8S41 | pdb_00008s41

The structure of the copia retrotransposon icosahedral capsid (T=9)

External Resource: Annotation

Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B [auth F], C [auth G], D [auth L], E [auth Q], A, B [auth F], C [auth G], D [auth L], E [auth Q], F [auth V], G [auth X], H [auth a], I [auth d]	PF14223	gag-polypeptide of LTR copia-type (Retrotran_gag_2)	gag-polypeptide of LTR copia-type	This domain is found in Plants and fungi, including LTR-polyproteins, or retrotransposons of the copia-type.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B [auth F], C [auth G], D [auth L], E [auth Q], A, B [auth F], C [auth G], D [auth L], E [auth Q], F [auth V], G [auth X], H [auth a], I [auth d]	Copia VLP protein	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity aspartic-type endopeptidase activity catalytic activity endopeptidase activity nucleic acid binding cation binding transition metal ion binding zinc ion binding metal ion binding	primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process DNA biosynthetic process DNA integration proteolysis primary metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process metabolic process cellular process macromolecule metabolic process DNA biosynthetic process DNA integration proteolysis protein metabolic process	transferase complex, transferring phosphorus-containing groups protein-containing complex catalytic complex transferase complex DNA polymerase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B [auth F], C [auth G], D [auth L], E [auth Q], A, B [auth F], C [auth G], D [auth L], E [auth Q], F [auth V], G [auth X], H [auth a], I [auth d]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, B [auth F], C [auth G], D [auth L], E [auth Q], A, B [auth F], C [auth G], D [auth L], E [auth Q], F [auth V], G [auth X], H [auth a], I [auth d]	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
A, B [auth F], C [auth G], D [auth L], E [auth Q], A, B [auth F], C [auth G], D [auth L], E [auth Q], F [auth V], G [auth X], H [auth a], I [auth d]	IPR001584	Integrase, catalytic core	Domain
A, B [auth F], C [auth G], D [auth L], E [auth Q], A, B [auth F], C [auth G], D [auth L], E [auth Q], F [auth V], G [auth X], H [auth a], I [auth d]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B [auth F], C [auth G], D [auth L], E [auth Q], A, B [auth F], C [auth G], D [auth L], E [auth Q], F [auth V], G [auth X], H [auth a], I [auth d]	IPR039537	Retrotransposon Ty1/copia-like	Family
A, B [auth F], C [auth G], D [auth L], E [auth Q], A, B [auth F], C [auth G], D [auth L], E [auth Q], F [auth V], G [auth X], H [auth a], I [auth d]	IPR001878	Zinc finger, CCHC-type	Domain
A, B [auth F], C [auth G], D [auth L], E [auth Q], A, B [auth F], C [auth G], D [auth L], E [auth Q], F [auth V], G [auth X], H [auth a], I [auth d]	IPR054722	Retrovirus-related Pol polyprotein from transposon TNT 1-94-like, beta-barrel domain	Domain
A, B [auth F], C [auth G], D [auth L], E [auth Q], A, B [auth F], C [auth G], D [auth L], E [auth Q], F [auth V], G [auth X], H [auth a], I [auth d]	IPR025724	GAG-pre-integrase domain	Domain
A, B [auth F], C [auth G], D [auth L], E [auth Q], A, B [auth F], C [auth G], D [auth L], E [auth Q], F [auth V], G [auth X], H [auth a], I [auth d]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, B [auth F], C [auth G], D [auth L], E [auth Q], A, B [auth F], C [auth G], D [auth L], E [auth Q], F [auth V], G [auth X], H [auth a], I [auth d]	IPR013103	Reverse transcriptase, RNA-dependent DNA polymerase	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.