Annotations: 6U8Q

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	N-terminal Zn binding domain of HIV integrase-like	8037847	3001203	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease H-like	8044526	3000143	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribonuclease H-like	8044526	3000143	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	N-terminal Zn binding domain of HIV integrase-like	8037847	3001203	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	N-terminal Zn binding domain of HIV integrase-like	8037847	3001203	SCOP2B (2022-06-29)
E [auth C]	SCOP2B Superfamily	Ribonuclease H-like	8044526	3000143	SCOP2B (2022-06-29)
F [auth D]	SCOP2B Superfamily	N-terminal Zn binding domain of HIV integrase-like	8037847	3001203	SCOP2B (2022-06-29)
F [auth D]	SCOP2B Superfamily	Ribonuclease H-like	8044526	3000143	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Ribonuclease H-like	8044526	3000143	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Ribonuclease H-like	8044526	3000143	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Ribonuclease H-like	8044526	3000143	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Ribonuclease H-like	8044526	3000143	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Ribonuclease H-like	8044526	3000143	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Ribonuclease H-like	8044526	3000143	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Ribonuclease H-like	8044526	3000143	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	Ribonuclease H-like	8044526	3000143	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)
A	PF00552	e6u8qA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF00552	ECOD (1.6)
A	PF02022	e6u8qA3	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF02022	ECOD (1.6)
A	PF00665	e6u8qA2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF00665	ECOD (1.6)
B	PF00552	e6u8qB3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF00552	ECOD (1.6)
B	PF02022	e6u8qB2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF02022	ECOD (1.6)
B	PF00665	e6u8qB1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF00665	ECOD (1.6)
E [auth C]	PF00552	e6u8qC1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF00552	ECOD (1.6)
E [auth C]	PF02022	e6u8qC2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF02022	ECOD (1.6)
E [auth C]	PF00665	e6u8qC3	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF00665	ECOD (1.6)
F [auth D]	PF00552	e6u8qD2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF00552	ECOD (1.6)
F [auth D]	PF02022	e6u8qD3	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: PF02022	ECOD (1.6)
F [auth D]	PF00665	e6u8qD1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF00665	ECOD (1.6)
I	PF00552	e6u8qI1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF00552	ECOD (1.6)
I	PF00665	e6u8qI2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF00665	ECOD (1.6)
J	PF00552	e6u8qJ1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF00552	ECOD (1.6)
J	PF00665	e6u8qJ2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF00665	ECOD (1.6)
K	PF00665	e6u8qK1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF00665	ECOD (1.6)
L	PF00665	e6u8qL1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF00665	ECOD (1.6)
M	PF00552	e6u8qM2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF00552	ECOD (1.6)
M	PF00665	e6u8qM1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF00665	ECOD (1.6)
N	PF00665	e6u8qN1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF00665	ECOD (1.6)
O	PF00665	e6u8qO1	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF00665	ECOD (1.6)
P	PF00552	e6u8qP1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: PF00552	ECOD (1.6)
P	PF00665	e6u8qP2	A: mixed a+b and a/b	X: Ribonuclease H-like	H: Ribonuclease H-like (From Topology)	T: Ribonuclease H-like	F: PF00665	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, K, L, M, N, O, P	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, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, K, L, M, N, O, P	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 do ...	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, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, K, L, M, N, O, P	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, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, K, L, M, N, O, P	Integrase	catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid RNA exonuclease activity RNA nuclease activity hydrolase activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds exoribonuclease H activity exonuclease activity catalytic activity catalytic activity, acting on DNA DNA-directed DNA polymerase activity catalytic activity, acting on RNA RNA exonuclease activity, producing 5'-phosphomonoesters catalytic activity, acting on a nucleic acid RNA exonuclease activity RNA nuclease activity hydrolase activity exonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters nuclease activity hydrolase activity, acting on ester bonds exoribonuclease H activity exonuclease activity catalytic activity catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups DNA binding binding organic cyclic compound binding nucleic acid binding RNA-directed DNA polymerase activity RNA binding aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein aspartic-type endopeptidase activity endopeptidase activity lipid binding endonuclease activity RNA endonuclease activity, producing 5'-phosphomonoesters RNA-DNA hybrid ribonuclease activity RNA endonuclease activity endonuclease activity, active with either ribo- or deoxyribonucleic acids and producing 5'-phosphomonoesters structural molecule activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	viral genome integration into host DNA viral process viral life cycle viral penetration into host nucleus intracellular transport of virus transport of virus biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host biological process involved in interaction with host biological process involved in symbiotic interaction nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process viral genome integration into host DNA viral process viral life cycle viral penetration into host nucleus intracellular transport of virus transport of virus biological process involved in interspecies interaction between organisms symbiont entry into host cell symbiont entry into host biological process involved in interaction with host biological process involved in symbiotic interaction nucleobase-containing compound metabolic process organic cyclic compound metabolic process organic substance metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process DNA integration nucleic acid metabolic process establishment of integrated proviral latency viral latency establishment of viral latency DNA recombination symbiont-mediated perturbation of host cellular process symbiont-mediated suppression of host gene expression modulation by symbiont of host process symbiont-mediated perturbation of host gene expression cellular process modulation of process of another organism organonitrogen compound metabolic process proteolysis protein metabolic process	membrane cellular anatomical entity host intracellular membrane-bounded organelle host cellular component host intracellular part host multivesicular body host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part host cell late endosome host cell endosome host intracellular region viral nucleocapsid membrane cellular anatomical entity host intracellular membrane-bounded organelle host cellular component host intracellular part host multivesicular body host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell part host cell late endosome host cell endosome host intracellular region viral nucleocapsid viral capsid virion component host cell plasma membrane host cell membrane virion membrane host cell nucleus
C [auth E], G	DNA (27-MER)	-	-	-
D [auth F], H	DNA (25-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, K, L, M, N, O, P	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, K, L, M, N, O, P	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, K, L, M, N, O, P	IPR001995	Peptidase A2A, retrovirus, catalytic	Domain
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, K, L, M, N, O, P	IPR001878	Zinc finger, CCHC-type	Domain
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, K, L, M, N, O, P	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, K, L, M, N, O, P	IPR012344	Matrix protein, lentiviral and alpha-retroviral, N-terminal	Homologous Superfamily
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, K, L, M, N, O, P	IPR036862	Integrase, C-terminal domain superfamily, retroviral	Homologous Superfamily
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, K, L, M, N, O, P	IPR018061	Retropepsins	Domain
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, K, L, M, N, O, P	IPR010661	Reverse transcriptase thumb	Domain
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, K, L, M, N, O, P	IPR002156	Ribonuclease H domain	Domain
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, K, L, M, N, O, P	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, K, L, M, N, O, P	IPR003308	Integrase, N-terminal zinc-binding domain	Domain
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, K, L, M, N, O, P	IPR001584	Integrase, catalytic core	Domain
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, K, L, M, N, O, P	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, K, L, M, N, O, P	IPR010999	Retroviral matrix protein	Homologous Superfamily
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, K, L, M, N, O, P	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, K, L, M, N, O, P	IPR001969	Aspartic peptidase, active site	Active Site
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, K, L, M, N, O, P	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, K, L, M, N, O, P	IPR017856	Integrase-like, N-terminal	Homologous Superfamily
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, K, L, M, N, O, P	IPR000071	Immunodeficiency lentiviral matrix, N-terminal	Domain
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, K, L, M, N, O, P	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, K, L, M, N, O, P	IPR001037	Integrase, C-terminal, retroviral	Domain
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, K, L, M, N, O, P	IPR034170	Retropepsin-like catalytic domain	Domain
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, K, L, M, N, O, P	IPR000477	Reverse transcriptase domain	Domain
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, K, L, M, N, O, P	IPR010659	Reverse transcriptase connection	Domain
A, B, E [auth C], F [auth D], I, A, B, E [auth C], F [auth D], I, J, K, L, M, N, O, P	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily

6U8Q

CryoEM structure of HIV-1 cleaved synaptic complex (CSC) intasome

External Resource: Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Domain Annotation: ECOD Classification ECOD Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

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6U8Q

CryoEM structure of HIV-1 cleaved synaptic complex (CSC) intasome

External Resource: Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Domain Annotation: ECOD Classification ECOD Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage