7KSE | pdb_00007kse

Crystal structure of Prototype Foamy Virus Protease-Reverse Transcriptase CSH mutant (selenomethionine-labeled)

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)
A	Spuma_A9PTase	e7kseA5	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Spuma_A9PTase	ECOD (1.6)
A	EUF08093	e7kseA4	A: alpha bundles	X: helical bundle domain in reverse transcriptase-like polymerases (From Topology)	H: helical bundle domain in reverse transcriptase-like polymerases (From Topology)	T: helical bundle domain in reverse transcriptase-like polymerases	F: EUF08093	ECOD (1.6)
A	RVT_1	e7kseA1	A: a+b two layers	X: Alpha-beta plaits	H: Adenylyl and guanylyl cyclase catalytic domain-like	T: Adenylyl and guanylyl cyclase catalytic domain-like	F: RVT_1	ECOD (1.6)
A	RNase_H	e7kseA2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: RNase_H	ECOD (1.6)
A	RNase_HI_RT_Ty3	e7kseA3	A: mixed a+b and a/b	X: Ribonuclease H-like	H: RNaseH-like domain in reverse transcriptase (From Topology)	T: RNaseH-like domain in reverse transcriptase	F: RNase_HI_RT_Ty3	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.40.70.10	Mainly Beta	Beta Barrel	Cathepsin D, subunit A	domain 1	CATH (utative)
A	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF03539	Spumavirus aspartic protease (A9) (Spuma_A9PTase)	Spumavirus aspartic protease (A9)	-	Family
A	PF17919	RNase H-like domain found in reverse transcriptase (RT_RNaseH_2)	RNase H-like domain found in reverse transcriptase		Domain
A	PF00075	RNase H (RNase_H)	RNase H	RNase H digests the RNA strand of an RNA/DNA hybrid. Important enzyme in retroviral replication cycle, and often found as a domain associated with reverse transcriptases. Structure is a mixed alpha+beta fold with three a/b/a layers.	Domain
A	PF00078	Reverse transcriptase (RNA-dependent DNA polymerase) (RVT_1)	Reverse transcriptase (RNA-dependent DNA polymerase)	A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs ...	A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	Peptidase A9/Reverse transcriptase/RNase H	RNA binding binding nucleic acid binding catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein RNA binding binding nucleic acid binding catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein hydrolase activity aspartic-type endopeptidase activity endopeptidase activity endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism catalytic activity, acting on RNA RNA-DNA hybrid ribonuclease activity RNA nuclease activity hydrolase activity, acting on ester bonds nuclease activity RNA endonuclease activity RNA-directed DNA polymerase activity cation binding ion binding metal ion binding small molecule binding	biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction establishment of integrated proviral latency viral latency establishment of viral latency viral genome integration into host DNA nucleobase-containing compound metabolic process DNA recombination metabolic process biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction establishment of integrated proviral latency viral latency establishment of viral latency viral genome integration into host DNA nucleobase-containing compound metabolic process DNA recombination metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process viral penetration into host nucleus intracellular transport of virus transport of virus DNA integration proteolysis protein metabolic process	host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host intracellular region other organism part host cell host intracellular membrane-bounded organelle host cell nucleus host intracellular organelle virion component

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A	IPR041588	Integrase zinc-binding domain	Domain
A	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A	IPR001641	Spumavirus aspartic protease A9	Domain
A	IPR040903	Retroviral integrase, C-terminal SH3 domain	Domain
A	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
A	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A	IPR050951	Retrovirus-related Pol polyprotein	Family
A	IPR002156	Ribonuclease H domain	Domain
A	IPR001584	Integrase, catalytic core	Domain
A	IPR041577	Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain	Domain
A	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A	IPR000477	Reverse transcriptase domain	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.