9G8S | pdb_00009g8s

C3 reconstruction of extended phiCD508 needle

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth Z], FA [auth c], K [auth Y], MA [auth d], R [auth a], D [auth Z], FA [auth c], K [auth Y], MA [auth d], R [auth a], Y [auth b]	PF09393	Phage tail tube protein (DUF2001)	Phage tail tube protein	This is a family of phage tail tube proteins including protein XkdM from phage-like element PBSX protein (Swiss:P54332) whose structure adopts a beta barrel flanked with alpha helical regions.	Domain
C [auth T], EA [auth W], J [auth S], LA [auth X], Q [auth U], C [auth T], EA [auth W], J [auth S], LA [auth X], Q [auth U], X [auth V]	PF24032	YQBQ-like (YQBQ)	YQBQ-like	This entry represents a domain found standalone in the Uncharacterized protein YqbQ, Phage-like element PBSX protein XkdQ and other related proteins. This domain is also found N-terminal in Clostridioides difficile endolysin (Ecd09610). It is predict ...	This entry represents a domain found standalone in the Uncharacterized protein YqbQ, Phage-like element PBSX protein XkdQ and other related proteins. This domain is also found N-terminal in Clostridioides difficile endolysin (Ecd09610). It is predicted to adopt a globular structure comprised mainly of two beta-barrels arranged in a head-to-tail manner. The function of this domain is unknown.	Domain
C [auth T], EA [auth W], J [auth S], LA [auth X], Q [auth U], C [auth T], EA [auth W], J [auth S], LA [auth X], Q [auth U], X [auth V]	PF01476	LysM domain (LysM)	LysM domain	The LysM (lysin motif) domain is about 40 residues long. It is found in a variety of enzymes involved in bacterial cell wall degradation [1]. This domain may have a general peptidoglycan binding function. The structure of this domain is known [2].	Domain
B [auth N], DA [auth Q], I [auth M], KA [auth R], P [auth O], B [auth N], DA [auth Q], I [auth M], KA [auth R], P [auth O], W [auth P]	PF10076	Bacteriophage Mu-like, Gp48 (Phage_Mu_Gp48)	Bacteriophage Mu-like, Gp48	-	Family
B [auth N], DA [auth Q], I [auth M], KA [auth R], P [auth O], B [auth N], DA [auth Q], I [auth M], KA [auth R], P [auth O], W [auth P]	PF24032	YQBQ-like (YQBQ)	YQBQ-like	This entry represents a domain found standalone in the Uncharacterized protein YqbQ, Phage-like element PBSX protein XkdQ and other related proteins. This domain is also found N-terminal in Clostridioides difficile endolysin (Ecd09610). It is predict ...	This entry represents a domain found standalone in the Uncharacterized protein YqbQ, Phage-like element PBSX protein XkdQ and other related proteins. This domain is also found N-terminal in Clostridioides difficile endolysin (Ecd09610). It is predicted to adopt a globular structure comprised mainly of two beta-barrels arranged in a head-to-tail manner. The function of this domain is unknown.	Domain
B [auth N], DA [auth Q], I [auth M], KA [auth R], P [auth O], B [auth N], DA [auth Q], I [auth M], KA [auth R], P [auth O], W [auth P]	PF10934	Contractile injection system sheath initiator (Sheath_initiator)	Contractile injection system sheath initiator	-	Family
A [auth C], BA [auth J], CA [auth E], G, H [auth A], A [auth C], BA [auth J], CA [auth E], G, H [auth A], IA [auth K], JA [auth F], N [auth H], O [auth B], PA [auth L], U [auth I], V [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
A [auth C], BA [auth J], CA [auth E], G, H [auth A], A [auth C], BA [auth J], CA [auth E], G, H [auth A], IA [auth K], JA [auth F], N [auth H], O [auth B], PA [auth L], U [auth I], V [auth D]	PF17481	Phage tail sheath protein beta-sandwich domain (Phage_sheath_domII)	Phage tail sheath protein beta-sandwich domain	This entry represents a two-layer beta sandwich domain found in a variety of phage tail sheath proteins, referred to as domain II in [4,5]. Domain I and II form the protease-resistant fragment [5].	Domain
A [auth C], BA [auth J], CA [auth E], G, H [auth A], A [auth C], BA [auth J], CA [auth E], G, H [auth A], IA [auth K], JA [auth F], N [auth H], O [auth B], PA [auth L], U [auth I], V [auth D]	PF26079	Baseplate J-like protein C-terminal domain (Baseplate_J_C)	Baseplate J-like protein C-terminal 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 C-terminal domain found in these protein.	Domain
A [auth C], BA [auth J], CA [auth E], G, H [auth A], A [auth C], BA [auth J], CA [auth E], G, H [auth A], IA [auth K], JA [auth F], N [auth H], O [auth B], PA [auth L], U [auth I], V [auth D]	PF26078	Baseplate J-like central domain (Baseplate_J_M)	Baseplate J-like central 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 domain found in baseplate J-like proteins. ...	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 domain found in baseplate J-like proteins.	Domain
A [auth C], BA [auth J], CA [auth E], G, H [auth A], A [auth C], BA [auth J], CA [auth E], G, H [auth A], IA [auth K], JA [auth F], N [auth H], O [auth B], PA [auth L], U [auth I], V [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
A [auth C], BA [auth J], CA [auth E], G, H [auth A], A [auth C], BA [auth J], CA [auth E], G, H [auth A], IA [auth K], JA [auth F], N [auth H], O [auth B], PA [auth L], U [auth I], V [auth D]	PF09393	Phage tail tube protein (DUF2001)	Phage tail tube protein	This is a family of phage tail tube proteins including protein XkdM from phage-like element PBSX protein (Swiss:P54332) whose structure adopts a beta barrel flanked with alpha helical regions.	Domain
A [auth C], BA [auth J], CA [auth E], G, H [auth A], A [auth C], BA [auth J], CA [auth E], G, H [auth A], IA [auth K], JA [auth F], N [auth H], O [auth B], PA [auth L], U [auth I], V [auth D]	PF10934	Contractile injection system sheath initiator (Sheath_initiator)	Contractile injection system sheath initiator	-	Family
A [auth C], BA [auth J], CA [auth E], G, H [auth A], A [auth C], BA [auth J], CA [auth E], G, H [auth A], IA [auth K], JA [auth F], N [auth H], O [auth B], PA [auth L], U [auth I], V [auth D]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
WA [auth w], XA [auth x], YA [auth y]	Tail tape measure	-	virion assembly viral tail assembly viral process viral life cycle	cellular anatomical structure membrane
SA [auth q], UA [auth t], VA [auth u]	XkdQ-related protein	-	-	-
QA [auth r], RA [auth v], TA [auth s]	Phage protein	-	-	-
AA [auth n], F [auth m], HA [auth o], M [auth k], OA [auth p], AA [auth n], F [auth m], HA [auth o], M [auth k], OA [auth p], T [auth l]	XkdS-related protein	-	-	-
E [auth g], GA [auth i], L [auth e], NA [auth j], S [auth f], E [auth g], GA [auth i], L [auth e], NA [auth j], S [auth f], Z [auth h]	Tail sheath	-	symbiont genome ejection through host cell envelope biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle symbiont genome ejection through host cell envelope, contractile tail mechanism biological process involved in interaction with host biological process involved in symbiotic interaction	virus tail virion component virus tail, sheath
D [auth Z], FA [auth c], K [auth Y], MA [auth d], R [auth a], D [auth Z], FA [auth c], K [auth Y], MA [auth d], R [auth a], Y [auth b]	XkdM-related protein	-	-	-
C [auth T], EA [auth W], J [auth S], LA [auth X], Q [auth U], C [auth T], EA [auth W], J [auth S], LA [auth X], Q [auth U], X [auth V]	Peptidoglycan-binding LysM protein	-	-	-
B [auth N], DA [auth Q], I [auth M], KA [auth R], P [auth O], B [auth N], DA [auth Q], I [auth M], KA [auth R], P [auth O], W [auth P]	XkdT-related protein	-	-	-
A [auth C], BA [auth J], CA [auth E], G, H [auth A], A [auth C], BA [auth J], CA [auth E], G, H [auth A], IA [auth K], JA [auth F], N [auth H], O [auth B], PA [auth L], U [auth I], V [auth D]	Baseplate J family protein	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
WA [auth w], XA [auth x], YA [auth y]	IPR010090	Phage tail tape measure protein	Domain
SA [auth q], UA [auth t], VA [auth u]	IPR056937	YqbQ/XkdQ	Domain
AA [auth n], F [auth m], HA [auth o], M [auth k], OA [auth p], AA [auth n], F [auth m], HA [auth o], M [auth k], OA [auth p], T [auth l]	IPR020288	Contractile injection system sheath initiator	Family
E [auth g], GA [auth i], L [auth e], NA [auth j], S [auth f], E [auth g], GA [auth i], L [auth e], NA [auth j], S [auth f], Z [auth h]	IPR020287	Tail sheath protein, C-terminal domain	Domain
E [auth g], GA [auth i], L [auth e], NA [auth j], S [auth f], E [auth g], GA [auth i], L [auth e], NA [auth j], S [auth f], Z [auth h]	IPR035089	Tail sheath protein, subtilisin-like domain	Domain
E [auth g], GA [auth i], L [auth e], NA [auth j], S [auth f], E [auth g], GA [auth i], L [auth e], NA [auth j], S [auth f], Z [auth h]	IPR035326	Phage tail sheath protein-like, beta-sandwich domain	Domain
D [auth Z], FA [auth c], K [auth Y], MA [auth d], R [auth a], D [auth Z], FA [auth c], K [auth Y], MA [auth d], R [auth a], Y [auth b]	IPR018989	Phage tail tube protein	Family
D [auth Z], FA [auth c], K [auth Y], MA [auth d], R [auth a], D [auth Z], FA [auth c], K [auth Y], MA [auth d], R [auth a], Y [auth b]	IPR038628	XkdM-like superfamily	Homologous Superfamily
C [auth T], EA [auth W], J [auth S], LA [auth X], Q [auth U], C [auth T], EA [auth W], J [auth S], LA [auth X], Q [auth U], X [auth V]	IPR036779	LysM domain superfamily	Homologous Superfamily
C [auth T], EA [auth W], J [auth S], LA [auth X], Q [auth U], C [auth T], EA [auth W], J [auth S], LA [auth X], Q [auth U], X [auth V]	IPR052196	Bacterial Potassium Binding	Family
C [auth T], EA [auth W], J [auth S], LA [auth X], Q [auth U], C [auth T], EA [auth W], J [auth S], LA [auth X], Q [auth U], X [auth V]	IPR018392	LysM domain	Domain
B [auth N], DA [auth Q], I [auth M], KA [auth R], P [auth O], B [auth N], DA [auth Q], I [auth M], KA [auth R], P [auth O], W [auth P]	IPR018755	Bacteriophage Mu-like, Gp48	Family
A [auth C], BA [auth J], CA [auth E], G, H [auth A], A [auth C], BA [auth J], CA [auth E], G, H [auth A], IA [auth K], JA [auth F], N [auth H], O [auth B], PA [auth L], U [auth I], V [auth D]	IPR052399	Phage Baseplate Assembly Protein	Family
A [auth C], BA [auth J], CA [auth E], G, H [auth A], A [auth C], BA [auth J], CA [auth E], G, H [auth A], IA [auth K], JA [auth F], N [auth H], O [auth B], PA [auth L], U [auth I], V [auth D]	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.