4JMR | pdb_00004jmr

A unique spumavirus gag N-terminal domain with functional properties of orthoretroviral Matrix and Capsid

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
D	Gag_spuma_1st	e4jmrD1	A: a+b two layers	X: N-terminal domain of spumavirus gag protein (From Topology)	H: N-terminal domain of spumavirus gag protein (From Topology)	T: N-terminal domain of spumavirus gag protein	F: Gag_spuma_1st	ECOD (1.6)
C	Gag_spuma_1st	e4jmrC1	A: a+b two layers	X: N-terminal domain of spumavirus gag protein (From Topology)	H: N-terminal domain of spumavirus gag protein (From Topology)	T: N-terminal domain of spumavirus gag protein	F: Gag_spuma_1st	ECOD (1.6)
B	Gag_spuma_1st	e4jmrB1	A: a+b two layers	X: N-terminal domain of spumavirus gag protein (From Topology)	H: N-terminal domain of spumavirus gag protein (From Topology)	T: N-terminal domain of spumavirus gag protein	F: Gag_spuma_1st	ECOD (1.6)
A	Gag_spuma_1st	e4jmrA1	A: a+b two layers	X: N-terminal domain of spumavirus gag protein (From Topology)	H: N-terminal domain of spumavirus gag protein (From Topology)	T: N-terminal domain of spumavirus gag protein	F: Gag_spuma_1st	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	1.20.5.1500	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
C	1.20.5.1500	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
B	1.20.5.1500	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
A	1.20.5.1500	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF03276	Spumavirus gag protein, N-terminal (Gag_spuma_N)	Spumavirus gag protein, N-terminal	This is the conserved N-terminal 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 region corresponds to the En ...	This is the conserved N-terminal 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 region corresponds to the Env-binding domain containing the cytoplasmic targeting and retention sequence (CTRS) [1,2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth F], F [auth E], G, H	Env protein	-	-	host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum host cell membrane other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host cell endomembrane system host intracellular region host cell endoplasmic reticulum membrane host intracellular membrane-bounded organelle host cellular component host intracellular part host cell endoplasmic reticulum host cell membrane other organism part host cell cytoplasm part host intracellular organelle cellular anatomical structure host cell cytoplasm host cell part host cell endomembrane system host intracellular region host cell endoplasmic reticulum membrane virion component viral membrane viral envelope membrane virion membrane
A, B, C, D	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
E [auth F], F [auth E], G, H	IPR005070	Foamy virus envelope protein	Family
A, B, C, D	IPR004957	Gag polyprotein, N-terminal domain	Domain
A, B, C, D	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.