5TIP

The Structure of the Major Capsid protein of PBCV-1

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
A	SCOP2 Family	Major capsid protein vp54	8030894	4002513	SCOP2 (2022-06-29)
A	SCOP2 Family	Major capsid protein vp54	8030895	4002513	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Group II dsDNA viruses VP	8043273	3001214	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Group II dsDNA viruses VP	8043274	3001214	SCOP2 (2022-06-29)
C	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)
D	SCOP2B Superfamily	Group II dsDNA viruses VP	8043273	3001214	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Group II dsDNA viruses VP	8043274	3001214	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Group II dsDNA viruses VP	8043274	3001214	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Group II dsDNA viruses VP	8043273	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)
A	Capsid_NCLDV	e5tipA1	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	e5tipA2	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	e5tipC2	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	e5tipC1	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	e5tipD1	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	e5tipD2	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)
B	Capsid_NCLDV	e5tipB2	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	e5tipB1	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)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.70.9.10	Mainly Beta	Distorted Sandwich	Adenovirus Type 2 Hexon	domain 4	CATH (4.3.0)
A	2.70.9.20	Mainly Beta	Distorted Sandwich	Adenovirus Type 2 Hexon	domain 4	CATH (4.3.0)
C	2.70.9.10	Mainly Beta	Distorted Sandwich	Adenovirus Type 2 Hexon	domain 4	CATH (4.3.0)
C	2.70.9.20	Mainly Beta	Distorted Sandwich	Adenovirus Type 2 Hexon	domain 4	CATH (4.3.0)
D	2.70.9.10	Mainly Beta	Distorted Sandwich	Adenovirus Type 2 Hexon	domain 4	CATH (4.3.0)
D	2.70.9.20	Mainly Beta	Distorted Sandwich	Adenovirus Type 2 Hexon	domain 4	CATH (4.3.0)
B	2.70.9.10	Mainly Beta	Distorted Sandwich	Adenovirus Type 2 Hexon	domain 4	CATH (4.3.0)
B	2.70.9.20	Mainly Beta	Distorted Sandwich	Adenovirus Type 2 Hexon	domain 4	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	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	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	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	IPR031654	Major capsid protein, N-terminal	Domain
A, B, C, D	IPR007542	Major capsid protein, C-terminal	Domain
A, B, C, D	IPR038519	Major capsid protein, C-terminal domain superfamily	Homologous Superfamily
A, B, C, D	IPR016112	Group II dsDNA virus coat/capsid protein	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.