5M1H | pdb_00005m1h

Structure of a Spumaretrovirus Gag central domain reveals an ancient retroviral capsid

External Resource: Annotation

Domain Annotation: ECOD Classification
Protein Family Annotation
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)
A	Gag_spuma_3rd	e5m1hA2	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein-C (From Topology)	T: Retrovirus capsid protein-C	F: Gag_spuma_3rd	ECOD (1.6)
A	Gag_spuma_2nd	e5m1hA1	A: alpha bundles	X: Retrovirus capsid protein	H: Retrovirus capsid protein N-terminal domain (From Topology)	T: Retrovirus capsid protein N-terminal domain	F: Gag_spuma_2nd	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF20672	Spumavirus Gag polyprotein, conserved central domain (Gag_FV_central)	Spumavirus Gag polyprotein, conserved central domain	This is the conserved central domain of the Gag polyprotein from Foamyviruses (FVs) or Spuma-retroviruses. Gag is the major structural protein required for genome packaging virion assembly, trafficking and egress. This domain has an all alpha-helical ...	This is the conserved central domain of the Gag polyprotein from Foamyviruses (FVs) or Spuma-retroviruses. Gag is the major structural protein required for genome packaging virion assembly, trafficking and egress. This domain has an all alpha-helical fold and contains the highly conserved PGQA and YxxLGL sequences [1]. The Gag polyprotein is a core viral polyprotein that undergoes specific enzymatic cleavages in vivo to yield the mature protein. It is involved in capsid formation and genome binding. Shortly after infection, interaction between incoming particle-associated Gag proteins and host dynein allows centrosomal targeting of the viral genome (associated to Gag), prior to nucleus translocation and integration into host genome [2, 3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Gag protein	DNA binding binding nucleic acid binding RNA binding	exit from host cell biological process involved in interspecies interaction between organisms viral process viral release from host cell viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell symbiont entry into host microtubule-dependent intracellular transport of viral material microtubule-dependent intracellular transport of viral material towards nucleus intracellular transport of virus transport of virus transport of viral material towards nucleus exit from host cell biological process involved in interspecies interaction between organisms viral process viral release from host cell viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell symbiont entry into host microtubule-dependent intracellular transport of viral material microtubule-dependent intracellular transport of viral material towards nucleus intracellular transport of virus transport of virus transport of viral material towards nucleus virion assembly viral budding viral budding via host ESCRT complex	host cellular component host intracellular part host cytoskeleton cellular anatomical structure host cell part host intracellular region other organism part host intracellular organelle host cell host intracellular membrane-bounded organelle host cell nucleus viral nucleocapsid viral capsid virion component host cellular component host intracellular part host cytoskeleton cellular anatomical structure host cell part host intracellular region other organism part host intracellular organelle host cell host intracellular membrane-bounded organelle host cell nucleus viral nucleocapsid viral capsid virion component host cell cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR004957	Gag polyprotein, N-terminal domain	Domain
A	IPR049099	Gag polyprotein, C-terminal	Domain

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.