1BMV

PROTEIN-RNA INTERACTIONS IN AN ICOSAHEDRAL VIRUS AT 3.0 ANGSTROMS RESOLUTION

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
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: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
B [auth 1]	d1bmv11	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Positive stranded ssRNA viruses	Comoviridae-like VP	Comovirus coat proteins (VP37 and VP23)	(Bean pod mottle virus ) [TaxId: 12260 ],	SCOPe (2.08)
C [auth 2]	d1bmv21	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Positive stranded ssRNA viruses	Comoviridae-like VP	Comovirus coat proteins (VP37 and VP23)	(Bean pod mottle virus ) [TaxId: 12260 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth 2]	SCOP2B Superfamily	Positive stranded ssRNA viruses-like	8038733	3000918	SCOP2B (2022-06-29)
C [auth 2]	SCOP2B Superfamily	Positive stranded ssRNA viruses-like	8038731	3000918	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 [auth 1]	PF02248	e1bmv11	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: PF02248	ECOD (1.6)
C [auth 2]	PF02247	e1bmv22	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: PF02247	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth 1]	2.60.120.20	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
C [auth 2]	2.60.120.20	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B [auth 1]	PF02248	Small coat protein (Como_SCP)	Small coat protein	This family contains the small coat protein (SCP) [1] of the comoviridae viral family.	Domain
C [auth 2]	PF02247	Large coat protein (Como_LCP)	Large coat protein	This family contains the large coat protein (LCP) [1] of the comoviridae viral family.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth M]	RNA (5'-R(GPGPUPCPAPAPAPAPUPGP*C)-3')	-	-	-
B [auth 1]	PROTEIN (ICOSAHEDRAL VIRUS - A DOMAIN)	DNA binding binding organic cyclic compound binding nucleic acid binding structural molecule activity RNA binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding DNA binding binding organic cyclic compound binding nucleic acid binding structural molecule activity RNA binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding	transport of virus in host, cell to cell transport of virus in multicellular host biological process involved in interspecies interaction between organisms migration in host viral process transport of virus biological process involved in interaction with host biological process involved in symbiotic interaction	viral capsid T=3 icosahedral viral capsid icosahedral viral capsid virion component host cell plasmodesma host cell plasma membrane host cellular component host cell part host cell junction host cell membrane cellular anatomical entity
C [auth 2]	PROTEIN (ICOSAHEDRAL VIRUS - B AND C DOMAIN)	DNA binding binding organic cyclic compound binding nucleic acid binding structural molecule activity RNA binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding DNA binding binding organic cyclic compound binding nucleic acid binding structural molecule activity RNA binding guanyl nucleotide binding GTP binding nucleotide binding guanyl ribonucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding	transport of virus in host, cell to cell transport of virus in multicellular host biological process involved in interspecies interaction between organisms migration in host viral process transport of virus biological process involved in interaction with host biological process involved in symbiotic interaction	viral capsid T=3 icosahedral viral capsid icosahedral viral capsid virion component host cell plasmodesma host cell plasma membrane host cellular component host cell part host cell junction host cell membrane cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth 1]	IPR003181	Large coat protein	Family
B [auth 1]	IPR029053	Viral coat protein subunit	Homologous Superfamily
B [auth 1]	IPR003182	RNA2 polyprotein	Family
C [auth 2]	IPR003181	Large coat protein	Family
C [auth 2]	IPR029053	Viral coat protein subunit	Homologous Superfamily
C [auth 2]	IPR003182	RNA2 polyprotein	Family

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.