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)
VA [auth s]	MIF	e7aefs1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: MIF	ECOD (v295.2)
UA [auth r]	MIF	e7aefr1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: MIF	ECOD (v295.2)
TA [auth q]	Alg8_N	e7aefq01	A: alpha arrays	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: Alg8_N	ECOD (v295.2)
TA [auth q]	TrkA_C	e7aefq04	A: alpha arrays	X: Rossmann-like	H: Rossmann-related	T: FAD/NAD(P)-binding domain	F: TrkA_C	ECOD (v295.2)
PA [auth p]	UCR_UQCRX_QCR9	e7aefp1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: UCR_UQCRX_QCR9	ECOD (v295.2)
OA [auth o]	UCR_UQCRX_QCR9	e7aefo1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: UCR_UQCRX_QCR9	ECOD (v295.2)
NA [auth n]	UCR_UQCRX_QCR9	e7aefn1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: UCR_UQCRX_QCR9	ECOD (v295.2)
MA [auth m]	UCR_UQCRX_QCR9	e7aefm1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: UCR_UQCRX_QCR9	ECOD (v295.2)
LA [auth l]	UCR_UQCRX_QCR9	e7aefl1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: UCR_UQCRX_QCR9	ECOD (v295.2)
KA [auth k]	Ribosomal_L36	e7aefk1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Ribosomal_L36	ECOD (v295.2)
JA [auth j]	MIF	e7aefj1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: MIF	ECOD (v295.2)
IA [auth i]	MIF	e7aefi1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: MIF	ECOD (v295.2)
HA [auth h]	MIF	e7aefh1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: MIF	ECOD (v295.2)
GA [auth g]	MIF	e7aefg1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: MIF	ECOD (v295.2)
FA [auth f]	MIF	e7aeff1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: MIF	ECOD (v295.2)
EA [auth e]	MIF	e7aefe1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: MIF	ECOD (v295.2)
Z	UCR_UQCRX_QCR9	e7aefZ1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: UCR_UQCRX_QCR9	ECOD (v295.2)
Y	Ribosomal_L36	e7aefY1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: Ribosomal_L36	ECOD (v295.2)
DA [auth d]	UCR_UQCRX_QCR9	e7aefd1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: UCR_UQCRX_QCR9	ECOD (v295.2)
CA [auth c]	UCR_UQCRX_QCR9	e7aefc1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: UCR_UQCRX_QCR9	ECOD (v295.2)
BA [auth b]	UCR_UQCRX_QCR9	e7aefb1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: UCR_UQCRX_QCR9	ECOD (v295.2)
AA [auth a]	UCR_UQCRX_QCR9	e7aefa1	A: alpha arrays	X: putative RnfG subunit of electron transport complex	H: putative RnfG subunit of electron transport complex	T: Aspartate/ornithine carbamoyltransferase	F: UCR_UQCRX_QCR9	ECOD (v295.2)
X	MlaD	e7aefX1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: MlaD	ECOD (v295.2)
W	MlaD	e7aefW1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: MlaD	ECOD (v295.2)
V	MlaD	e7aefV1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: MlaD	ECOD (v295.2)
U	MlaD	e7aefU1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: MlaD	ECOD (v295.2)
T	MlaD	e7aefT1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: MlaD	ECOD (v295.2)
S	MlaD	e7aefS1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: FMN-binding split barrel	F: MlaD	ECOD (v295.2)

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
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	-	-
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]	IPR063691	Phage baseplate V, C-terminal trimerisation domain	Domain
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
TA [auth q], UA [auth r], VA [auth s]	IPR063554	Alg8, N-terminal domain	Domain
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	IPR063260	Baseplate protein PVC11-like	Family
A, B, C, D, E A, B, C, D, E, F	IPR062935	Baseplate wedge Pvc12-like domain 3	Domain

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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.