6QOZ | pdb_00006qoz

CryoEM reconstruction of Cowpea Mosaic Virus (CPMV) bound to an Affimer reagent

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)
H [auth I]	SCOP2B Superfamily	Positive stranded ssRNA viruses-like	8033718	3000918	SCOP2B (2022-06-29)
H [auth I]	SCOP2B Superfamily	Positive stranded ssRNA viruses-like	8033728	3000918	SCOP2B (2022-06-29)
F [auth G]	SCOP2B Superfamily	Positive stranded ssRNA viruses-like	8033728	3000918	SCOP2B (2022-06-29)
F [auth G]	SCOP2B Superfamily	Positive stranded ssRNA viruses-like	8033718	3000918	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	Positive stranded ssRNA viruses-like	8033728	3000918	SCOP2B (2022-06-29)
D [auth E]	SCOP2B Superfamily	Positive stranded ssRNA viruses-like	8033718	3000918	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Positive stranded ssRNA viruses-like	8033718	3000918	SCOP2B (2022-06-29)
B	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)
H [auth I]	Como_LCP_C	e6qozI1	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: Como_LCP_C	ECOD (1.6)
H [auth I]	Como_LCP_N	e6qozI2	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: Como_LCP_N	ECOD (1.6)
F [auth G]	Como_LCP_C	e6qozG1	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: Como_LCP_C	ECOD (1.6)
F [auth G]	Como_LCP_N	e6qozG2	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: Como_LCP_N	ECOD (1.6)
D [auth E]	Como_LCP_C	e6qozE2	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: Como_LCP_C	ECOD (1.6)
D [auth E]	Como_LCP_N	e6qozE1	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: Como_LCP_N	ECOD (1.6)
B	Como_LCP_C	e6qozB2	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: Como_LCP_C	ECOD (1.6)
B	Como_LCP_N	e6qozB1	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: Como_LCP_N	ECOD (1.6)
I [auth C]	Cystatin	e6qozC1	A: a+b two layers	X: Cystatin-like	H: Cystatin/monellin (From Topology)	T: Cystatin/monellin	F: Cystatin	ECOD (1.6)
G [auth H]	Como_SCP	e6qozH1	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: Como_SCP	ECOD (1.6)
E [auth F]	Como_SCP	e6qozF1	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: Como_SCP	ECOD (1.6)
C [auth D]	Como_SCP	e6qozD1	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: Como_SCP	ECOD (1.6)
A	Como_SCP	e6qozA1	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: Como_SCP	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H [auth I]	2.60.120.20	Mainly Beta	Sandwich	Jelly Rolls		CATH (utative)
F [auth G]	2.60.120.20	Mainly Beta	Sandwich	Jelly Rolls		CATH (utative)
D [auth E]	2.60.120.20	Mainly Beta	Sandwich	Jelly Rolls		CATH (utative)
B	2.60.120.20	Mainly Beta	Sandwich	Jelly Rolls		CATH (utative)
G [auth H]	2.60.120.20	Mainly Beta	Sandwich	Jelly Rolls		CATH (utative)
E [auth F]	2.60.120.20	Mainly Beta	Sandwich	Jelly Rolls		CATH (utative)
C [auth D]	2.60.120.20	Mainly Beta	Sandwich	Jelly Rolls		CATH (utative)
A	2.60.120.20	Mainly Beta	Sandwich	Jelly Rolls		CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, D [auth E], F [auth G], H [auth I]	PF02247	Large coat protein (Como_LCP)	Large coat protein	This family contains the large coat protein (LCP) [1] of the comoviridae viral family.	Domain
A, C [auth D], E [auth F], G [auth H]	PF02248	Small coat protein (Como_SCP)	Small coat protein	This family contains the small coat protein (SCP) [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, D [auth E], F [auth G], H [auth I]	Cowpea mosaic virus large subunit	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
I [auth C]	Affimer binding protein	-	-	-
A, C [auth D], E [auth F], G [auth H]	RNA2 polyprotein	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, D [auth E], F [auth G], H [auth I]	IPR003181	Large coat protein	Family
B, D [auth E], F [auth G], H [auth I]	IPR029053	Viral coat protein subunit	Homologous Superfamily
B, D [auth E], F [auth G], H [auth I]	IPR003182	RNA2 polyprotein	Family
A, C [auth D], E [auth F], G [auth H]	IPR003181	Large coat protein	Family
A, C [auth D], E [auth F], G [auth H]	IPR029053	Viral coat protein subunit	Homologous Superfamily
A, C [auth D], E [auth F], G [auth H]	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.