5TC1 | pdb_00005tc1

In situ structures of the genome and genome-delivery apparatus in ssRNA bacteriophage MS2

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	RNA bacteriophage capsid protein	8038606	3001853	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	RNA bacteriophage capsid protein	8038606	3001853	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	RNA bacteriophage capsid protein	8038606	3001853	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	RNA bacteriophage capsid protein	8038606	3001853	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	RNA bacteriophage capsid protein	8038606	3001853	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	RNA bacteriophage capsid protein	8038606	3001853	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	RNA bacteriophage capsid protein	8038606	3001853	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	RNA bacteriophage capsid protein	8038606	3001853	SCOP2B (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 [auth M]	Phage_mat-A	e5tc1M1	A: a+b complex topology	X: ssRNA bacteriophage MS2 maturation protein (From Topology)	H: ssRNA bacteriophage MS2 maturation protein (From Topology)	T: ssRNA bacteriophage MS2 maturation protein	F: Phage_mat-A	ECOD (1.6)
A	Levi_coat	e5tc1A1	A: a+b two layers	X: RNA bacteriophage capsid protein (From Topology)	H: RNA bacteriophage capsid protein (From Topology)	T: RNA bacteriophage capsid protein	F: Levi_coat	ECOD (1.6)
C	Levi_coat	e5tc1C1	A: a+b two layers	X: RNA bacteriophage capsid protein (From Topology)	H: RNA bacteriophage capsid protein (From Topology)	T: RNA bacteriophage capsid protein	F: Levi_coat	ECOD (1.6)
F	Levi_coat	e5tc1F1	A: a+b two layers	X: RNA bacteriophage capsid protein (From Topology)	H: RNA bacteriophage capsid protein (From Topology)	T: RNA bacteriophage capsid protein	F: Levi_coat	ECOD (1.6)
H	Levi_coat	e5tc1H1	A: a+b two layers	X: RNA bacteriophage capsid protein (From Topology)	H: RNA bacteriophage capsid protein (From Topology)	T: RNA bacteriophage capsid protein	F: Levi_coat	ECOD (1.6)
G	Levi_coat	e5tc1G1	A: a+b two layers	X: RNA bacteriophage capsid protein (From Topology)	H: RNA bacteriophage capsid protein (From Topology)	T: RNA bacteriophage capsid protein	F: Levi_coat	ECOD (1.6)
E	Levi_coat	e5tc1E1	A: a+b two layers	X: RNA bacteriophage capsid protein (From Topology)	H: RNA bacteriophage capsid protein (From Topology)	T: RNA bacteriophage capsid protein	F: Levi_coat	ECOD (1.6)
D	Levi_coat	e5tc1D1	A: a+b two layers	X: RNA bacteriophage capsid protein (From Topology)	H: RNA bacteriophage capsid protein (From Topology)	T: RNA bacteriophage capsid protein	F: Levi_coat	ECOD (1.6)
B	Levi_coat	e5tc1B1	A: a+b two layers	X: RNA bacteriophage capsid protein (From Topology)	H: RNA bacteriophage capsid protein (From Topology)	T: RNA bacteriophage capsid protein	F: Levi_coat	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.30.380.10	Alpha Beta	2-Layer Sandwich	MS2 Viral Coat Protein	MS2 Viral Coat Protein	CATH (4.3.0)
C	3.30.380.10	Alpha Beta	2-Layer Sandwich	MS2 Viral Coat Protein	MS2 Viral Coat Protein	CATH (4.3.0)
F	3.30.380.10	Alpha Beta	2-Layer Sandwich	MS2 Viral Coat Protein	MS2 Viral Coat Protein	CATH (4.3.0)
H	3.30.380.10	Alpha Beta	2-Layer Sandwich	MS2 Viral Coat Protein	MS2 Viral Coat Protein	CATH (4.3.0)
G	3.30.380.10	Alpha Beta	2-Layer Sandwich	MS2 Viral Coat Protein	MS2 Viral Coat Protein	CATH (4.3.0)
E	3.30.380.10	Alpha Beta	2-Layer Sandwich	MS2 Viral Coat Protein	MS2 Viral Coat Protein	CATH (4.3.0)
D	3.30.380.10	Alpha Beta	2-Layer Sandwich	MS2 Viral Coat Protein	MS2 Viral Coat Protein	CATH (4.3.0)
B	3.30.380.10	Alpha Beta	2-Layer Sandwich	MS2 Viral Coat Protein	MS2 Viral Coat Protein	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
I [auth M]	PF03863	Phage maturation protein (Phage_mat-A)	Phage maturation protein	-	Family
A, B, C, D, E A, B, C, D, E, F, G, H	PF01819	Levivirus coat protein (Levi_coat)	Levivirus coat protein	The Levivirus coat protein forms the bacteriophage coat that encapsidates the viral RNA. 180 copies of this protein form the virion shell. The MS2 bacteriophage coat protein controls two distinct processes: sequence-specific RNA encapsidation and re ...	The Levivirus coat protein forms the bacteriophage coat that encapsidates the viral RNA. 180 copies of this protein form the virion shell. The MS2 bacteriophage coat protein controls two distinct processes: sequence-specific RNA encapsidation and repression of replicase translation-by binding to an RNA stem-loop structure of 19 nucleotides containing the initiation codon of the replicase gene. The binding of a coat protein dimer to this hairpin shuts off synthesis of the viral replicase, switching the viral replication cycle to virion assembly rather than continued replication [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
J [auth R]	phage MS2 genome	-	-	-
I [auth M]	Maturation protein	RNA binding binding nucleic acid binding	viral process viral genome circularization virion attachment to host cell biological process involved in interspecies interaction between organisms adhesion of symbiont to host cell viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction virion attachment to host cell pilus symbiont entry into host cell symbiont entry into host	virion component
A, B, C, D, E A, B, C, D, E, F, G, H	Capsid protein	structural molecule activity RNA binding binding nucleic acid binding identical protein binding protein binding	viral gene expression regulation of viral translation regulation of biological process regulation of viral process negative regulation of viral process negative regulation of viral translation viral process biological regulation negative regulation of biological process viral translation regulation of biosynthetic process regulation of cellular process regulation of protein metabolic process primary metabolic process viral gene expression regulation of viral translation regulation of biological process regulation of viral process negative regulation of viral process negative regulation of viral translation viral process biological regulation negative regulation of biological process viral translation regulation of biosynthetic process regulation of cellular process regulation of protein metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process protein biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of gene expression biosynthetic process regulation of translation regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process protein metabolic process regulation of metabolic process	viral capsid T=3 icosahedral viral capsid icosahedral viral capsid virion component

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
I [auth M]	IPR005563	Assembly protein	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR002703	Levivirus coat protein	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR015954	Bacteriophage RNA-type, capsid	Homologous Superfamily

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.