9RMU | pdb_00009rmu

SIVtal integrase in complex with RNA stem-loop (focused refinement of the filament repeat unit)

External Resource: Annotation

Domain Annotation: ECOD Classification
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)
L [auth f]		e9rmuf1	A: ATPD N-terminal domain-like	X: N-terminal domain of the delta subunit of the F1F0-ATP synthase	H: Galactose-binding domain-like	T: Med26	F:	ECOD (20:10:01)
J [auth H]		e9rmuH1	A: ATPD N-terminal domain-like	X: N-terminal domain of the delta subunit of the F1F0-ATP synthase	H: N-terminal domain of the delta subunit of the F1F0-ATP synthase	T: IBR	F:	ECOD (20:10:01)
I [auth G]		e9rmuG1	A: ATPD N-terminal domain-like	X: N-terminal domain of the delta subunit of the F1F0-ATP synthase	H: N-terminal domain of the delta subunit of the F1F0-ATP synthase	T: IBR	F:	ECOD (20:10:01)
H [auth F]		e9rmuF1	A: ATPD N-terminal domain-like	X: N-terminal domain of the delta subunit of the F1F0-ATP synthase	H: N-terminal domain of the delta subunit of the F1F0-ATP synthase	T: IBR	F:	ECOD (20:10:01)
G [auth E]		e9rmuE1	A: ATPD N-terminal domain-like	X: N-terminal domain of the delta subunit of the F1F0-ATP synthase	H: N-terminal domain of the delta subunit of the F1F0-ATP synthase	T: IBR	F:	ECOD (20:10:01)
F [auth b]		e9rmub1	A: ATPD N-terminal domain-like	X: N-terminal domain of the delta subunit of the F1F0-ATP synthase	H: N-terminal domain of the delta subunit of the F1F0-ATP synthase	T: IBR	F:	ECOD (20:10:01)
D		e9rmuD1	A: ATPD N-terminal domain-like	X: N-terminal domain of the delta subunit of the F1F0-ATP synthase	H: N-terminal domain of the delta subunit of the F1F0-ATP synthase	T: IBR	F:	ECOD (20:10:01)
C		e9rmuC1	A: ATPD N-terminal domain-like	X: N-terminal domain of the delta subunit of the F1F0-ATP synthase	H: Galactose-binding domain-like	T: Med26	F:	ECOD (20:10:01)
B		e9rmuB1	A: ATPD N-terminal domain-like	X: N-terminal domain of the delta subunit of the F1F0-ATP synthase	H: N-terminal domain of the delta subunit of the F1F0-ATP synthase	T: IBR	F:	ECOD (20:10:01)
A		e9rmuA1	A: ATPD N-terminal domain-like	X: N-terminal domain of the delta subunit of the F1F0-ATP synthase	H: N-terminal domain of the delta subunit of the F1F0-ATP synthase	T: IBR	F:	ECOD (20:10:01)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth J], K [auth I], M [auth j], N [auth i]	RNA	-	-	-
A, B, C, D, F [auth b], A, B, C, D, F [auth b], G [auth E], H [auth F], I [auth G], J [auth H], L [auth f]	Pol protein	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 DNA binding binding nucleic acid binding 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 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 catalytic activity, acting on DNA DNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups 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 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 DNA integration proteolysis protein metabolic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, F [auth b], A, B, C, D, F [auth b], G [auth E], H [auth F], I [auth G], J [auth H], L [auth f]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, B, C, D, F [auth b], A, B, C, D, F [auth b], G [auth E], H [auth F], I [auth G], J [auth H], L [auth f]	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A, B, C, D, F [auth b], A, B, C, D, F [auth b], G [auth E], H [auth F], I [auth G], J [auth H], L [auth f]	IPR001995	Peptidase A2A, retrovirus, catalytic	Domain
A, B, C, D, F [auth b], A, B, C, D, F [auth b], G [auth E], H [auth F], I [auth G], J [auth H], L [auth f]	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
A, B, C, D, F [auth b], A, B, C, D, F [auth b], G [auth E], H [auth F], I [auth G], J [auth H], L [auth f]	IPR001969	Aspartic peptidase, active site	Active Site
A, B, C, D, F [auth b], A, B, C, D, F [auth b], G [auth E], H [auth F], I [auth G], J [auth H], L [auth f]	IPR036862	Integrase, C-terminal domain superfamily, retroviral	Homologous Superfamily
A, B, C, D, F [auth b], A, B, C, D, F [auth b], G [auth E], H [auth F], I [auth G], J [auth H], L [auth f]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, B, C, D, F [auth b], A, B, C, D, F [auth b], G [auth E], H [auth F], I [auth G], J [auth H], L [auth f]	IPR018061	Retropepsins	Domain
A, B, C, D, F [auth b], A, B, C, D, F [auth b], G [auth E], H [auth F], I [auth G], J [auth H], L [auth f]	IPR017856	Integrase-like, N-terminal	Homologous Superfamily
A, B, C, D, F [auth b], A, B, C, D, F [auth b], G [auth E], H [auth F], I [auth G], J [auth H], L [auth f]	IPR010661	Reverse transcriptase thumb	Domain
A, B, C, D, F [auth b], A, B, C, D, F [auth b], G [auth E], H [auth F], I [auth G], J [auth H], L [auth f]	IPR002156	Ribonuclease H domain	Domain
A, B, C, D, F [auth b], A, B, C, D, F [auth b], G [auth E], H [auth F], I [auth G], J [auth H], L [auth f]	IPR003308	Integrase, N-terminal zinc-binding domain	Domain
A, B, C, D, F [auth b], A, B, C, D, F [auth b], G [auth E], H [auth F], I [auth G], J [auth H], L [auth f]	IPR001584	Integrase, catalytic core	Domain
A, B, C, D, F [auth b], A, B, C, D, F [auth b], G [auth E], H [auth F], I [auth G], J [auth H], L [auth f]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, B, C, D, F [auth b], A, B, C, D, F [auth b], G [auth E], H [auth F], I [auth G], J [auth H], L [auth f]	IPR001037	Integrase, C-terminal, retroviral	Domain
A, B, C, D, F [auth b], A, B, C, D, F [auth b], G [auth E], H [auth F], I [auth G], J [auth H], L [auth f]	IPR000477	Reverse transcriptase domain	Domain
A, B, C, D, F [auth b], A, B, C, D, F [auth b], G [auth E], H [auth F], I [auth G], J [auth H], L [auth f]	IPR010659	Reverse transcriptase connection	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.