5FMO | pdb_00005fmo

Crystal structure and proteomics analysis of empty virus like particles of Cowpea mosaic virus

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 S]	d5fmos_	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Positive stranded ssRNA viruses	Comoviridae-like VP	automated matches	CPMV (Cowpea mosaic virus ) [TaxId: 12264 ],	SCOPe (2.08)
A [auth L]	d5fmol1	All beta proteins	Nucleoplasmin-like/VP (viral coat and capsid proteins)	Positive stranded ssRNA viruses	Comoviridae-like VP	automated matches	CPMV (Cowpea mosaic virus ) [TaxId: 12264 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth L]	SCOP2B Superfamily	Positive stranded ssRNA viruses-like	8033718	3000918	SCOP2B (2022-06-29)
A [auth L]	SCOP2B Superfamily	Positive stranded ssRNA viruses-like	8033728	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 S]	Como_SCP	e5fmoS1	A: a/b three-layered sandwiches	X: HTH	H: Baseplate wedge protein gp6 helical domain	T: Baseplate wedge protein gp6 helical domain	F: Como_SCP	ECOD (v294.1)
A [auth L]	Como_SCP	e5fmoL1	A: a/b three-layered sandwiches	X: HTH	H: Baseplate wedge protein gp6 helical domain	T: Baseplate wedge protein gp6 helical domain	F: Como_SCP	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth S]	2.60.120.20	Mainly Beta	Sandwich	Jelly Rolls		CATH (4.3.0)
A [auth L]	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 S]	PF02248	Small coat protein (Como_SCP)	Small coat protein	This family contains the small coat protein (SCP) [1] of the comoviridae viral family.	Domain
A [auth L]	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
B [auth S]	EMPTY VIRUS LIKE PARTICLES OF COWPEA MOSAIC VIRUS	DNA binding 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 DNA binding 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	symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host immune response biological process involved in interspecies interaction between organisms symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host process symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host innate immune response modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction transport of virus in host, cell to cell transport of virus in multicellular host migration in host viral process symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host immune response biological process involved in interspecies interaction between organisms symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host process symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host innate immune response modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction transport of virus in host, cell to cell transport of virus in multicellular host migration in host viral process transport of virus	viral capsid T=3 icosahedral viral capsid icosahedral viral capsid virion component host intracellular membrane-bounded organelle host cellular component host intracellular part cellular anatomical structure host cell part host intracellular region host cell nucleus other organism part host intracellular organelle host cell plasmodesma viral capsid T=3 icosahedral viral capsid icosahedral viral capsid virion component host intracellular membrane-bounded organelle host cellular component host intracellular part cellular anatomical structure host cell part host intracellular region host cell nucleus other organism part host intracellular organelle host cell plasmodesma host cell plasma membrane host cell junction host cell membrane
A [auth L]	EMPTY VIRUS LIKE PARTICLES OF COWPEA MOSAIC VIRUS	DNA binding 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 DNA binding 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	symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host immune response biological process involved in interspecies interaction between organisms symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host process symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host innate immune response modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction transport of virus in host, cell to cell transport of virus in multicellular host migration in host viral process symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host immune response biological process involved in interspecies interaction between organisms symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host process symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host innate immune response modulation of process of another organism biological process involved in interaction with host biological process involved in symbiotic interaction transport of virus in host, cell to cell transport of virus in multicellular host migration in host viral process transport of virus	viral capsid T=3 icosahedral viral capsid icosahedral viral capsid virion component host intracellular membrane-bounded organelle host cellular component host intracellular part cellular anatomical structure host cell part host intracellular region host cell nucleus other organism part host intracellular organelle host cell plasmodesma viral capsid T=3 icosahedral viral capsid icosahedral viral capsid virion component host intracellular membrane-bounded organelle host cellular component host intracellular part cellular anatomical structure host cell part host intracellular region host cell nucleus other organism part host intracellular organelle host cell plasmodesma host cell plasma membrane host cell junction host cell membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth S]	IPR003181	Large coat protein	Family
B [auth S]	IPR029053	Viral coat protein subunit	Homologous Superfamily
B [auth S]	IPR003182	RNA2 polyprotein	Family
A [auth L]	IPR003181	Large coat protein	Family
A [auth L]	IPR029053	Viral coat protein subunit	Homologous Superfamily
A [auth L]	IPR003182	RNA2 polyprotein	Family

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.