8OPG | pdb_00008opg

Virus-like Particle based on PVY coat protein with dC79 deletion with RNA-free helical architecture

External Resource: Annotation

Domain Annotation: ECOD Classification
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
S [auth As]	DNA_topoisoIV	e8opgAs1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
R [auth Ar]	DNA_topoisoIV	e8opgAr1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
Q [auth Aq]	DNA_topoisoIV	e8opgAq1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
P [auth Ap]	DNA_topoisoIV	e8opgAp1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
O [auth Ao]	DNA_topoisoIV	e8opgAo1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
N [auth An]	DNA_topoisoIV	e8opgAn1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
M [auth Am]	DNA_topoisoIV	e8opgAm1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
L [auth Al]	DNA_topoisoIV	e8opgAl1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
K [auth Ak]	DNA_topoisoIV	e8opgAk1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
J [auth Aj]	DNA_topoisoIV	e8opgAj1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
I [auth Ai]	DNA_topoisoIV	e8opgAi1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
H [auth Ah]	DNA_topoisoIV	e8opgAh1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
G [auth Ag]	DNA_topoisoIV	e8opgAg1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
F [auth Af]	DNA_topoisoIV	e8opgAf1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
E [auth Ae]	DNA_topoisoIV	e8opgAe1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
D [auth Ad]	DNA_topoisoIV	e8opgAd1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
C [auth Ac]	DNA_topoisoIV	e8opgAc1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
B [auth Ab]	DNA_topoisoIV	e8opgAb1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
A [auth Aa]	Kringle	e8opgAa01	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Kringle	ECOD (v294.2)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], F [auth Af], G [auth Ag], H [auth Ah], I [auth Ai], J [auth Aj], K [auth Ak], L [auth Al], M [auth Am], N [auth An], O [auth Ao], P [auth Ap], Q [auth Aq], R [auth Ar], S [auth As]	Genome polyprotein (Fragment)	nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on a nucleic acid helicase activity macromolecular conformation isomerase activity catalytic activity ATP-dependent activity cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity endopeptidase activity RNA-directed RNA polymerase activity nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on a nucleic acid helicase activity macromolecular conformation isomerase activity catalytic activity ATP-dependent activity cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity endopeptidase activity RNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA RNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups serine hydrolase activity serine-type peptidase activity RNA binding binding nucleic acid binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides structural molecule activity	RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process cellular process macromolecule metabolic process gene expression DNA-templated transcription proteolysis protein metabolic 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	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 viral capsid virion component helical viral capsid host cell cytoplasm part host cell cytoplasmic vesicle 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 viral capsid virion component helical viral capsid host cell cytoplasm part host cell cytoplasmic vesicle host cell cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], F [auth Af], G [auth Ag], H [auth Ah], I [auth Ai], J [auth Aj], K [auth Ak], L [auth Al], M [auth Am], N [auth An], O [auth Ao], P [auth Ap], Q [auth Aq], R [auth Ar], S [auth As]	IPR001205	RNA-directed RNA polymerase, C-terminal domain	Domain
A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], F [auth Af], G [auth Ag], H [auth Ah], I [auth Ai], J [auth Aj], K [auth Ak], L [auth Al], M [auth Am], N [auth An], O [auth Ao], P [auth Ap], Q [auth Aq], R [auth Ar], S [auth As]	IPR001456	Helper component proteinase	Family
A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], F [auth Af], G [auth Ag], H [auth Ah], I [auth Ai], J [auth Aj], K [auth Ak], L [auth Al], M [auth Am], N [auth An], O [auth Ao], P [auth Ap], Q [auth Aq], R [auth Ar], S [auth As]	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], F [auth Af], G [auth Ag], H [auth Ah], I [auth Ai], J [auth Aj], K [auth Ak], L [auth Al], M [auth Am], N [auth An], O [auth Ao], P [auth Ap], Q [auth Aq], R [auth Ar], S [auth As]	IPR002540	Peptidase S30, polyprotein P1, potyvirus	Domain
A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], F [auth Af], G [auth Ag], H [auth Ah], I [auth Ai], J [auth Aj], K [auth Ak], L [auth Al], M [auth Am], N [auth An], O [auth Ao], P [auth Ap], Q [auth Aq], R [auth Ar], S [auth As]	IPR013648	Polyprotein, Potyviridae	Domain
A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], F [auth Af], G [auth Ag], H [auth Ah], I [auth Ai], J [auth Aj], K [auth Ak], L [auth Al], M [auth Am], N [auth An], O [auth Ao], P [auth Ap], Q [auth Aq], R [auth Ar], S [auth As]	IPR001730	Potyvirus NIa protease (NIa-pro) domain	Domain
A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], F [auth Af], G [auth Ag], H [auth Ah], I [auth Ai], J [auth Aj], K [auth Ak], L [auth Al], M [auth Am], N [auth An], O [auth Ao], P [auth Ap], Q [auth Aq], R [auth Ar], S [auth As]	IPR011545	DEAD/DEAH-box helicase domain	Domain
A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], F [auth Af], G [auth Ag], H [auth Ah], I [auth Ai], J [auth Aj], K [auth Ak], L [auth Al], M [auth Am], N [auth An], O [auth Ao], P [auth Ap], Q [auth Aq], R [auth Ar], S [auth As]	IPR031159	Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain	Domain
A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], F [auth Af], G [auth Ag], H [auth Ah], I [auth Ai], J [auth Aj], K [auth Ak], L [auth Al], M [auth Am], N [auth An], O [auth Ao], P [auth Ap], Q [auth Aq], R [auth Ar], S [auth As]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], F [auth Af], G [auth Ag], H [auth Ah], I [auth Ai], J [auth Aj], K [auth Ak], L [auth Al], M [auth Am], N [auth An], O [auth Ao], P [auth Ap], Q [auth Aq], R [auth Ar], S [auth As]	IPR043504	Peptidase_S1_PA_chymotrypsin	Unknown
A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], F [auth Af], G [auth Ag], H [auth Ah], I [auth Ai], J [auth Aj], K [auth Ak], L [auth Al], M [auth Am], N [auth An], O [auth Ao], P [auth Ap], Q [auth Aq], R [auth Ar], S [auth As]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], F [auth Af], G [auth Ag], H [auth Ah], I [auth Ai], J [auth Aj], K [auth Ak], L [auth Al], M [auth Am], N [auth An], O [auth Ao], P [auth Ap], Q [auth Aq], R [auth Ar], S [auth As]	IPR001650	Helicase, C-terminal domain-like	Domain
A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], F [auth Af], G [auth Ag], H [auth Ah], I [auth Ai], J [auth Aj], K [auth Ak], L [auth Al], M [auth Am], N [auth An], O [auth Ao], P [auth Ap], Q [auth Aq], R [auth Ar], S [auth As]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], F [auth Af], G [auth Ag], H [auth Ah], I [auth Ai], J [auth Aj], K [auth Ak], L [auth Al], M [auth Am], N [auth An], O [auth Ao], P [auth Ap], Q [auth Aq], R [auth Ar], S [auth As]	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], F [auth Af], G [auth Ag], H [auth Ah], I [auth Ai], J [auth Aj], K [auth Ak], L [auth Al], M [auth Am], N [auth An], O [auth Ao], P [auth Ap], Q [auth Aq], R [auth Ar], S [auth As]	IPR001592	Potyvirus coat protein	Family
A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], F [auth Af], G [auth Ag], H [auth Ah], I [auth Ai], J [auth Aj], K [auth Ak], L [auth Al], M [auth Am], N [auth An], O [auth Ao], P [auth Ap], Q [auth Aq], R [auth Ar], S [auth As]	IPR039560	Potyviral polyprotein protein 3	Domain
A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], F [auth Af], G [auth Ag], H [auth Ah], I [auth Ai], J [auth Aj], K [auth Ak], L [auth Al], M [auth Am], N [auth An], O [auth Ao], P [auth Ap], Q [auth Aq], R [auth Ar], S [auth As]	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain
A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], A [auth Aa], B [auth Ab], C [auth Ac], D [auth Ad], E [auth Ae], F [auth Af], G [auth Ag], H [auth Ah], I [auth Ai], J [auth Aj], K [auth Ak], L [auth Al], M [auth Am], N [auth An], O [auth Ao], P [auth Ap], Q [auth Aq], R [auth Ar], S [auth As]	IPR042308	Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain superfamily	Homologous Superfamily

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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.