5M0R | pdb_00005m0r

Cryo-EM reconstruction of the maedi-visna virus (MVV) strand transfer complex

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
P	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8072259	3000355	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8072259	3000355	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8072259	3000355	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8072259	3000355	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8072259	3000355	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8072259	3000355	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8072259	3000355	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8072259	3000355	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8072259	3000355	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8072259	3000355	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8072259	3000355	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8072259	3000355	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8072259	3000355	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	DNA-binding domain of retroviral integrase	8072259	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)
P	IN_DBD_C	e5m0rP2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
P	rve	e5m0rP1	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)
O	Integrase_Zn	e5m0rO2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
O	rve	e5m0rO1	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)
N	IN_DBD_C	e5m0rN1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
N	Integrase_Zn	e5m0rN3	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
N	rve	e5m0rN2	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)
M	IN_DBD_C	e5m0rM3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
M	Integrase_Zn	e5m0rM2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
M	rve	e5m0rM1	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)
L	IN_DBD_C	e5m0rL2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
L	rve	e5m0rL1	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)
K	IN_DBD_C	e5m0rK3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
K	Integrase_Zn	e5m0rK2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
K	rve	e5m0rK1	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)
J	IN_DBD_C	e5m0rJ3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
J	Integrase_Zn	e5m0rJ1	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
J	rve	e5m0rJ2	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)
I	IN_DBD_C	e5m0rI3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
I	Integrase_Zn	e5m0rI2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
I	rve	e5m0rI1	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)
H	IN_DBD_C	e5m0rH2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
H	rve	e5m0rH1	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	Integrase_Zn	e5m0rG2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
G	rve	e5m0rG1	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	e5m0rF1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
F	Integrase_Zn	e5m0rF2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
F	rve	e5m0rF3	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	e5m0rE3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
E	Integrase_Zn	e5m0rE2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
E	rve	e5m0rE1	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	e5m0rD2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
D	rve	e5m0rD1	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	e5m0rC3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
C	Integrase_Zn	e5m0rC2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
C	rve	e5m0rC1	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	e5m0rB2	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
B	Integrase_Zn	e5m0rB3	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
B	rve	e5m0rB1	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	e5m0rA3	A: beta barrels	X: SH3	H: SH3	T: SH3	F: IN_DBD_C	ECOD (1.6)
A	Integrase_Zn	e5m0rA2	A: alpha arrays	X: HTH	H: HTH	T: tri-helical	F: Integrase_Zn	ECOD (1.6)
A	rve	e5m0rA1	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)

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, 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, C, D, E A, B, C, D, E, F, G, H, 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
S [auth U], V	tDNA	-	-	-
R, U [auth T]	vDNA-tDNA, transferred strand, joined to a model tDNA	-	-	-
Q, T [auth S]	vDNA, non-transfered strand	-	-	-
A, B, C, D, E A, B, C, D, E, F, G, H, 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 hydrolase activity, acting on ester bonds nuclease activity exoribonuclease H activity exonuclease activity catalytic activity catalytic activity, acting on DNA DNA-directed DNA polymerase activity 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 hydrolase activity, acting on ester bonds nuclease activity 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 nucleic acid binding aspartic-type peptidase activity peptidase activity catalytic activity, acting on a protein aspartic-type endopeptidase activity endopeptidase activity endonuclease activity RNA endonuclease activity producing 5'-phosphomonoesters, hydrolytic mechanism RNA-DNA hybrid ribonuclease activity RNA endonuclease activity RNA-directed DNA polymerase activity RNA binding RNA stem-loop binding pyrophosphatase activity nucleoside triphosphate diphosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides dUTP diphosphatase activity hydrolase activity, acting on acid anhydrides 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 nucleoside phosphate metabolic process nucleotide metabolic process organophosphate metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process DNA integration proteolysis protein metabolic process	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, I, J, K, L, M, N, O, P	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR045345	Retroviral nucleocapsid Gag protein p24, C-terminal domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR036157	dUTPase-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR001995	Peptidase A2A, retrovirus, catalytic	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR001878	Zinc finger, CCHC-type	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR001969	Aspartic peptidase, active site	Active Site
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR029054	dUTPase-like	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR036862	Integrase, C-terminal domain superfamily, retroviral	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR018061	Retropepsins	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR017856	Integrase-like, N-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR002156	Ribonuclease H domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR003308	Integrase, N-terminal zinc-binding domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR001584	Integrase, catalytic core	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR033704	dUTPase, trimeric	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR001037	Integrase, C-terminal, retroviral	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR000477	Reverse transcriptase domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P	IPR008916	Retrovirus capsid, C-terminal	Homologous Superfamily