5EJK | pdb_00005ejk

Crystal structure of the Rous sarcoma virus intasome

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
H	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8041682	3000355	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8041682	3000355	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8041682	3000355	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8041682	3000355	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8041682	3000355	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8041682	3000355	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8041682	3000355	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8041682	3000355	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
H	IN_DBD_C	e5ejkH1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
H	Integrase_Zn	e5ejkH3	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
H	rve	e5ejkH2	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)
G	IN_DBD_C	e5ejkG1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
G	Integrase_Zn	e5ejkG3	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
G	rve	e5ejkG2	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)
F	IN_DBD_C	e5ejkF2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
F	Integrase_Zn	e5ejkF4	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
F	rve	e5ejkF3	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)
E	IN_DBD_C	e5ejkE1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
E	Integrase_Zn	e5ejkE3	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
E	rve	e5ejkE2	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)
D	IN_DBD_C	e5ejkD2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
D	Integrase_Zn	e5ejkD4	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
D	rve	e5ejkD3	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)
C	IN_DBD_C	e5ejkC2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
C	Integrase_Zn	e5ejkC4	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
C	rve	e5ejkC3	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)
B	IN_DBD_C	e5ejkB2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
B	Integrase_Zn	e5ejkB4	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
B	rve	e5ejkB3	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	IN_DBD_C	e5ejkA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
A	Integrase_Zn	e5ejkA3	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
A	rve	e5ejkA2	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)
H	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)
H	2.30.30.10	Mainly Beta	Roll	SH3 type barrels.	Integrase, C-terminal domain superfamily, retroviral	CATH (utative)
G	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)
G	2.30.30.10	Mainly Beta	Roll	SH3 type barrels.	Integrase, C-terminal domain superfamily, retroviral	CATH (utative)
F	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)
F	2.30.30.10	Mainly Beta	Roll	SH3 type barrels.	Integrase, C-terminal domain superfamily, retroviral	CATH (utative)
E	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)
E	2.30.30.10	Mainly Beta	Roll	SH3 type barrels.	Integrase, C-terminal domain superfamily, retroviral	CATH (utative)
D	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)
D	2.30.30.10	Mainly Beta	Roll	SH3 type barrels.	Integrase, C-terminal domain superfamily, retroviral	CATH (utative)
C	2.30.30.10	Mainly Beta	Roll	SH3 type barrels.	Integrase, C-terminal domain superfamily, retroviral	CATH (utative)
B	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)
B	2.30.30.10	Mainly Beta	Roll	SH3 type barrels.	Integrase, C-terminal domain superfamily, retroviral	CATH (utative)
A	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (utative)
A	2.30.30.10	Mainly Beta	Roll	SH3 type barrels.	Integrase, C-terminal domain superfamily, retroviral	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF02022	Integrase Zinc binding domain (Integrase_Zn)	Integrase Zinc binding domain	Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain Pfam:PF00665 ...	Integrase mediates integration of a DNA copy of the viral genome into the host chromosome. Integrase is composed of three domains. This domain is the amino-terminal domain zinc binding domain. The central domain is the catalytic domain Pfam:PF00665. The carboxyl terminal domain is a DNA binding domain Pfam:PF00552.	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	PF00552	Integrase DNA binding domain (IN_DBD_C)	Integrase DNA binding 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. The central domain is the catalytic domain Pfam:PF00665. This dom ...	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. The central domain is the catalytic domain Pfam:PF00665. This domain is the carboxyl terminal domain that is a non-specific DNA binding domain [1].	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	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
O [auth k], P [auth n]	DNA (5'-D(APGPTPGPTPCPTPT)-3')	-	-	-
K, N	DNA (5'-D(CPTPTPCPTPCPTPC)-3')	-	-	-
J, M	DNA (5'-D(APAPTPGPTPTPGPTPCPTPTPAPTPGPCPAPAPTPAPCPTPC)-3')	-	-	-
I, L	RSV Integrase	-	-	-
A, B, C, D, E A, B, C, D, E, F, G, H	Gag-Pro-Pol polyprotein	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 DNA binding binding nucleic acid binding aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein 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 DNA binding binding nucleic acid binding 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 RNA binding RNA stem-loop binding cation binding transition metal ion binding zinc ion 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 gene expression viral translational frameshifting viral translation viral genome integration into host DNA 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 gene expression viral translational frameshifting viral translation 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 DNA integration proteolysis protein metabolic process	viral nucleocapsid viral capsid virion component

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001995	Peptidase A2A, retrovirus, catalytic	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001878	Zinc finger, CCHC-type	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR010999	Retroviral matrix protein	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR012344	Matrix protein, lentiviral and alpha-retroviral, N-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001969	Aspartic peptidase, active site	Active Site
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036862	Integrase, C-terminal domain superfamily, retroviral	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR018061	Retropepsins	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR017856	Integrase-like, N-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR010661	Reverse transcriptase thumb	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR004028	Retroviral Gag polyprotein, M	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR002156	Ribonuclease H domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR003308	Integrase, N-terminal zinc-binding domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001584	Integrase, catalytic core	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR001037	Integrase, C-terminal, retroviral	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR034170	Retropepsin-like catalytic domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR000477	Reverse transcriptase domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily