5A20 | pdb_00005a20

Structure of bacteriophage SPP1 head-to-tail interface filled with DNA and tape measure protein

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C	SCOP2B Superfamily	YqbG/phage connector protein-like	8104059	3001980	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	YqbG/phage connector protein-like	8104059	3001980	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Phage head-tail joining protein-like	8106666	3002861	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Phage head-tail joining protein-like	8106666	3002861	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	T6SS-like	8091258	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)
A	Phage_prot_Gp6	e5a20A1	A: a/b three-layered sandwiches	X: OB-fold	H: OB domain in putative lipoprotein BF3042-related proteins	T: OB domain in putative lipoprotein BF3042-related proteins	F: Phage_prot_Gp6	ECOD (v294.1)
A	SAS-6_N	e5a20A2	A: a/b three-layered sandwiches	X: OB-fold	H: OB domain in putative lipoprotein BF3042-related proteins	T: OB domain in putative lipoprotein BF3042-related proteins	F: SAS-6_N	ECOD (v294.1)
B	Lactamase_B_2	e5a20B1	A: a/b three-layered sandwiches	X: Cytidine deaminase-like	H: Cytidine deaminase-like	T: Cytidine deaminase-like	F: Lactamase_B_2	ECOD (v294.1)
C	DUF3168	e5a20C1	A: a/b three-layered sandwiches	X: OB-fold	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: DUF3168	ECOD (v294.1)
D	DUF3168	e5a20D1	A: a/b three-layered sandwiches	X: OB-fold	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: DUF3168	ECOD (v294.1)
E	DUF3168	e5a20E1	A: a/b three-layered sandwiches	X: OB-fold	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: DUF3168	ECOD (v294.1)
F	DUF3168	e5a20F1	A: a/b three-layered sandwiches	X: OB-fold	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: DUF3168	ECOD (v294.1)
G	DUF3168	e5a20G1	A: a/b three-layered sandwiches	X: OB-fold	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: DUF3168	ECOD (v294.1)
H	Arena_glycoprot	e5a20H1	A: a/b three-layered sandwiches	X: OB-fold	H: Phage tail fiber protein trimerization domain	T: Phage tail fiber protein trimerization domain	F: Arena_glycoprot	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF05133	Phage portal protein, SPP1 Gp6-like (SPP1_portal)	Phage portal protein, SPP1 Gp6-like	-	Family
E, F	PF05521	Phage head completion protein (Phage_HCP)	Phage head completion protein	This entry represents the head completion protein (gp16) found in Siphoviridae bacteriophages. This protein functions as a stopper in the portal-tail connector complex, locking the viral DNA inside the capsid. During infection, it undergoes a conform ...	This entry represents the head completion protein (gp16) found in Siphoviridae bacteriophages. This protein functions as a stopper in the portal-tail connector complex, locking the viral DNA inside the capsid. During infection, it undergoes a conformational change, opening by a diaphragm-like motion to allow the genome to exit the capsid through the tail tube to the host cell. The protein also functions as a docking platform for the preassembled tail. The connector complex is essential for stable viral particle assembly and controlled genome release during host infection.	Domain
G	PF11367	Tail completion protein gp17 (Tail_completion_gp17)	Tail completion protein gp17	This entry includes Tail completion protein gp17 from Siphoviridae bacteriophage SPP1 Swiss:O48448, a tail completion protein which caps the tail and interacts with the connector gp16, thereby attaching the tail to the capsid [1,2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	PORTAL PROTEIN	-	symbiont genome ejection through host cell envelope biological process involved in interspecies interaction between organisms symbiont genome ejection through host cell envelope, long flexible tail mechanism symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction virion assembly viral DNA genome packaging, headful viral genome packaging viral DNA genome packaging	viral procapsid virion component protein-containing complex viral capsid viral portal complex
C, D	15 PROTEIN	-	symbiont genome ejection through host cell envelope biological process involved in interspecies interaction between organisms symbiont genome ejection through host cell envelope, long flexible tail mechanism symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction	virion component
E, F	HEAD COMPLETION PROTEIN GP16	-	symbiont genome ejection through host cell envelope biological process involved in interspecies interaction between organisms symbiont genome ejection through host cell envelope, long flexible tail mechanism symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction	virion component
G	TAIL-TO-HEAD JOINING PROTEIN GP17	-	virion assembly viral tail assembly virus tail fiber assembly viral process viral life cycle	virus tail virion component
H	MAJOR TAIL PROTEIN GP17.1	-	viral gene expression viral process viral translational frameshifting viral translation symbiont genome ejection through host cell envelope biological process involved in interspecies interaction between organisms symbiont genome ejection through host cell envelope, long flexible tail mechanism symbiont entry into host cell symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction virion assembly viral head-tail joining	virus tail, tube virus tail virion component

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR006428	Portal protein, SPP1-type	Family
A, B	IPR021145	Portal protein SPP1 Gp6-like	Family
C, D	IPR021146	Phage gp6-like head-tail connector protein	Family
C, D	IPR047186	Head-tail connector protein gp6/gp15-like	Family
C, D	IPR053746	Viral Head-Tail Connector Assembly Factor	Homologous Superfamily
E, F	IPR008767	Bacteriophage SPP1, head-tail adaptor	Family
E, F	IPR038666	Bacteriophage SPP1, head-tail adaptor superfamily	Homologous Superfamily
G	IPR053745	Viral Tail Completion Superfamily	Homologous Superfamily
G	IPR021508	Tail completion protein gp17	Family
H	IPR011855	Phage major tail protein TP901-1	Family
H	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
H	IPR003961	Fibronectin type III	Domain
H	IPR036116	Fibronectin type III superfamily	Homologous Superfamily

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.