e7aefZ1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: F_UNCLASSIFIED	ECOD (1.6)
Y	F_UNCLASSIFIED	e7aefY1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: F_UNCLASSIFIED	ECOD (1.6)
DA [auth d]	F_UNCLASSIFIED	e7aefd1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: F_UNCLASSIFIED	ECOD (1.6)
CA [auth c]	F_UNCLASSIFIED	e7aefc1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: F_UNCLASSIFIED	ECOD (1.6)
BA [auth b]	F_UNCLASSIFIED	e7aefb1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: F_UNCLASSIFIED	ECOD (1.6)
AA [auth a]	F_UNCLASSIFIED	e7aefa1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: F_UNCLASSIFIED	ECOD (1.6)
X	GPW_gp25	e7aefX1	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)
W	GPW_gp25	e7aefW1	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)
V	GPW_gp25	e7aefV1	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)
U	GPW_gp25	e7aefU1	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)
T	GPW_gp25	e7aefT1	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)
S	GPW_gp25	e7aefS1	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
AA [auth a], BA [auth b], CA [auth c], DA [auth d], Y, AA [auth a], BA [auth b], CA [auth c], DA [auth d], Y, Z	PF06841	T4-like virus tail tube protein gp19 (Phage_T4_gp19)	T4-like virus tail tube protein gp19	-	Family
S, T, U, V, W S, T, U, V, W, X	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
M, N, O, P, Q M, N, O, P, Q, R	PF19266	Contractile injection system tube protein (CIS_tube)	Contractile injection system tube protein	-	Family
M, N, O, P, Q M, N, O, P, Q, R	PF06841	T4-like virus tail tube protein gp19 (Phage_T4_gp19)	T4-like virus tail tube protein gp19	-	Family
G, H, I, J, K G, H, I, J, K, L	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
G, H, I, J, K G, H, I, J, K, L	PF06841	T4-like virus tail tube protein gp19 (Phage_T4_gp19)	T4-like virus tail tube protein gp19	-	Family
G, H, I, J, K G, H, I, J, K, L	PF04865	Baseplate J-like protein barrel domain (Baseplate_J)	Baseplate J-like protein barrel domain	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 six stranded beta barrel domain found in va ...	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 six stranded beta barrel domain found in various baseplate J-like proteins.	Domain
A, B, C, D, E A, B, C, D, E, F	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
A, B, C, D, E A, B, C, D, E, F	PF06841	T4-like virus tail tube protein gp19 (Phage_T4_gp19)	T4-like virus tail tube protein gp19	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
TA [auth q], UA [auth r], VA [auth s]	Phosphoserine phosphatase SerB	-	-	-
QA [auth t], RA [auth u], SA [auth v]	inner protein (Algo6)	-	-	-
KA [auth k], LA [auth l], MA [auth m], NA [auth n], OA [auth o], KA [auth k], LA [auth l], MA [auth m], NA [auth n], OA [auth o], PA [auth p]	Phage tail protein	structural molecule activity	-	-
EA [auth e], FA [auth f], GA [auth g], HA [auth h], IA [auth i], EA [auth e], FA [auth f], GA [auth g], HA [auth h], IA [auth i], JA [auth j]	Putative phage tail sheath protein FI	-	-	-
AA [auth a], BA [auth b], CA [auth c], DA [auth d], Y, AA [auth a], BA [auth b], CA [auth c], DA [auth d], Y, Z	Phospholipid/glycerol acyltransferase	structural molecule activity acyltransferase activity transferase activity catalytic activity	-	-
S, T, U, V, W S, T, U, V, W, X	Putative tail lysozyme	-	-	-
M, N, O, P, Q M, N, O, P, Q, R	LysM domain-containing protein	-	-	-
G, H, I, J, K G, H, I, J, K, L	Baseplate_J domain-containing protein	-	-	-
A, B, C, D, E A, B, C, D, E, F	baseplate protein (Algo12)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
TA [auth q], UA [auth r], VA [auth s]	IPR006531	Gp5/Type VI secretion system Vgr protein, OB-fold domain	Domain
TA [auth q], UA [auth r], VA [auth s]	IPR037026	Vgr protein, OB-fold domain superfamily	Homologous Superfamily
TA [auth q], UA [auth r], VA [auth s]	IPR006533	Type VI secretion system, RhsGE-associated Vgr protein	Family
QA [auth t], RA [auth u], SA [auth v]	IPR045459	Protein of unknown function DUF5908	Family
KA [auth k], LA [auth l], MA [auth m], NA [auth n], OA [auth o], KA [auth k], LA [auth l], MA [auth m], NA [auth n], OA [auth o], PA [auth p]	IPR011747	Conserved hypothetical protein CHP02241	Family
KA [auth k], LA [auth l], MA [auth m], NA [auth n], OA [auth o], KA [auth k], LA [auth l], MA [auth m], NA [auth n], OA [auth o], PA [auth p]	IPR010667	Bacteriophage T4, Gp19, tail tube	Family
EA [auth e], FA [auth f], GA [auth g], HA [auth h], IA [auth i], EA [auth e], FA [auth f], GA [auth g], HA [auth h], IA [auth i], JA [auth j]	IPR052042	Tail sheath structural protein	Family
EA [auth e], FA [auth f], GA [auth g], HA [auth h], IA [auth i], EA [auth e], FA [auth f], GA [auth g], HA [auth h], IA [auth i], JA [auth j]	IPR020287	Tail sheath protein, C-terminal domain	Domain
AA [auth a], BA [auth b], CA [auth c], DA [auth d], Y, AA [auth a], BA [auth b], CA [auth c], DA [auth d], Y, Z	IPR011747	Conserved hypothetical protein CHP02241	Family
AA [auth a], BA [auth b], CA [auth c], DA [auth d], Y, AA [auth a], BA [auth b], CA [auth c], DA [auth d], Y, Z	IPR010667	Bacteriophage T4, Gp19, tail tube	Family
S, T, U, V, W S, T, U, V, W, X	IPR007048	IraD/Gp25-like	Domain
M, N, O, P, Q M, N, O, P, Q, R	IPR045361	Contractile injection system tube protein, N-terminal domain	Domain
M, N, O, P, Q M, N, O, P, Q, R	IPR018392	LysM domain	Domain
G, H, I, J, K G, H, I, J, K, L	IPR006949	Baseplate protein J-like, barrel domain	Domain

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.