8WUT

SpCas9-MMLV RT-pegRNA-target DNA complex (initiation)

External Resource: Annotation

Domain Annotation: SCOP2 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)
A	SCOP2B Superfamily	Ribonuclease H-like	8092300	3000143	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cas9 REC domain-like	8045843	3002580	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease H-like	8092300	3000143	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease H-like	8092300	3000143	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	His-Me finger endonucleases	8048679	3001893	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cas9 PI domain-like	8092301	3002581	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cas9 BH domain-like	8045840	3002579	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF16592	REC lobe of CRISPR-associated endonuclease Cas9 (Cas9_REC)	REC lobe of CRISPR-associated endonuclease Cas9	-	Family
A	PF16593	Bridge helix of CRISPR-associated endonuclease Cas9 (Cas9-BH)	Bridge helix of CRISPR-associated endonuclease Cas9	-	Family
A	PF13395	HNH endonuclease (HNH_4)	HNH endonuclease	This HNH nuclease domain is found in CRISPR-related proteins.	Domain
A	PF16595	PAM-interacting domain of CRISPR-associated endonuclease Cas9 (Cas9_PI)	PAM-interacting domain of CRISPR-associated endonuclease Cas9	Cas9_PI is a family found at the C-terminal of bacterial type II CRISPR system Cas9 endonuclease. This domain adopts a novel protein fold that is unique to the Cas9 family. It is positioned in the structure-DNA-complex to recognise the PAM sequence o ...	Cas9_PI is a family found at the C-terminal of bacterial type II CRISPR system Cas9 endonuclease. This domain adopts a novel protein fold that is unique to the Cas9 family. It is positioned in the structure-DNA-complex to recognise the PAM sequence on the non-complementary DNA strand of the crRNA. PAM sequence is protospacer-adjacent motifs on DNA. See family CRISPR-DR2, Rfam:RF01315. Cas9 carries two nuclease domains, HNH and RuvC, which cleave the DNA strands that are complementary and non-complementary to the 20 nucleotide guide sequence in crRNAs, respectively [1].	Domain
A	PF22702	Cas9 RuvC domain (Cas9_RuvC)	Cas9 RuvC domain	This entry represent a RuvC endonuclease domain (RNAseH-like) domain found in CRISPR-Cas9 from Streptococcus pyogenes and related sequences [1-5]. This domain, and the HNH (Pfam:PF13395) domain of Cas9, are used to cleave the DNA strands complementar ...	This entry represent a RuvC endonuclease domain (RNAseH-like) domain found in CRISPR-Cas9 from Streptococcus pyogenes and related sequences [1-5]. This domain, and the HNH (Pfam:PF13395) domain of Cas9, are used to cleave the DNA strands complementary (target) and non-complementary (non-target) to the crRNA, respectively [5]. This domain is related to Pfam:PF18541.	Domain
B [auth E]	PF17919	RNase H-like domain found in reverse transcriptase (RT_RNaseH_2)	RNase H-like domain found in reverse transcriptase	-	Domain
B [auth E]	PF00078	Reverse transcriptase (RNA-dependent DNA polymerase) (RVT_1)	Reverse transcriptase (RNA-dependent DNA polymerase)	A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs ...	A reverse transcriptase gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. Reverse transcriptases occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	CRISPR-associated endonuclease Cas9/Csn1	DNA binding binding organic cyclic compound binding nucleic acid binding nuclease activity hydrolase activity, acting on ester bonds 3'-5' exonuclease activity hydrolase activity exonuclease activity catalytic activity DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid DNA binding binding organic cyclic compound binding nucleic acid binding nuclease activity hydrolase activity, acting on ester bonds 3'-5' exonuclease activity hydrolase activity exonuclease activity catalytic activity DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid DNA nuclease activity RNA binding cation binding ion binding metal ion binding small molecule binding	maintenance of CRISPR repeat elements chromosome organization primary metabolic process DNA metabolic process maintenance of DNA repeat elements nucleic acid metabolic process cellular component organization nucleobase-containing compound metabolic process organelle organization cellular process metabolic process cellular component organization or biogenesis macromolecule metabolic process biological process involved in interspecies interaction between organisms maintenance of CRISPR repeat elements chromosome organization primary metabolic process DNA metabolic process maintenance of DNA repeat elements nucleic acid metabolic process cellular component organization nucleobase-containing compound metabolic process organelle organization cellular process metabolic process cellular component organization or biogenesis macromolecule metabolic process biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response defense response to symbiont response to external stimulus response to biotic stimulus defense response to virus defense response to other organism response to stress response to external biotic stimulus response to virus	-
B [auth E]	Gag-Pol polyprotein	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 DNA binding aspartic-type 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 DNA 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 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 structural constituent of virion structural molecule activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	virion assembly viral process viral life cycle 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 establishment of integrated proviral latency viral latency establishment of viral latency viral genome integration into host DNA nucleobase-containing compound metabolic process DNA recombination virion assembly viral process viral life cycle 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 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 primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA integration proteolysis protein metabolic process	cell periphery plasma membrane membrane cellular anatomical entity host cell plasma membrane host cellular component host cell part host cell membrane host intracellular membrane-bounded organelle host intracellular part host multivesicular body host cell cytoplasm part host intracellular organelle host cell cytoplasm cell periphery plasma membrane membrane cellular anatomical entity host cell plasma membrane host cellular component host cell part host cell membrane host intracellular membrane-bounded organelle host intracellular part host multivesicular body host cell cytoplasm part host intracellular organelle host cell cytoplasm host cell late endosome host cell endosome host intracellular region host cell late endosome membrane host cell endosome membrane
C	DNA (51-MER)	-	-	-
D	DNA (5'-D(TPGPAPTPGPGPCPAPGPAPGPTPAPCPTPAP*G)-3')	-	-	-
E [auth B]	RNA (115-MER)	-	-	-
F	DNA/RNA (35-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A	IPR032240	CRISPR-associated endonuclease Cas9, REC lobe	Domain
A	IPR032239	CRISPR-associated endonuclease Cas9, bridge helix	Domain
A	IPR033114	Cas9-type HNH domain	Domain
A	IPR028629	CRISPR-associated endonuclease Cas9	Family
A	IPR003615	HNH nuclease	Domain
A	IPR032237	CRISPR-associated endonuclease Cas9, PAM-interacting domain	Domain
B [auth E]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
B [auth E]	IPR040643	Murine leukemia virus integrase, C-terminal	Domain
B [auth E]	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
B [auth E]	IPR001995	Peptidase A2A, retrovirus, catalytic	Domain
B [auth E]	IPR001878	Zinc finger, CCHC-type	Domain
B [auth E]	IPR008919	Retrovirus capsid, N-terminal	Homologous Superfamily
B [auth E]	IPR010999	Retroviral matrix protein	Homologous Superfamily
B [auth E]	IPR021109	Aspartic peptidase domain superfamily	Homologous Superfamily
B [auth E]	IPR002079	Gag polyprotein, inner coat protein p12	Domain
B [auth E]	IPR001969	Aspartic peptidase, active site	Active Site
B [auth E]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
B [auth E]	IPR018061	Retropepsins	Domain
B [auth E]	IPR050462	Retroviral Gag-Pol polyproteins	Family
B [auth E]	IPR002156	Ribonuclease H domain	Domain
B [auth E]	IPR036875	Zinc finger, CCHC-type superfamily	Homologous Superfamily
B [auth E]	IPR000840	Gamma-retroviral matrix protein	Domain
B [auth E]	IPR001584	Integrase, catalytic core	Domain
B [auth E]	IPR041577	Reverse transcriptase/retrotransposon-derived protein, RNase H-like domain	Domain
B [auth E]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
B [auth E]	IPR000477	Reverse transcriptase domain	Domain
B [auth E]	IPR036946	Gamma-retroviral matrix domain superfamily	Homologous Superfamily
B [auth E]	IPR039464	Gag-Pol polyprotein, Zinc-finger like domain	Domain
B [auth E]	IPR003036	Core shell protein Gag P30	Domain