Annotations: 3IYL

Atomic CryoEM Structure of a Nonenveloped Virus Suggests How Membrane Penetration Protein is Primed for Cell Entry

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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	zf-C2H2_6	e3iylY1	A: alpha arrays	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: zf-C2H2_6	ECOD (v295.2)
X	MR_MLE_N	e3iylX1	A: alpha arrays	X: Thioredoxin-like	H: Thioredoxin-like	T: Thioredoxin-like	F: MR_MLE_N	ECOD (v295.2)
W	Reovirus_L2_N	e3iylW1	A: alpha arrays	X: HIT-like	H: HIT-related	T: HIT-related	F: Reovirus_L2_N	ECOD (v295.2)
W	Reovirus_L2_GTase	e3iylW2	A: alpha arrays	X: HIT-like	H: HIT-related	T: HIT-related	F: Reovirus_L2_GTase	ECOD (v295.2)
W	Reovirus_L2_4th	e3iylW3	A: alpha arrays	X: CH domain-like	H: Calponin-homology domain-like	T: Calponin-homology domain-like	F: Reovirus_L2_4th	ECOD (v295.2)
W	Reovirus_L2_MT1	e3iylW4	A: alpha arrays	X: CH domain-like	H: Calponin-homology domain-like	T: Calponin-homology domain-like	F: Reovirus_L2_MT1	ECOD (v295.2)
W	Reovirus_L2_MT2	e3iylW5	A: alpha arrays	X: CH domain-like	H: Calponin-homology domain-like	T: Calponin-homology domain-like	F: Reovirus_L2_MT2	ECOD (v295.2)
W	Reovirus_L2_6th	e3iylW6	A: alpha arrays	X: CH domain-like	H: Calponin-homology domain-like	T: Calponin-homology domain-like	F: Reovirus_L2_6th	ECOD (v295.2)
W	Reovirus_L2_7th	e3iylW7	A: alpha arrays	X: CH domain-like	H: Calponin-homology domain-like	T: Calponin-homology domain-like	F: Reovirus_L2_7th	ECOD (v295.2)
W	Reovirus_L2_8th	e3iylW8	A: alpha arrays	X: CH domain-like	H: Calponin-homology domain-like	T: Calponin-homology domain-like	F: Reovirus_L2_8th	ECOD (v295.2)
V	Cytochrome_CBB3	e3iylV1	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: Cytochrome_CBB3	ECOD (v295.2)
U	Sigma_1_2	e3iylU1	A: alpha arrays	X: Outer capsid protein sigma 3-related	H: PsV capsid protein	T: PsV capsid protein	F: Sigma_1_2	ECOD (v295.2)
T	KAsynt_C_assoc	e3iylT2	A: alpha arrays	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: KAsynt_C_assoc	ECOD (v295.2)
S	Med6	e3iylS1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: Med6	ECOD (v295.2)
R	KAsynt_C_assoc	e3iylR2	A: alpha arrays	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: KAsynt_C_assoc	ECOD (v295.2)
Q	Med6	e3iylQ1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: Med6	ECOD (v295.2)
P	KAsynt_C_assoc	e3iylP2	A: alpha arrays	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: KAsynt_C_assoc	ECOD (v295.2)
O	Med6	e3iylO1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: Med6	ECOD (v295.2)
N	KAsynt_C_assoc	e3iylN2	A: alpha arrays	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: KAsynt_C_assoc	ECOD (v295.2)
M	Med6	e3iylM1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: Med6	ECOD (v295.2)
L	KAsynt_C_assoc	e3iylL2	A: alpha arrays	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: KAsynt_C_assoc	ECOD (v295.2)
K	Med6	e3iylK1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: Med6	ECOD (v295.2)
J	KAsynt_C_assoc	e3iylJ2	A: alpha arrays	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: KAsynt_C_assoc	ECOD (v295.2)
I	Med6	e3iylI1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: Med6	ECOD (v295.2)
H	KAsynt_C_assoc	e3iylH2	A: alpha arrays	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: KAsynt_C_assoc	ECOD (v295.2)
G	Med6	e3iylG1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: Med6	ECOD (v295.2)
F	KAsynt_C_assoc	e3iylF2	A: alpha arrays	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: KAsynt_C_assoc	ECOD (v295.2)
E	Med6	e3iylE1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: Med6	ECOD (v295.2)
D	KAsynt_C_assoc	e3iylD2	A: alpha arrays	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: KAsynt_C_assoc	ECOD (v295.2)
C	Med6	e3iylC1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: Med6	ECOD (v295.2)
B	Biotin_carb_C	e3iylB1	A: alpha arrays	X: Repetitive alpha hairpins	H: Phage tail fiber protein trimerization domain	T: CO dehydrogenase molybdoprotein N-domain-like	F: Biotin_carb_C	ECOD (v295.2)
A	Med6	e3iylA1	A: alpha arrays	X: Hypothetical protein YqbG-like	H: Hypothetical protein YqbG-like	T: alpha/beta-Hydrolases	F: Med6	ECOD (v295.2)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
W	3.90.1810.10	Alpha Beta	Alpha-Beta Complex	Reovirus components fold	Reovirus components	CATH (4.3.0)
W	3.55.60.10	Alpha Beta	3-Layer(bab) Sandwich	Reovirus components fold	Reovirus components	CATH (4.3.0)
W	3.40.50.10760	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Reovirus core	CATH (4.3.0)
W	3.40.50.150	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Vaccinia Virus protein VP39	CATH (4.3.0)
W	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
V	1.10.287.1520	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
U	1.10.287.1520	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
T	1.10.2050.10	Mainly Alpha	Orthogonal Bundle	Protein mu-1, chain B, domain 3	Protein mu-1, chain B, domain 3	CATH (4.3.0)
T	2.60.120.420	Mainly Beta	Sandwich	Jelly Rolls	Membrane penetration protein mu1, Chain B, domain 4	CATH (4.3.0)
R	1.10.2050.10	Mainly Alpha	Orthogonal Bundle	Protein mu-1, chain B, domain 3	Protein mu-1, chain B, domain 3	CATH (4.3.0)
R	2.60.120.420	Mainly Beta	Sandwich	Jelly Rolls	Membrane penetration protein mu1, Chain B, domain 4	CATH (4.3.0)
P	1.10.2050.10	Mainly Alpha	Orthogonal Bundle	Protein mu-1, chain B, domain 3	Protein mu-1, chain B, domain 3	CATH (4.3.0)
P	2.60.120.420	Mainly Beta	Sandwich	Jelly Rolls	Membrane penetration protein mu1, Chain B, domain 4	CATH (4.3.0)
N	1.10.2050.10	Mainly Alpha	Orthogonal Bundle	Protein mu-1, chain B, domain 3	Protein mu-1, chain B, domain 3	CATH (4.3.0)
N	2.60.120.420	Mainly Beta	Sandwich	Jelly Rolls	Membrane penetration protein mu1, Chain B, domain 4	CATH (4.3.0)
L	1.10.2050.10	Mainly Alpha	Orthogonal Bundle	Protein mu-1, chain B, domain 3	Protein mu-1, chain B, domain 3	CATH (4.3.0)
L	2.60.120.420	Mainly Beta	Sandwich	Jelly Rolls	Membrane penetration protein mu1, Chain B, domain 4	CATH (4.3.0)
J	1.10.2050.10	Mainly Alpha	Orthogonal Bundle	Protein mu-1, chain B, domain 3	Protein mu-1, chain B, domain 3	CATH (4.3.0)
J	2.60.120.420	Mainly Beta	Sandwich	Jelly Rolls	Membrane penetration protein mu1, Chain B, domain 4	CATH (4.3.0)
H	1.10.2050.10	Mainly Alpha	Orthogonal Bundle	Protein mu-1, chain B, domain 3	Protein mu-1, chain B, domain 3	CATH (4.3.0)
H	2.60.120.420	Mainly Beta	Sandwich	Jelly Rolls	Membrane penetration protein mu1, Chain B, domain 4	CATH (4.3.0)
F	1.10.2050.10	Mainly Alpha	Orthogonal Bundle	Protein mu-1, chain B, domain 3	Protein mu-1, chain B, domain 3	CATH (4.3.0)
F	2.60.120.420	Mainly Beta	Sandwich	Jelly Rolls	Membrane penetration protein mu1, Chain B, domain 4	CATH (4.3.0)
D	1.10.2050.10	Mainly Alpha	Orthogonal Bundle	Protein mu-1, chain B, domain 3	Protein mu-1, chain B, domain 3	CATH (4.3.0)
D	2.60.120.420	Mainly Beta	Sandwich	Jelly Rolls	Membrane penetration protein mu1, Chain B, domain 4	CATH (4.3.0)
B	1.10.2050.10	Mainly Alpha	Orthogonal Bundle	Protein mu-1, chain B, domain 3	Protein mu-1, chain B, domain 3	CATH (4.3.0)
B	2.60.120.420	Mainly Beta	Sandwich	Jelly Rolls	Membrane penetration protein mu1, Chain B, domain 4	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
X, Y	VP3	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 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 catalytic activity nucleic acid conformation isomerase activity isomerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid helicase activity RNA helicase activity ATP-dependent activity, acting on RNA macromolecular conformation isomerase activity ATP-dependent activity cation binding transition metal ion binding zinc ion binding metal ion binding	7-methylguanosine mRNA capping RNA metabolic process primary metabolic process 7-methylguanosine RNA capping RNA capping gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process 7-methylguanosine mRNA capping RNA metabolic process primary metabolic process 7-methylguanosine RNA capping RNA capping gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process mRNA processing mRNA metabolic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process RNA 5'-end processing metabolic process cellular process RNA processing macromolecule metabolic process	viral capsid icosahedral viral capsid virion component viral inner capsid T=2 icosahedral viral capsid
W	VP1	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 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 guanylyltransferase activity mRNA guanylyltransferase activity RNA guanylyltransferase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid transferase activity catalytic activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups RNA methyltransferase activity transferase activity, transferring one-carbon groups S-adenosylmethionine-dependent methyltransferase activity mRNA 5'-cap (guanine-N7-)-methyltransferase activity N-methyltransferase activity methyltransferase activity mRNA methyltransferase activity guanyl nucleotide binding GTP binding guanyl ribonucleotide binding	-	viral capsid icosahedral viral capsid virion component viral outer capsid
U, V	Core protein VP6	-	-	viral capsid virion component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	Outer capsid VP4	host cell surface binding binding	symbiont-mediated disruption of host anatomical structure biological process involved in interspecies interaction between organisms symbiont entry into host cell via permeabilization of host membrane viral life cycle symbiont-mediated disruption of host cellular anatomical structure biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated perturbation of host membrane symbiont entry into host cell viral process symbiont entry into host disruption of anatomical structure in another organism	viral capsid icosahedral viral capsid virion component viral outer capsid

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
X, Y	IPR044949	Inner capsid protein lambda-1/ VP3 superfamily	Homologous Superfamily
X, Y	IPR013087	Zinc finger C2H2-type	Domain
X, Y	IPR054176	Inner capsid protein lambda-1/VP3	Domain
W	IPR048601	Reovirus core-spike protein lambda-2-like, GTase domain	Domain
W	IPR048602	Reovirus core-spike protein lambda-2-like, 7th domain	Domain
W	IPR048604	Reovirus core-spike protein lambda-2-like, ferredoxin-like domain	Domain
W	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily	Homologous Superfamily
W	IPR048598	Reovirus core-spike protein lambda-2-like, first methyltransferase domain	Domain
W	IPR048596	Reovirus core-spike protein lambda-2-like, N-terminal domain	Domain
W	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
W	IPR048603	Reovirus core-spike protein lambda-2-like, 6th domain	Domain
W	IPR010311	Reovirus core-spike lambda-2	Family
W	IPR048597	Reovirus core-spike protein lambda-2-like, second methyltransferase domain	Domain
W	IPR048294	Reovirus core-spike protein lambda-2-like, C-terminal domain	Domain
U, V	IPR004317	Sigma1/sigma2, reoviral	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	IPR015960	Mu1 membrane penetration protein, domain IV	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	IPR036256	Mu1/VP4 superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	IPR009113	Outer capsid protein Mu1/VP4	Family
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	IPR015962	Mu1 membrane penetration protein, domain II	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T	IPR044937	Mu1 membrane penetration protein, domain III	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.

3IYL | pdb_00003iyl

Atomic CryoEM Structure of a Nonenveloped Virus Suggests How Membrane Penetration Protein is Primed for Cell Entry

External Resource: Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Domain Annotation: CATH CATH Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage