7ADZ | pdb_00007adz

Cryo-EM structure of an extracellular contractile injection system in marine bacterium Algoriphagus machipongonensis, the cap portion in extended state.

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)
AA [auth 2c]	Ribosomal_L19	e7adz2c1	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ribosomal_L19	ECOD (v294.2)
BA [auth 2d]	Ribosomal_L19	e7adz2d1	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ribosomal_L19	ECOD (v294.2)
CA [auth 2e]	Ribosomal_L19	e7adz2e1	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ribosomal_L19	ECOD (v294.2)
DA [auth 2f]	Ribosomal_L19	e7adz2f1	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ribosomal_L19	ECOD (v294.2)
M [auth 1a]	GST_C	e7adz1a1	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: GST_C	ECOD (v294.2)
N [auth 1b]	Ribosomal_L19	e7adz1b1	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ribosomal_L19	ECOD (v294.2)
O [auth 1c]	Ribosomal_L19	e7adz1c1	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ribosomal_L19	ECOD (v294.2)
P [auth 1d]	Ribosomal_L19	e7adz1d1	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ribosomal_L19	ECOD (v294.2)
Q [auth 1e]	Ribosomal_L19	e7adz1e1	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ribosomal_L19	ECOD (v294.2)
R [auth 1f]	Ribosomal_L19	e7adz1f1	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ribosomal_L19	ECOD (v294.2)
Y [auth 2a]	Ribosomal_L19	e7adz2a1	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ribosomal_L19	ECOD (v294.2)
Z [auth 2b]	Ribosomal_L19	e7adz2b1	A: beta barrels	X: Nuclear receptor ligand-binding domain	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: Ribosomal_L19	ECOD (v294.2)
S [auth 2A]	MIF4G	e7adz2A1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)
T [auth 2B]	MIF4G	e7adz2B1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)
U [auth 2C]	MIF4G	e7adz2C1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)
V [auth 2D]	MIF4G	e7adz2D1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)
W [auth 2E]	MIF4G	e7adz2E1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)
X [auth 2F]	MIF4G	e7adz2F1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: MIF4G	ECOD (v294.2)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth 0A], B [auth 0B], C [auth 0C], D [auth 0D], E [auth 0E], A [auth 0A], B [auth 0B], C [auth 0C], D [auth 0D], E [auth 0E], F [auth 0F]	PF14065	Pvc16 N-terminal domain (Pvc16_N)	Pvc16 N-terminal domain	This protein forms part of a contractile injection system [1]. Photorhabdus virulence cassette (PVC) represents one group of extracellular CISs that are present in both bacteria and archaea [1]. This entry include Pvc16. This family of proteins is f ...	This protein forms part of a contractile injection system [1]. Photorhabdus virulence cassette (PVC) represents one group of extracellular CISs that are present in both bacteria and archaea [1]. This entry include Pvc16. This family of proteins is found in bacteria and archaea. Proteins in this family are typically between 190 and 320 amino acids in length. This domain alone in Pvc16 is able to produce PVC particles with normal length but without the outer sheath, indicating the main function of this N-terminal domain in terminating the tube growth [1].	Domain
G [auth 1A], H [auth 1B], I [auth 1C], J [auth 1D], K [auth 1E], G [auth 1A], H [auth 1B], I [auth 1C], J [auth 1D], K [auth 1E], L [auth 1F]	PF06841	T4-like virus tail tube protein gp19 (Phage_T4_gp19)	T4-like virus tail tube protein gp19	-	Family
S [auth 2A], T [auth 2B], U [auth 2C], V [auth 2D], W [auth 2E], S [auth 2A], T [auth 2B], U [auth 2C], V [auth 2D], W [auth 2E], X [auth 2F]	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
S [auth 2A], T [auth 2B], U [auth 2C], V [auth 2D], W [auth 2E], S [auth 2A], T [auth 2B], U [auth 2C], V [auth 2D], W [auth 2E], X [auth 2F]	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
A [auth 0A], B [auth 0B], C [auth 0C], D [auth 0D], E [auth 0E], A [auth 0A], B [auth 0B], C [auth 0C], D [auth 0D], E [auth 0E], F [auth 0F]	cap protein (Algo1)	-	-	-
G [auth 1A], H [auth 1B], I [auth 1C], J [auth 1D], K [auth 1E], G [auth 1A], H [auth 1B], I [auth 1C], J [auth 1D], K [auth 1E], L [auth 1F]	cap adaptor protein (Algo2)	-	-	-
AA [auth 2c], BA [auth 2d], CA [auth 2e], DA [auth 2f], M [auth 1a], AA [auth 2c], BA [auth 2d], CA [auth 2e], DA [auth 2f], M [auth 1a], N [auth 1b], O [auth 1c], P [auth 1d], Q [auth 1e], R [auth 1f], Y [auth 2a], Z [auth 2b]	Phage tail protein	structural molecule activity	-	-
S [auth 2A], T [auth 2B], U [auth 2C], V [auth 2D], W [auth 2E], S [auth 2A], T [auth 2B], U [auth 2C], V [auth 2D], W [auth 2E], X [auth 2F]	Putative phage tail sheath protein FI	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth 0A], B [auth 0B], C [auth 0C], D [auth 0D], E [auth 0E], A [auth 0A], B [auth 0B], C [auth 0C], D [auth 0D], E [auth 0E], F [auth 0F]	IPR025351	Pvc16, N-terminal	Domain
AA [auth 2c], BA [auth 2d], CA [auth 2e], DA [auth 2f], M [auth 1a], AA [auth 2c], BA [auth 2d], CA [auth 2e], DA [auth 2f], M [auth 1a], N [auth 1b], O [auth 1c], P [auth 1d], Q [auth 1e], R [auth 1f], Y [auth 2a], Z [auth 2b]	IPR011747	Conserved hypothetical protein CHP02241	Family
AA [auth 2c], BA [auth 2d], CA [auth 2e], DA [auth 2f], M [auth 1a], AA [auth 2c], BA [auth 2d], CA [auth 2e], DA [auth 2f], M [auth 1a], N [auth 1b], O [auth 1c], P [auth 1d], Q [auth 1e], R [auth 1f], Y [auth 2a], Z [auth 2b]	IPR010667	Bacteriophage T4, Gp19, tail tube	Family
S [auth 2A], T [auth 2B], U [auth 2C], V [auth 2D], W [auth 2E], S [auth 2A], T [auth 2B], U [auth 2C], V [auth 2D], W [auth 2E], X [auth 2F]	IPR052042	Tail sheath structural protein	Family
S [auth 2A], T [auth 2B], U [auth 2C], V [auth 2D], W [auth 2E], S [auth 2A], T [auth 2B], U [auth 2C], V [auth 2D], W [auth 2E], X [auth 2F]	IPR020287	Tail sheath protein, C-terminal domain	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.