3L2U

Crystal structure of the Prototype Foamy Virus (PFV) intasome in complex with magnesium and GS9137 (Elvitegravir)

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3l2ua1	All alpha proteins	DNA/RNA-binding 3-helical bundle	Retroviral integrase, N-terminal Zn binding domain	automated matches	automated matches	SFVcpz(hu) (Human spumaretrovirus ) [TaxId: 11963 ],	SCOPe (2.08)
A	d3l2ua3	All beta proteins	SH3-like barrel	DNA-binding domain of retroviral integrase	DNA-binding domain of retroviral integrase	DNA-binding domain of retroviral integrase	SFVcpz(hu) (Human spumaretrovirus ) [TaxId: 11963 ],	SCOPe (2.08)
A	d3l2ua2	Alpha and beta proteins (a/b)	Ribonuclease H-like motif	Ribonuclease H-like	Retroviral integrase, catalytic domain	Retroviral integrase, catalytic domain	SFVcpz(hu) (Human spumaretrovirus ) [TaxId: 11963 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	rve	e3l2uB1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: rve	ECOD (1.6)
A	EUF07571	e3l2uA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: EUF07571	ECOD (1.6)
A	zf-H2C2_like	e3l2uA2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: zf-H2C2_like	ECOD (1.6)
A	rve	e3l2uA3	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: rve	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	1.10.340.70	Mainly Alpha	Orthogonal Bundle	Endonuclease III	domain 1	CATH (4.3.0)
A	2.30.30.140	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
A	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	6.10.20.110	Special	Helix non-globular	Arc Repressor Mutant, subunit A		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF18103	Retroviral integrase C-terminal SH3 domain (SH3_11)	Retroviral integrase C-terminal SH3 domain	This is the carboxy-terminal domain (CTD) found in retroviral integrase, an essential retroviral enzyme that binds both termini of linear viral DNA and inserts them into a host cell chromosome. The CTD adopts an SH3-like fold. Each CTD makes contact ...	This is the carboxy-terminal domain (CTD) found in retroviral integrase, an essential retroviral enzyme that binds both termini of linear viral DNA and inserts them into a host cell chromosome. The CTD adopts an SH3-like fold. Each CTD makes contact with the phosphodiester backbone of both viral DNA molecules, essentially crosslinking the structure [1].	Domain
A, B	PF17921	Integrase zinc binding domain (Integrase_H2C2)	Integrase zinc binding domain	This zinc binding domain is found in a wide variety of integrase proteins.	Domain
A, B	PF00665	Integrase core domain (rve)	Integrase core domain	Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain Pfam:PF02022. This domain is the central catalytic domain. The ca ...	Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. The amino-terminal domain is a zinc binding domain Pfam:PF02022. This domain is the central catalytic domain. The carboxyl terminal domain that is a non-specific DNA binding domain Pfam:PF00552. The catalytic domain acts as an endonuclease when two nucleotides are removed from the 3' ends of the blunt-ended viral DNA made by reverse transcription. This domain also catalyses the DNA strand transfer reaction of the 3' ends of the viral DNA to the 5' ends of the integration site [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Integrase	RNA binding binding organic cyclic compound 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 RNA binding binding organic cyclic compound 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 catalytic activity, acting on RNA RNA-DNA hybrid ribonuclease activity RNA nuclease activity nuclease activity hydrolase activity, acting on ester bonds RNA endonuclease activity endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters 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 host cell host intracellular membrane-bounded organelle host cell nucleus host intracellular organelle virion component
C	5'-D(APTPTPGPTPCPAPTPGPGPAPAPTPTPTPTPGPTP*A)-3'	-	-	-
D	5'-D(TPAPCPAPAPAPAPTPTPCPCPAPTPGPAPCP*A)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

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