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
Protein Family Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
J	PF05993	e3iylJ2	A: beta sandwiches	X: jelly-roll	H: Jelly-roll domain in membrane penetration protein mu1 (From Topology)	T: Jelly-roll domain in membrane penetration protein mu1	F: PF05993	ECOD (1.6)
J	PF05993	e3iylJ3	A: alpha arrays	X: Alpha-helical domain in membrane penetration protein mu1 (From Topology)	H: Alpha-helical domain in membrane penetration protein mu1 (From Topology)	T: Alpha-helical domain in membrane penetration protein mu1	F: PF05993	ECOD (1.6)
L	PF05993	e3iylL2	A: beta sandwiches	X: jelly-roll	H: Jelly-roll domain in membrane penetration protein mu1 (From Topology)	T: Jelly-roll domain in membrane penetration protein mu1	F: PF05993	ECOD (1.6)
L	PF05993	e3iylL3	A: alpha arrays	X: Alpha-helical domain in membrane penetration protein mu1 (From Topology)	H: Alpha-helical domain in membrane penetration protein mu1 (From Topology)	T: Alpha-helical domain in membrane penetration protein mu1	F: PF05993	ECOD (1.6)
P	PF05993	e3iylP2	A: beta sandwiches	X: jelly-roll	H: Jelly-roll domain in membrane penetration protein mu1 (From Topology)	T: Jelly-roll domain in membrane penetration protein mu1	F: PF05993	ECOD (1.6)
P	PF05993	e3iylP3	A: alpha arrays	X: Alpha-helical domain in membrane penetration protein mu1 (From Topology)	H: Alpha-helical domain in membrane penetration protein mu1 (From Topology)	T: Alpha-helical domain in membrane penetration protein mu1	F: PF05993	ECOD (1.6)
T	PF05993	e3iylT2	A: beta sandwiches	X: jelly-roll	H: Jelly-roll domain in membrane penetration protein mu1 (From Topology)	T: Jelly-roll domain in membrane penetration protein mu1	F: PF05993	ECOD (1.6)
T	PF05993	e3iylT3	A: alpha arrays	X: Alpha-helical domain in membrane penetration protein mu1 (From Topology)	H: Alpha-helical domain in membrane penetration protein mu1 (From Topology)	T: Alpha-helical domain in membrane penetration protein mu1	F: PF05993	ECOD (1.6)
B	PF05993	e3iylB2	A: beta sandwiches	X: jelly-roll	H: Jelly-roll domain in membrane penetration protein mu1 (From Topology)	T: Jelly-roll domain in membrane penetration protein mu1	F: PF05993	ECOD (1.6)
B	PF05993	e3iylB1	A: alpha arrays	X: Alpha-helical domain in membrane penetration protein mu1 (From Topology)	H: Alpha-helical domain in membrane penetration protein mu1 (From Topology)	T: Alpha-helical domain in membrane penetration protein mu1	F: PF05993	ECOD (1.6)
D	PF05993	e3iylD2	A: beta sandwiches	X: jelly-roll	H: Jelly-roll domain in membrane penetration protein mu1 (From Topology)	T: Jelly-roll domain in membrane penetration protein mu1	F: PF05993	ECOD (1.6)
D	PF05993	e3iylD3	A: alpha arrays	X: Alpha-helical domain in membrane penetration protein mu1 (From Topology)	H: Alpha-helical domain in membrane penetration protein mu1 (From Topology)	T: Alpha-helical domain in membrane penetration protein mu1	F: PF05993	ECOD (1.6)
F	PF05993	e3iylF2	A: beta sandwiches	X: jelly-roll	H: Jelly-roll domain in membrane penetration protein mu1 (From Topology)	T: Jelly-roll domain in membrane penetration protein mu1	F: PF05993	ECOD (1.6)
F	PF05993	e3iylF3	A: alpha arrays	X: Alpha-helical domain in membrane penetration protein mu1 (From Topology)	H: Alpha-helical domain in membrane penetration protein mu1 (From Topology)	T: Alpha-helical domain in membrane penetration protein mu1	F: PF05993	ECOD (1.6)
H	PF05993	e3iylH2	A: beta sandwiches	X: jelly-roll	H: Jelly-roll domain in membrane penetration protein mu1 (From Topology)	T: Jelly-roll domain in membrane penetration protein mu1	F: PF05993	ECOD (1.6)
H	PF05993	e3iylH3	A: alpha arrays	X: Alpha-helical domain in membrane penetration protein mu1 (From Topology)	H: Alpha-helical domain in membrane penetration protein mu1 (From Topology)	T: Alpha-helical domain in membrane penetration protein mu1	F: PF05993	ECOD (1.6)
N	PF05993	e3iylN2	A: beta sandwiches	X: jelly-roll	H: Jelly-roll domain in membrane penetration protein mu1 (From Topology)	T: Jelly-roll domain in membrane penetration protein mu1	F: PF05993	ECOD (1.6)
N	PF05993	e3iylN3	A: alpha arrays	X: Alpha-helical domain in membrane penetration protein mu1 (From Topology)	H: Alpha-helical domain in membrane penetration protein mu1 (From Topology)	T: Alpha-helical domain in membrane penetration protein mu1	F: PF05993	ECOD (1.6)
R	PF05993	e3iylR2	A: beta sandwiches	X: jelly-roll	H: Jelly-roll domain in membrane penetration protein mu1 (From Topology)	T: Jelly-roll domain in membrane penetration protein mu1	F: PF05993	ECOD (1.6)
R	PF05993	e3iylR3	A: alpha arrays	X: Alpha-helical domain in membrane penetration protein mu1 (From Topology)	H: Alpha-helical domain in membrane penetration protein mu1 (From Topology)	T: Alpha-helical domain in membrane penetration protein mu1	F: PF05993	ECOD (1.6)
U	PF03084	e3iylU1	A: alpha complex topology	X: Core protein VP6 (From Topology)	H: Core protein VP6 (From Topology)	T: Core protein VP6	F: PF03084	ECOD (1.6)
V	PF03084	e3iylV1	A: alpha complex topology	X: Core protein VP6 (From Topology)	H: Core protein VP6 (From Topology)	T: Core protein VP6	F: PF03084	ECOD (1.6)
W	PF06016	e3iylW8	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF06016	ECOD (1.6)
W	PF21060	e3iylW6	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF21060	ECOD (1.6)
W	PF21061	e3iylW7	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF21061	ECOD (1.6)
W	PF21062,PF21065	e3iylW3	A: a+b two layers	X: ferredoxin-like domain in VP1 (From Topology)	H: ferredoxin-like domain in VP1 (From Topology)	T: ferredoxin-like domain in VP1	F: PF21062,PF21065	ECOD (1.6)
W	PF21063	e3iylW2	A: a+b three layers	X: HIT-like	H: HIT-related (From Topology)	T: HIT-related	F: PF21063	ECOD (1.6)
W	PF21064	e3iylW1	A: a+b complex topology	X: Rotavirus NSP2 fragment, N-terminal domain (From Topology)	H: Rotavirus NSP2 fragment, N-terminal domain (From Topology)	T: Rotavirus NSP2 fragment, N-terminal domain	F: PF21064	ECOD (1.6)
W	PF21065	e3iylW4	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PF21065	ECOD (1.6)
W	PF21066	e3iylW5	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: S-adenosyl-L-methionine-dependent methyltransferases	F: PF21066	ECOD (1.6)
X	PF22033	e3iylX1	A: a+b complex topology	X: Inner layer core protein p3-related (From Topology)	H: Inner layer core protein p3-related (From Topology)	T: Inner layer core protein p3-related	F: PF22033	ECOD (1.6)
Y	PF22033	e3iylY1	A: a+b complex topology	X: Inner layer core protein p3-related (From Topology)	H: Inner layer core protein p3-related (From Topology)	T: Inner layer core protein p3-related	F: PF22033	ECOD (1.6)
Y	PF13912	e3iylY2	A: few secondary structure elements	X: beta-beta-alpha zinc fingers	H: beta-beta-alpha zinc fingers (From Topology)	T: beta-beta-alpha zinc fingers	F: PF13912	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
U	1.10.287.1520	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
V	1.10.287.1520	Mainly Alpha	Orthogonal Bundle	Helix Hairpins		CATH (4.3.0)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
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	PF05993	Reovirus major virion structural protein Mu-1/Mu-1C (M2) (Reovirus_M2)	Reovirus major virion structural protein Mu-1/Mu-1C (M2)	-	Family
U, V	PF03084	Reoviral Sigma1/Sigma2 family (Sigma_1_2)	Reoviral Sigma1/Sigma2 family	-	Family
W	PF21064	Reovirus core-spike protein lambda-2 (L2), N-terminal (Reovirus_L2_N)	Reovirus core-spike protein lambda-2 (L2), N-terminal	Reovirus core-spike protein VP1/lambda-2 (VP1/L2) forms a pentamer that mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts [1]. It forms a hollow cylinder with projecting turrets. Each VP1/L2 monomer consists of eight dom ...	Reovirus core-spike protein VP1/lambda-2 (VP1/L2) forms a pentamer that mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts [1]. It forms a hollow cylinder with projecting turrets. Each VP1/L2 monomer consists of eight domains with the most N-terminal domain at the base of the turret and the most C-terminal domain at the top [2]. This entry represents the N-terminal domain which adopts an alpha/beta topology.	Domain
W	PF21063	Reovirus core-spike protein lambda-2 (L2), GTase domain (Reovirus_L2_GTase)	Reovirus core-spike protein lambda-2 (L2), GTase domain	Reovirus core-spike protein VP1/lambda-2 (VP1/L2) forms a pentamer that mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts [1]. It forms a hollow cylinder with projecting turrets. Each VP1/L2 monomer consists of eight dom ...	Reovirus core-spike protein VP1/lambda-2 (VP1/L2) forms a pentamer that mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts [1]. It forms a hollow cylinder with projecting turrets. Each VP1/L2 monomer consists of eight domains with the most N-terminal domain at the base of the turret and the most C-terminal domain at the top. This entry represents the second one, which contains the nucleotide-binding histidine triad (HIT)-like motif from the GTase (guanylyltransferase) domain [2].	Domain
W	PF21066	Reovirus core-spike protein lambda-2 (L2), methyltransferase-2 (Reovirus_L2_MT2)	Reovirus core-spike protein lambda-2 (L2), methyltransferase-2	Reovirus core-spike protein VP1/lambda-2 (VP1/L2) forms a pentamer that mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts [1]. It forms a hollow cylinder with projecting turrets. Each VP1/L2 monomer consists of eight dom ...	Reovirus core-spike protein VP1/lambda-2 (VP1/L2) forms a pentamer that mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts [1]. It forms a hollow cylinder with projecting turrets. Each VP1/L2 monomer consists of eight domains with the most N-terminal domain at the base of the turret and the most C-terminal domain at the top. This entry represents the second methyltransferase domain (MT2), which catalyses the last reaction, 2'O-methylation [2].	Domain
W	PF21065	Reovirus core-spike protein lambda-2 (L2), methyltransferase-1 (Reovirus_L2_MT1)	Reovirus core-spike protein lambda-2 (L2), methyltransferase-1	Reovirus core-spike protein VP1/lambda-2 (VP1/L2) forms a pentamer that mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts [1]. It forms a hollow cylinder with projecting turrets. Each VP1/L2 monomer consists of eight dom ...	Reovirus core-spike protein VP1/lambda-2 (VP1/L2) forms a pentamer that mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts [1]. It forms a hollow cylinder with projecting turrets. Each VP1/L2 monomer consists of eight domains with the most N-terminal domain at the base of the turret and the most C-terminal domain at the top. This entry represents the methyltransferase-1 domain [2] which adds a methyl group to the N7 of the guanosine added by the GTase [2].	Domain
W	PF21060	Reovirus core-spike protein lambda-2 (L2), 6th domain (Reovirus_L2_6th)	Reovirus core-spike protein lambda-2 (L2), 6th domain	Reovirus core-spike protein VP1/lambda-2 (VP1/L2) forms a pentamer that mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts [1]. It forms a hollow cylinder with projecting turrets. Each VP1/L2 monomer consists of eight dom ...	Reovirus core-spike protein VP1/lambda-2 (VP1/L2) forms a pentamer that mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts [1]. It forms a hollow cylinder with projecting turrets. Each VP1/L2 monomer consists of eight domains with the most N-terminal domain at the base of the turret and the most C-terminal domain at the top. This entry represents the sixth domain which, together with the seventh and eighth (Pfam:PF06016) domains forms a three-domain flap at the top of the turret, that may serve as a gate to retard exit of the 5' terminus of the mRNA [2]. This domain has a Ig-like fold, resembling the V of an antibody light chain [2].	Domain
W	PF06016	Reovirus core-spike protein lambda-2 (L2), C-terminal (Reovirus_L2_8th)	Reovirus core-spike protein lambda-2 (L2), C-terminal	Reovirus core-spike protein VP1/lambda-2 (VP1/L2) forms a pentamer that mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts [1]. It forms a hollow cylinder with projecting turrets. Each VP1/L2 monomer consists of eight dom ...	Reovirus core-spike protein VP1/lambda-2 (VP1/L2) forms a pentamer that mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts [1]. It forms a hollow cylinder with projecting turrets. Each VP1/L2 monomer consists of eight domains with the most N-terminal domain at the base of the turret and the most C-terminal domain at the top. This entry represents the C-terminal (eighth) domain which, together with the sixth and seventh domains, forms a three-domain flap at the top of the turret, that may serve as a gate to retard exit of the 5' terminus of the mRNA [2]. This domain has a Ig-like, resembling a truncated V region of an antibody light chain.	Domain
W	PF21062	Reovirus core-spike protein lambda-2 (L2), ferredoxin-like domain (Reovirus_L2_4th)	Reovirus core-spike protein lambda-2 (L2), ferredoxin-like domain	Reovirus core-spike protein VP1/lambda-2 (VP1/L2) forms a pentamer that mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts [1]. It forms a hollow cylinder with projecting turrets. Each VP1/L2 monomer consists of eight dom ...	Reovirus core-spike protein VP1/lambda-2 (VP1/L2) forms a pentamer that mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts [1]. It forms a hollow cylinder with projecting turrets. Each VP1/L2 monomer consists of eight domains with the most N-terminal domain at the base of the turret and the most C-terminal domain at the top. This entry represents the fourth domain, which adopts a ferredoxin-like fold consisting of four beta-strands protected by alpha-helices that probably functions as a structural support for the three enzyme domains (two methyltransferase and GTase domains) [2].	Domain
W	PF21061	Reovirus core-spike protein lambda-2 (L2), 7th domain (Reovirus_L2_7th)	Reovirus core-spike protein lambda-2 (L2), 7th domain	Reovirus core-spike protein VP1/lambda-2 (VP1/L2) forms a pentamer that mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts [1]. It forms a hollow cylinder with projecting turrets. Each VP1/L2 monomer consists of eight dom ...	Reovirus core-spike protein VP1/lambda-2 (VP1/L2) forms a pentamer that mediates enzymatic reactions in 5' capping of the viral plus-strand transcripts [1]. It forms a hollow cylinder with projecting turrets. Each VP1/L2 monomer consists of eight domains with the most N-terminal domain at the base of the turret and the most C-terminal domain at the top. This entry represents the seventh domain which, together with the sixth (Pfam:PF21060) and eighth (Pfam:PF06016) domains forms a three-domain flap at the top of the turret, that may serve as a gate to retard exit of the 5' terminus of the mRNA [2]. This domain has a Ig-like fold, resembling the C region of an antibody light chain [2].	Domain

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.

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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 ECOD Database Homepage

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage