3KK5

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


Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

ChainsTypeFamily Name Domain Identifier Family IdentifierProvenance Source (Version)
CSCOP2B SuperfamilyGroup II dsDNA viruses VP8043273 3001214 SCOP2B (2022-06-29)
CSCOP2B SuperfamilyGroup II dsDNA viruses VP8043274 3001214 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyGroup II dsDNA viruses VP8043274 3001214 SCOP2B (2022-06-29)
DSCOP2B SuperfamilyGroup II dsDNA viruses VP8043273 3001214 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyGroup II dsDNA viruses VP8043273 3001214 SCOP2B (2022-06-29)
GSCOP2B SuperfamilyGroup II dsDNA viruses VP8043274 3001214 SCOP2B (2022-06-29)
HSCOP2B SuperfamilyGroup II dsDNA viruses VP8043274 3001214 SCOP2B (2022-06-29)
HSCOP2B SuperfamilyGroup II dsDNA viruses VP8043273 3001214 SCOP2B (2022-06-29)
ISCOP2B SuperfamilyGroup II dsDNA viruses VP8043274 3001214 SCOP2B (2022-06-29)
ISCOP2B SuperfamilyGroup II dsDNA viruses VP8043273 3001214 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyGroup II dsDNA viruses VP8043273 3001214 SCOP2B (2022-06-29)
ASCOP2B SuperfamilyGroup II dsDNA viruses VP8043274 3001214 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyGroup II dsDNA viruses VP8043273 3001214 SCOP2B (2022-06-29)
BSCOP2B SuperfamilyGroup II dsDNA viruses VP8043274 3001214 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyGroup II dsDNA viruses VP8043273 3001214 SCOP2B (2022-06-29)
ESCOP2B SuperfamilyGroup II dsDNA viruses VP8043274 3001214 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyGroup II dsDNA viruses VP8043273 3001214 SCOP2B (2022-06-29)
FSCOP2B SuperfamilyGroup II dsDNA viruses VP8043274 3001214 SCOP2B (2022-06-29)
JSCOP2B SuperfamilyGroup II dsDNA viruses VP8043273 3001214 SCOP2B (2022-06-29)
JSCOP2B SuperfamilyGroup II dsDNA viruses VP8043274 3001214 SCOP2B (2022-06-29)
KSCOP2B SuperfamilyGroup II dsDNA viruses VP8043273 3001214 SCOP2B (2022-06-29)
KSCOP2B SuperfamilyGroup II dsDNA viruses VP8043274 3001214 SCOP2B (2022-06-29)
LSCOP2B SuperfamilyGroup II dsDNA viruses VP8043273 3001214 SCOP2B (2022-06-29)
LSCOP2B SuperfamilyGroup II dsDNA viruses VP8043274 3001214 SCOP2B (2022-06-29)
MSCOP2B SuperfamilyGroup II dsDNA viruses VP8043273 3001214 SCOP2B (2022-06-29)
MSCOP2B SuperfamilyGroup II dsDNA viruses VP8043274 3001214 SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
CPF04451e3kk5C2 A: beta sandwichesX: jelly-rollH: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)T: Nucleoplasmin-like/VP (viral coat and capsid proteins)F: PF04451ECOD (1.6)
CPF16903e3kk5C1 A: beta sandwichesX: jelly-rollH: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)T: Nucleoplasmin-like/VP (viral coat and capsid proteins)F: PF16903ECOD (1.6)
DPF04451e3kk5D2 A: beta sandwichesX: jelly-rollH: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)T: Nucleoplasmin-like/VP (viral coat and capsid proteins)F: PF04451ECOD (1.6)
DPF16903e3kk5D1 A: beta sandwichesX: jelly-rollH: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)T: Nucleoplasmin-like/VP (viral coat and capsid proteins)F: PF16903ECOD (1.6)
GPF04451e3kk5G2 A: beta sandwichesX: jelly-rollH: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)T: Nucleoplasmin-like/VP (viral coat and capsid proteins)F: PF04451ECOD (1.6)
GPF16903e3kk5G1 A: beta sandwichesX: jelly-rollH: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)T: Nucleoplasmin-like/VP (viral coat and capsid proteins)F: PF16903ECOD (1.6)
HPF04451e3kk5H2 A: beta sandwichesX: jelly-rollH: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)T: Nucleoplasmin-like/VP (viral coat and capsid proteins)F: PF04451ECOD (1.6)
HPF16903e3kk5H1 A: beta sandwichesX: jelly-rollH: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)T: Nucleoplasmin-like/VP (viral coat and capsid proteins)F: PF16903ECOD (1.6)
IPF04451e3kk5I2 A: beta sandwichesX: jelly-rollH: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)T: Nucleoplasmin-like/VP (viral coat and capsid proteins)F: PF04451ECOD (1.6)
IPF16903e3kk5I1 A: beta sandwichesX: jelly-rollH: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)T: Nucleoplasmin-like/VP (viral coat and capsid proteins)F: PF16903ECOD (1.6)
APF04451e3kk5A2 A: beta sandwichesX: jelly-rollH: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)T: Nucleoplasmin-like/VP (viral coat and capsid proteins)F: PF04451ECOD (1.6)
APF16903e3kk5A1 A: beta sandwichesX: jelly-rollH: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)T: Nucleoplasmin-like/VP (viral coat and capsid proteins)F: PF16903ECOD (1.6)
BPF04451e3kk5B2 A: beta sandwichesX: jelly-rollH: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)T: Nucleoplasmin-like/VP (viral coat and capsid proteins)F: PF04451ECOD (1.6)
BPF16903e3kk5B1 A: beta sandwichesX: jelly-rollH: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)T: Nucleoplasmin-like/VP (viral coat and capsid proteins)F: PF16903ECOD (1.6)
EPF04451e3kk5E2 A: beta sandwichesX: jelly-rollH: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)T: Nucleoplasmin-like/VP (viral coat and capsid proteins)F: PF04451ECOD (1.6)
EPF16903e3kk5E1 A: beta sandwichesX: jelly-rollH: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)T: Nucleoplasmin-like/VP (viral coat and capsid proteins)F: PF16903ECOD (1.6)
FPF04451e3kk5F2 A: beta sandwichesX: jelly-rollH: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)T: Nucleoplasmin-like/VP (viral coat and capsid proteins)F: PF04451ECOD (1.6)
FPF16903e3kk5F1 A: beta sandwichesX: jelly-rollH: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)T: Nucleoplasmin-like/VP (viral coat and capsid proteins)F: PF16903ECOD (1.6)
JPF04451e3kk5J2 A: beta sandwichesX: jelly-rollH: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)T: Nucleoplasmin-like/VP (viral coat and capsid proteins)F: PF04451ECOD (1.6)
JPF16903e3kk5J1 A: beta sandwichesX: jelly-rollH: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)T: Nucleoplasmin-like/VP (viral coat and capsid proteins)F: PF16903ECOD (1.6)
KPF04451e3kk5K2 A: beta sandwichesX: jelly-rollH: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)T: Nucleoplasmin-like/VP (viral coat and capsid proteins)F: PF04451ECOD (1.6)
KPF16903e3kk5K1 A: beta sandwichesX: jelly-rollH: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)T: Nucleoplasmin-like/VP (viral coat and capsid proteins)F: PF16903ECOD (1.6)
LPF04451e3kk5L2 A: beta sandwichesX: jelly-rollH: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)T: Nucleoplasmin-like/VP (viral coat and capsid proteins)F: PF04451ECOD (1.6)
LPF16903e3kk5L1 A: beta sandwichesX: jelly-rollH: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)T: Nucleoplasmin-like/VP (viral coat and capsid proteins)F: PF16903ECOD (1.6)
MPF04451e3kk5M2 A: beta sandwichesX: jelly-rollH: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)T: Nucleoplasmin-like/VP (viral coat and capsid proteins)F: PF04451ECOD (1.6)
MPF16903e3kk5M1 A: beta sandwichesX: jelly-rollH: Nucleoplasmin-like/VP (viral coat and capsid proteins) (From Topology)T: Nucleoplasmin-like/VP (viral coat and capsid proteins)F: PF16903ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
A, B, C, D, E
PF16903Major capsid protein N-terminus (Capsid_N)Major capsid protein N-terminusThis is the N-terminal domain of the major capsid protein in several dsDNA viruses [1].Domain
A, B, C, D, E
PF04451Large eukaryotic DNA virus major capsid protein (Capsid_NCLDV)Large eukaryotic DNA virus major capsid proteinThis 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

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
A, B, C, D, E
Major capsid protein -

InterPro: Protein Family Classification InterPro Database Homepage

ChainsAccessionNameType
A, B, C, D, E
IPR031654Major capsid protein, N-terminalDomain
A, B, C, D, E
IPR007542Major capsid protein, C-terminalDomain
A, B, C, D, E
IPR038519Major capsid protein, C-terminal domain superfamilyHomologous Superfamily
A, B, C, D, E
IPR016112Group II dsDNA virus coat/capsid proteinHomologous Superfamily