1JMU | pdb_00001jmu

Crystal Structure of the Reovirus mu1/sigma3 Complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
I	d1jmui_	Alpha and beta proteins (a+b)	Outer capsid protein sigma 3	Outer capsid protein sigma 3	Outer capsid protein sigma 3	Outer capsid protein sigma 3	(Reovirus sp. ) [TaxId: 10891 ],	SCOPe (2.08)
H	d1jmuh_	Alpha and beta proteins (a+b)	Outer capsid protein sigma 3	Outer capsid protein sigma 3	Outer capsid protein sigma 3	Outer capsid protein sigma 3	(Reovirus sp. ) [TaxId: 10891 ],	SCOPe (2.08)
G	d1jmug_	Alpha and beta proteins (a+b)	Outer capsid protein sigma 3	Outer capsid protein sigma 3	Outer capsid protein sigma 3	Outer capsid protein sigma 3	(Reovirus sp. ) [TaxId: 10891 ],	SCOPe (2.08)
F	d1jmu.3	Multi-domain proteins (alpha and beta)	Membrane penetration protein mu1	Membrane penetration protein mu1	Membrane penetration protein mu1	Membrane penetration protein mu1	(Reovirus sp. ) [TaxId: 10891 ],	SCOPe (2.08)
D	d1jmu.2	Multi-domain proteins (alpha and beta)	Membrane penetration protein mu1	Membrane penetration protein mu1	Membrane penetration protein mu1	Membrane penetration protein mu1	(Reovirus sp. ) [TaxId: 10891 ],	SCOPe (2.08)
B	d1jmu.1	Multi-domain proteins (alpha and beta)	Membrane penetration protein mu1	Membrane penetration protein mu1	Membrane penetration protein mu1	Membrane penetration protein mu1	(Reovirus sp. ) [TaxId: 10891 ],	SCOPe (2.08)
E	d1jmu.3	Multi-domain proteins (alpha and beta)	Membrane penetration protein mu1	Membrane penetration protein mu1	Membrane penetration protein mu1	Membrane penetration protein mu1	(Reovirus sp. ) [TaxId: 10891 ],	SCOPe (2.08)
C	d1jmu.2	Multi-domain proteins (alpha and beta)	Membrane penetration protein mu1	Membrane penetration protein mu1	Membrane penetration protein mu1	Membrane penetration protein mu1	(Reovirus sp. ) [TaxId: 10891 ],	SCOPe (2.08)
A	d1jmu.1	Multi-domain proteins (alpha and beta)	Membrane penetration protein mu1	Membrane penetration protein mu1	Membrane penetration protein mu1	Membrane penetration protein mu1	(Reovirus sp. ) [TaxId: 10891 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
I	SCOP2B Superfamily	Outer capsid protein sigma 3	8071741	3001282	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Outer capsid protein sigma 3	8071741	3001282	SCOP2B (2022-06-29)
G	SCOP2 Family	Outer capsid protein sigma 3	8071740	4003686	SCOP2 (2022-06-29)
G	SCOP2 Superfamily	Outer capsid protein sigma 3	8071741	3001282	SCOP2 (2022-06-29)
F	SCOP2B Superfamily	Reovirus mu1 protein-like	8091411	3002506	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Reovirus mu1 protein-like	8091411	3002506	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Reovirus mu1 protein-like	8091411	3002506	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Reovirus mu1 protein-like	8091411	3002506	SCOP2B (2022-06-29)
A	SCOP2 Family	Reovirus mu1 protein-like	8091410	4007739	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Reovirus mu1 protein-like	8091411	3002506	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
I	RNA_pol_Rpb2_2	e1jmuI1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: RNA_pol_Rpb2_2	ECOD (v294.1)
H	RNA_pol_Rpb2_2	e1jmuH1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: RNA_pol_Rpb2_2	ECOD (v294.1)
G	RNA_pol_Rpb2_2	e1jmuG1	A: a/b three-layered sandwiches	X: ETN0001 domain-like	H: ETN0001 domain-like	T: Mss4-like	F: RNA_pol_Rpb2_2	ECOD (v294.1)
F	Copper-bind	e1jmuF2	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (v294.1)
F	RrnaAD	e1jmuF1	A: a/b three-layered sandwiches	X: Alpha-beta plaits	H: Protease propeptides/inhibitors	T: Protease propeptides/inhibitors	F: RrnaAD	ECOD (v294.1)
D	Copper-bind	e1jmuD3	A: a/b three-layered sandwiches	X: Phage tail fiber protein trimerization domain	H: beta-Prism I	T: beta-Prism I	F: Copper-bind	ECOD (v294.1)
D	VipB_2	e1jmuD1	A: a/b three-layered sandwiches	X: Rossmann-like	H: Rossmann-related	T: DHS-like NAD/FAD-binding domain	F: VipB_2	ECOD (v294.1)
B	Reovirus_M2	e1jmuB1	A: beta sandwiches	X: jelly-roll	H: Jelly-roll domain in membrane penetration protein mu1	T: Jelly-roll domain in membrane penetration protein mu1	F: Reovirus_M2	ECOD (v294.1)
B	Reovirus_M2	e1jmuB7	A: a/b three-layered sandwiches	X: Alpha-helical domain in membrane penetration protein mu1	H: Alpha-helical domain in membrane penetration protein mu1	T: Alpha-helical domain in membrane penetration protein mu1	F: Reovirus_M2	ECOD (v294.1)
E	FANCI_S1-cap,FANCI_S1,FANCI_S2,FANCI_S3,FANCI_S4,FANCI_HD1,FANCI_HD2	e1jmuE1	A: a/b three-layered sandwiches	X: barrel domains in phase 1 flagellin	H: Class II aaRS and biotin synthetases	T: Class II aaRS and biotin synthetases	F: FANCI_S1-cap,FANCI_S1,FANCI_S2,FANCI_S3,FANCI_S4,FANCI_HD1,FANCI_HD2	ECOD (v294.1)
C	Docking	e1jmuC1	A: a/b three-layered sandwiches	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: Docking	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
I	3.90.1630.10	Alpha Beta	Alpha-Beta Complex	Outer-capsid protein sigma 3, small lobe	Outer-capsid protein sigma 3, small lobe	CATH (4.3.0)
I	3.90.1320.10	Alpha Beta	Alpha-Beta Complex	Outer-capsid protein sigma 3, large lobe	Outer-capsid protein sigma 3, large lobe	CATH (4.3.0)
H	3.90.1630.10	Alpha Beta	Alpha-Beta Complex	Outer-capsid protein sigma 3, small lobe	Outer-capsid protein sigma 3, small lobe	CATH (4.3.0)
H	3.90.1320.10	Alpha Beta	Alpha-Beta Complex	Outer-capsid protein sigma 3, large lobe	Outer-capsid protein sigma 3, large lobe	CATH (4.3.0)
G	3.90.1630.10	Alpha Beta	Alpha-Beta Complex	Outer-capsid protein sigma 3, small lobe	Outer-capsid protein sigma 3, small lobe	CATH (4.3.0)
G	3.90.1320.10	Alpha Beta	Alpha-Beta Complex	Outer-capsid protein sigma 3, large lobe	Outer-capsid protein sigma 3, large lobe	CATH (4.3.0)
F	3.90.1370.10	Alpha Beta	Alpha-Beta Complex	Protein mu-1, chain B, domain 1	Protein mu-1, chain B, domain 1	CATH (4.3.0)
F	1.10.2040.10	Mainly Alpha	Orthogonal Bundle	Protein mu-1, chain B, domain 2	Protein mu-1, chain B, domain 2	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	3.90.1370.10	Alpha Beta	Alpha-Beta Complex	Protein mu-1, chain B, domain 1	Protein mu-1, chain B, domain 1	CATH (4.3.0)
D	1.10.2040.10	Mainly Alpha	Orthogonal Bundle	Protein mu-1, chain B, domain 2	Protein mu-1, chain B, domain 2	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	3.90.1370.10	Alpha Beta	Alpha-Beta Complex	Protein mu-1, chain B, domain 1	Protein mu-1, chain B, domain 1	CATH (4.3.0)
B	1.10.2040.10	Mainly Alpha	Orthogonal Bundle	Protein mu-1, chain B, domain 2	Protein mu-1, chain B, domain 2	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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
G, H, I	PF00979	Reovirus outer capsid protein, Sigma 3 (Reovirus_cap)	Reovirus outer capsid protein, Sigma 3	-	Family
B, D, F	PF05993	Reovirus major virion structural protein Mu-1/Mu-1C (M2) (Reovirus_M2)	Reovirus major virion structural protein Mu-1/Mu-1C (M2)	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G, H, I	SIGMA 3 PROTEIN	enzyme regulator activity protein kinase inhibitor activity molecular function inhibitor activity molecular function regulator activity enzyme inhibitor activity protein kinase regulator activity protein serine/threonine kinase inhibitor activity kinase inhibitor activity kinase regulator activity structural molecule activity cation binding transition metal ion binding zinc ion binding ion binding enzyme regulator activity protein kinase inhibitor activity molecular function inhibitor activity molecular function regulator activity enzyme inhibitor activity protein kinase regulator activity protein serine/threonine kinase inhibitor activity kinase inhibitor activity kinase regulator activity structural molecule activity cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding RNA binding nucleic acid binding	symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms response to stimulus response to other organism symbiont-mediated perturbation of host defenses symbiont-mediated suppression of host PKR/eIFalpha signaling symbiont-mediated response to host defenses response to external stimulus response to biotic stimulus biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host signal transduction pathway symbiont-mediated perturbation of host process symbiont-mediated suppression of host-directed shutoff of host translation symbiont-mediated suppression of host defenses symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms response to stimulus response to other organism symbiont-mediated perturbation of host defenses symbiont-mediated suppression of host PKR/eIFalpha signaling symbiont-mediated response to host defenses response to external stimulus response to biotic stimulus biological process involved in interaction with host biological process involved in symbiotic interaction symbiont-mediated suppression of host signal transduction pathway symbiont-mediated perturbation of host process symbiont-mediated suppression of host-directed shutoff of host translation symbiont-mediated suppression of host defenses response to host response to external biotic stimulus symbiont-mediated perturbation of host signal transduction pathway modulation of process of another organism symbiont-mediated perturbation of host defense response symbiont-mediated suppression of host immune response symbiont-mediated suppression of host innate immune response symbiont-mediated perturbation of host immune response symbiont-mediated perturbation of host innate immune response viral process viral life cycle symbiont-mediated suppression of host interferon-mediated signaling pathway symbiont-mediated suppression of host type I interferon-mediated signaling pathway	viral capsid icosahedral viral capsid virion component viral outer capsid
B, D, F	PROTEIN MU-1	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	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host intracellular region host cell mitochondrion viral capsid virion component host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host intracellular region host cell mitochondrion viral capsid virion component host cell plasma membrane host cell membrane icosahedral viral capsid viral outer capsid
A, C, E	PROTEIN MU-1	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	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host intracellular region host cell mitochondrion viral capsid virion component host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host intracellular region host cell mitochondrion viral capsid virion component host cell plasma membrane host cell membrane icosahedral viral capsid viral outer capsid

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
G, H, I	IPR000153	Reovirus, outer capsid sigma 3	Family
G, H, I	IPR023634	Reovirus, outer capsid sigma-3 domain superfamily	Homologous Superfamily
B, D, F	IPR015961	Mu1 membrane penetration protein, domain I	Homologous Superfamily
B, D, F	IPR015960	Mu1 membrane penetration protein, domain IV	Homologous Superfamily
B, D, F	IPR036256	Mu1/VP4 superfamily	Homologous Superfamily
B, D, F	IPR009113	Outer capsid protein Mu1/VP4	Family
B, D, F	IPR015962	Mu1 membrane penetration protein, domain II	Homologous Superfamily
B, D, F	IPR044937	Mu1 membrane penetration protein, domain III	Homologous Superfamily
A, C, E	IPR015961	Mu1 membrane penetration protein, domain I	Homologous Superfamily
A, C, E	IPR015960	Mu1 membrane penetration protein, domain IV	Homologous Superfamily
A, C, E	IPR036256	Mu1/VP4 superfamily	Homologous Superfamily
A, C, E	IPR009113	Outer capsid protein Mu1/VP4	Family
A, C, E	IPR015962	Mu1 membrane penetration protein, domain II	Homologous Superfamily
A, C, E	IPR044937	Mu1 membrane penetration protein, domain III	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
G, H, I	ACE	RESID: AA0041 , AA0042 , AA0043 , AA0044 , AA0045 , AA0046 , AA0049 , AA0050 , AA0051 , AA0052 , AA0053 , AA0054 , AA0354 PSI-MOD : N-acetyl-L-alanine MOD:00050 , N-acetyl-L-aspartic acid MOD:00051 , N-acetyl-L-cysteine MOD:00052 , N-acetyl-S-archeol-cysteine MOD:00897 , N-acetyl-L-glutamic acid MOD:00053 , N-acetyl-L-glutamine MOD:00054 , N-acetylglycine MOD:00055 , N-acetyl-L-methionine MOD:00058 , N-acetyl-L-proline MOD:00059 , N-acetyl-L-serine MOD:00060 , N,O-diacetylated L-serine MOD:00648 , N-acetyl-L-threonine MOD:00061 , N-acetyl-L-tyrosine MOD:00062 , N-acetyl-L-valine MOD:00063 , N2-acetyl-L-arginine MOD:00359

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.