3KK5 | pdb_00003kk5

Crystal structure of PBCV-1 VP54 fitted into a cryo-EM reconstruction of the virophage Sputnik

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)
B	SCOP2B Superfamily	Group II dsDNA viruses VP	8043273	3001214	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Group II dsDNA viruses VP	8043274	3001214	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Group II dsDNA viruses VP	8043273	3001214	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Group II dsDNA viruses VP	8043274	3001214	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Group II dsDNA viruses VP	8043274	3001214	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Group II dsDNA viruses VP	8043273	3001214	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Group II dsDNA viruses VP	8043273	3001214	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Group II dsDNA viruses VP	8043274	3001214	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Group II dsDNA viruses VP	8043273	3001214	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Group II dsDNA viruses VP	8043274	3001214	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Group II dsDNA viruses VP	8043274	3001214	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Group II dsDNA viruses VP	8043273	3001214	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Group II dsDNA viruses VP	8043274	3001214	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Group II dsDNA viruses VP	8043273	3001214	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Group II dsDNA viruses VP	8043273	3001214	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Group II dsDNA viruses VP	8043274	3001214	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Group II dsDNA viruses VP	8043273	3001214	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Group II dsDNA viruses VP	8043274	3001214	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Group II dsDNA viruses VP	8043273	3001214	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Group II dsDNA viruses VP	8043274	3001214	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Group II dsDNA viruses VP	8043273	3001214	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Group II dsDNA viruses VP	8043274	3001214	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Group II dsDNA viruses VP	8043273	3001214	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Group II dsDNA viruses VP	8043274	3001214	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Group II dsDNA viruses VP	8043273	3001214	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Group II dsDNA viruses VP	8043274	3001214	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)
B	Capsid_NCLDV	e3kk5B2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Capsid_NCLDV	ECOD (1.6)
B	Capsid_N	e3kk5B1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Capsid_N	ECOD (1.6)
C	Capsid_NCLDV	e3kk5C2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Capsid_NCLDV	ECOD (1.6)
C	Capsid_N	e3kk5C1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Capsid_N	ECOD (1.6)
D	Capsid_NCLDV	e3kk5D2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Capsid_NCLDV	ECOD (1.6)
D	Capsid_N	e3kk5D1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Capsid_N	ECOD (1.6)
E	Capsid_NCLDV	e3kk5E2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Capsid_NCLDV	ECOD (1.6)
E	Capsid_N	e3kk5E1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Capsid_N	ECOD (1.6)
F	Capsid_NCLDV	e3kk5F2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Capsid_NCLDV	ECOD (1.6)
F	Capsid_N	e3kk5F1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Capsid_N	ECOD (1.6)
H	Capsid_NCLDV	e3kk5H2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Capsid_NCLDV	ECOD (1.6)
H	Capsid_N	e3kk5H1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Capsid_N	ECOD (1.6)
I	Capsid_NCLDV	e3kk5I2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Capsid_NCLDV	ECOD (1.6)
I	Capsid_N	e3kk5I1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Capsid_N	ECOD (1.6)
J	Capsid_NCLDV	e3kk5J2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Capsid_NCLDV	ECOD (1.6)
J	Capsid_N	e3kk5J1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Capsid_N	ECOD (1.6)
K	Capsid_NCLDV	e3kk5K2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Capsid_NCLDV	ECOD (1.6)
K	Capsid_N	e3kk5K1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Capsid_N	ECOD (1.6)
L	Capsid_NCLDV	e3kk5L2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Capsid_NCLDV	ECOD (1.6)
L	Capsid_N	e3kk5L1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Capsid_N	ECOD (1.6)
M	Capsid_NCLDV	e3kk5M2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Capsid_NCLDV	ECOD (1.6)
M	Capsid_N	e3kk5M1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Capsid_N	ECOD (1.6)
G	Capsid_NCLDV	e3kk5G2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Capsid_NCLDV	ECOD (1.6)
G	Capsid_N	e3kk5G1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Capsid_N	ECOD (1.6)
A	Capsid_NCLDV	e3kk5A2	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Capsid_NCLDV	ECOD (1.6)
A	Capsid_N	e3kk5A1	A: beta sandwiches	X: jelly-roll	H: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)	T: Nucleoplasmin-like/VP (viral coat and capsid proteins)	F: Capsid_N	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M	PF16903	Major capsid protein N-terminus (Capsid_N)	Major capsid protein N-terminus	This is the N-terminal domain of the major capsid protein in several dsDNA viruses [1].	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M	PF04451	Large eukaryotic DNA virus major capsid protein (Capsid_NCLDV)	Large eukaryotic DNA virus major capsid protein	This family includes the major capsid protein of iridoviruses, chlorella virus and Spodoptera ascovirus, which are all dsDNA viruses with no RNA stage. This is the most abundant structural protein and can account for up to 45% of virion protein [1]. ...	This family includes the major capsid protein of iridoviruses, chlorella virus and Spodoptera ascovirus, which are all dsDNA viruses with no RNA stage. This is the most abundant structural protein and can account for up to 45% of virion protein [1]. In Chlorella virus PBCV-1 the major capsid protein is a glycoprotein [2]. The four families of large eukaryotic DNA viruses, Poxviridae, Asfarviridae, Iridoviridae, and Phycodnaviridae, are referred to collectively as nucleocytoplasmic large DNA viruses or NCLDV. The virions of different NCLDV have dramatically different structures. The major capsid proteins of iridoviruses and phycodnaviruses, both of which have icosahedral capsids surrounding an inner lipid membrane, showed a high level of sequence conservation. A more limited, but statistically significant sequence similarity was observed between these proteins and the major capsid protein (p72) of ASFV, which also has an icosahedral capsid. It was surprising, however, to find that all of these proteins shared a conserved domain with the poxvirus protein D13L, which is an integral virion component thought to form a scaffold for the formation of viral crescents and immature virion [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M	Major capsid protein	structural molecule activity binding lipid binding	-	viral capsid virion component

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M	IPR031654	Major capsid protein, N-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M	IPR007542	Major capsid protein, C-terminal	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M	IPR038519	Major capsid protein, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M	IPR016112	Group II dsDNA virus coat/capsid protein	Homologous Superfamily