8OPE | pdb_00008ope

Virus-like Particle based on PVY coat protein with dC40 deletion with helical architecture encapsidating ssRNA

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)
Y [auth Ay]	DNA_topoisoIV	e8opeAy1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
W [auth Aw]	DNA_topoisoIV	e8opeAw1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
U [auth Au]	DNA_topoisoIV	e8opeAu1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
S [auth As]	DNA_topoisoIV	e8opeAs1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
Q [auth Aq]	DNA_topoisoIV	e8opeAq1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
OA [auth Bo]	DNA_topoisoIV	e8opeBo1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
O [auth Ao]	DNA_topoisoIV	e8opeAo1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
MA [auth Bm]	DNA_topoisoIV	e8opeBm1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
M [auth Am]	DNA_topoisoIV	e8opeAm1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
KA [auth Bk]	DNA_topoisoIV	e8opeBk1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
K [auth Ak]	DNA_topoisoIV	e8opeAk1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
IA [auth Bi]	DNA_topoisoIV	e8opeBi1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
I [auth Ai]	DNA_topoisoIV	e8opeAi1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
GA [auth Bg]	DNA_topoisoIV	e8opeBg1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
G [auth Ag]	DNA_topoisoIV	e8opeAg1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
EA [auth Be]	DNA_topoisoIV	e8opeBe1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
E [auth Ae]	DNA_topoisoIV	e8opeAe1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
CA [auth Bc]	DNA_topoisoIV	e8opeBc1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
C [auth Ac]	DNA_topoisoIV	e8opeAc1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
AA [auth Ba]	DNA_topoisoIV	e8opeBa1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)
A [auth Aa]	DNA_topoisoIV	e8opeAa1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: DNA_topoisoIV	ECOD (v294.2)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth Ab], BA [auth Bb], D [auth Ad], DA [auth Bd], F [auth Af], B [auth Ab], BA [auth Bb], D [auth Ad], DA [auth Bd], F [auth Af], FA [auth Bf], H [auth Ah], HA [auth Bh], J [auth Aj], JA [auth Bj], L [auth Al], LA [auth Bl], N [auth An], NA [auth Bn], P [auth Ap], PA [auth Bp], R [auth Ar], T [auth At], V [auth Av], X [auth Ax], Z [auth Az]	RNA (5'-R(PUPUPUPUP*U)-3')	-	-	-
A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], EA [auth Be], G [auth Ag], GA [auth Bg], I [auth Ai], IA [auth Bi], K [auth Ak], KA [auth Bk], M [auth Am], MA [auth Bm], O [auth Ao], OA [auth Bo], Q [auth Aq], S [auth As], U [auth Au], W [auth Aw], Y [auth Ay]	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], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], EA [auth Be], G [auth Ag], GA [auth Bg], I [auth Ai], IA [auth Bi], K [auth Ak], KA [auth Bk], M [auth Am], MA [auth Bm], O [auth Ao], OA [auth Bo], Q [auth Aq], S [auth As], U [auth Au], W [auth Aw], Y [auth Ay]	IPR001205	RNA-directed RNA polymerase, C-terminal domain	Domain
A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], EA [auth Be], G [auth Ag], GA [auth Bg], I [auth Ai], IA [auth Bi], K [auth Ak], KA [auth Bk], M [auth Am], MA [auth Bm], O [auth Ao], OA [auth Bo], Q [auth Aq], S [auth As], U [auth Au], W [auth Aw], Y [auth Ay]	IPR001456	Helper component proteinase	Family
A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], EA [auth Be], G [auth Ag], GA [auth Bg], I [auth Ai], IA [auth Bi], K [auth Ak], KA [auth Bk], M [auth Am], MA [auth Bm], O [auth Ao], OA [auth Bo], Q [auth Aq], S [auth As], U [auth Au], W [auth Aw], Y [auth Ay]	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], EA [auth Be], G [auth Ag], GA [auth Bg], I [auth Ai], IA [auth Bi], K [auth Ak], KA [auth Bk], M [auth Am], MA [auth Bm], O [auth Ao], OA [auth Bo], Q [auth Aq], S [auth As], U [auth Au], W [auth Aw], Y [auth Ay]	IPR002540	Peptidase S30, polyprotein P1, potyvirus	Domain
A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], EA [auth Be], G [auth Ag], GA [auth Bg], I [auth Ai], IA [auth Bi], K [auth Ak], KA [auth Bk], M [auth Am], MA [auth Bm], O [auth Ao], OA [auth Bo], Q [auth Aq], S [auth As], U [auth Au], W [auth Aw], Y [auth Ay]	IPR013648	Polyprotein, Potyviridae	Domain
A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], EA [auth Be], G [auth Ag], GA [auth Bg], I [auth Ai], IA [auth Bi], K [auth Ak], KA [auth Bk], M [auth Am], MA [auth Bm], O [auth Ao], OA [auth Bo], Q [auth Aq], S [auth As], U [auth Au], W [auth Aw], Y [auth Ay]	IPR001730	Potyvirus NIa protease (NIa-pro) domain	Domain
A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], EA [auth Be], G [auth Ag], GA [auth Bg], I [auth Ai], IA [auth Bi], K [auth Ak], KA [auth Bk], M [auth Am], MA [auth Bm], O [auth Ao], OA [auth Bo], Q [auth Aq], S [auth As], U [auth Au], W [auth Aw], Y [auth Ay]	IPR011545	DEAD/DEAH-box helicase domain	Domain
A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], EA [auth Be], G [auth Ag], GA [auth Bg], I [auth Ai], IA [auth Bi], K [auth Ak], KA [auth Bk], M [auth Am], MA [auth Bm], O [auth Ao], OA [auth Bo], Q [auth Aq], S [auth As], U [auth Au], W [auth Aw], Y [auth Ay]	IPR031159	Helper-component proteinase (HC-Pro) cysteine protease (CPD) domain	Domain
A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], EA [auth Be], G [auth Ag], GA [auth Bg], I [auth Ai], IA [auth Bi], K [auth Ak], KA [auth Bk], M [auth Am], MA [auth Bm], O [auth Ao], OA [auth Bo], Q [auth Aq], S [auth As], U [auth Au], W [auth Aw], Y [auth Ay]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], EA [auth Be], G [auth Ag], GA [auth Bg], I [auth Ai], IA [auth Bi], K [auth Ak], KA [auth Bk], M [auth Am], MA [auth Bm], O [auth Ao], OA [auth Bo], Q [auth Aq], S [auth As], U [auth Au], W [auth Aw], Y [auth Ay]	IPR043504	Peptidase_S1_PA_chymotrypsin	Unknown
A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], EA [auth Be], G [auth Ag], GA [auth Bg], I [auth Ai], IA [auth Bi], K [auth Ak], KA [auth Bk], M [auth Am], MA [auth Bm], O [auth Ao], OA [auth Bo], Q [auth Aq], S [auth As], U [auth Au], W [auth Aw], Y [auth Ay]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], EA [auth Be], G [auth Ag], GA [auth Bg], I [auth Ai], IA [auth Bi], K [auth Ak], KA [auth Bk], M [auth Am], MA [auth Bm], O [auth Ao], OA [auth Bo], Q [auth Aq], S [auth As], U [auth Au], W [auth Aw], Y [auth Ay]	IPR001650	Helicase, C-terminal domain-like	Domain
A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], EA [auth Be], G [auth Ag], GA [auth Bg], I [auth Ai], IA [auth Bi], K [auth Ak], KA [auth Bk], M [auth Am], MA [auth Bm], O [auth Ao], OA [auth Bo], Q [auth Aq], S [auth As], U [auth Au], W [auth Aw], Y [auth Ay]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], EA [auth Be], G [auth Ag], GA [auth Bg], I [auth Ai], IA [auth Bi], K [auth Ak], KA [auth Bk], M [auth Am], MA [auth Bm], O [auth Ao], OA [auth Bo], Q [auth Aq], S [auth As], U [auth Au], W [auth Aw], Y [auth Ay]	IPR014001	Helicase superfamily 1/2, ATP-binding domain	Domain
A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], EA [auth Be], G [auth Ag], GA [auth Bg], I [auth Ai], IA [auth Bi], K [auth Ak], KA [auth Bk], M [auth Am], MA [auth Bm], O [auth Ao], OA [auth Bo], Q [auth Aq], S [auth As], U [auth Au], W [auth Aw], Y [auth Ay]	IPR001592	Potyvirus coat protein	Family
A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], EA [auth Be], G [auth Ag], GA [auth Bg], I [auth Ai], IA [auth Bi], K [auth Ak], KA [auth Bk], M [auth Am], MA [auth Bm], O [auth Ao], OA [auth Bo], Q [auth Aq], S [auth As], U [auth Au], W [auth Aw], Y [auth Ay]	IPR039560	Potyviral polyprotein protein 3	Domain
A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], EA [auth Be], G [auth Ag], GA [auth Bg], I [auth Ai], IA [auth Bi], K [auth Ak], KA [auth Bk], M [auth Am], MA [auth Bm], O [auth Ao], OA [auth Bo], Q [auth Aq], S [auth As], U [auth Au], W [auth Aw], Y [auth Ay]	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain
A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], A [auth Aa], AA [auth Ba], C [auth Ac], CA [auth Bc], E [auth Ae], EA [auth Be], G [auth Ag], GA [auth Bg], I [auth Ai], IA [auth Bi], K [auth Ak], KA [auth Bk], M [auth Am], MA [auth Bm], O [auth Ao], OA [auth Bo], Q [auth Aq], S [auth As], U [auth Au], W [auth Aw], Y [auth Ay]	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.