8FLJ

Cas1-Cas2/3 integrase and IHF bound to CRISPR leader, repeat and foreign DNA

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	CRISPR associated protein Cas1	8053181	3002164	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CRISPR associated protein Cas1	8053181	3002164	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	CRISPR associated protein Cas1	8053181	3002164	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	CRISPR associated protein Cas1	8053181	3002164	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF01867	CRISPR associated protein Cas1 (Cas_Cas1)	CRISPR associated protein Cas1	-	Family
E, G	PF00216	Bacterial DNA-binding protein (Bac_DNA_binding)	Bacterial DNA-binding protein		Domain
F, H	PF00216	Bacterial DNA-binding protein (Bac_DNA_binding)	Bacterial DNA-binding protein		Domain
M, N	PF21384	CRISPR-associated nuclease/helicase Cas3, I-F/YPEST, Cas2 domain (Cas3_I-F_Cas2)	CRISPR-associated nuclease/helicase Cas3, I-F/YPEST, Cas2 domain	This domain is found at the N-terminal end of CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST from Pseudomonas aeruginosa and similar sequences predominantly found in proteobacteria. In the type I-F CRISPR-Cas system, Cas3 is fused with Ca ...	This domain is found at the N-terminal end of CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST from Pseudomonas aeruginosa and similar sequences predominantly found in proteobacteria. In the type I-F CRISPR-Cas system, Cas3 is fused with Cas2 at the N terminus. This entry represents the Cas2 domain of Cas3, which shows a four-stranded beta-sheet and two alpha-helices, in a structure that resembles that of Cas2 from the Escherichia coli. It appears N- terminal to the histidine-aspartate (HD)-type nuclease domain (Pfam:PF18019) [1,2].	Domain
M, N	PF21802	CRISPR-associated Cas3 subtype I-F/YPEST-like, C-terminal domain (Cas3-like_C)	CRISPR-associated Cas3 subtype I-F/YPEST-like, C-terminal domain	This domain is found at the C-terminal end of CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST from Pseudomonas aeruginosa. Cas3 contains an HD nuclease domain (Pfam:PF18019), RecA1, RecA2, a long linker region, and this C-terminal domain. ...	This domain is found at the C-terminal end of CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST from Pseudomonas aeruginosa. Cas3 contains an HD nuclease domain (Pfam:PF18019), RecA1, RecA2, a long linker region, and this C-terminal domain. This domain shows two alpha-helices and two six-stranded beta-blades [1,2].	Domain
M, N	PF18019	Cas3, HD domain (Cas3_HD)	Cas3, HD domain	This HD domain is found at the N-terminus of Cas3 enzymes fused to a helicase domain. This domain is sometimes found as a separate protein. It acts as a nuclease that cleaves ssDNA.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	CRISPR-associated endonuclease Cas1	DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on a nucleic acid hydrolase activity catalytic activity DNA nuclease activity DNA binding binding nucleic acid binding cation binding ion binding DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on a nucleic acid hydrolase activity catalytic activity DNA nuclease activity DNA binding binding nucleic acid binding cation binding ion binding metal ion binding small molecule binding identical protein binding protein binding	biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response 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 maintenance of CRISPR repeat elements chromosome organization primary metabolic process biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response 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 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	-
E, G	Integration host factor subunit alpha	DNA binding binding nucleic acid binding structural molecule activity structural constituent of chromatin	regulation of biosynthetic process regulation of biological process regulation of cellular process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of gene expression biosynthetic process regulation of translation regulation of biosynthetic process regulation of biological process regulation of cellular process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of gene expression biosynthetic process regulation of translation regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process protein metabolic process regulation of metabolic process RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription DNA recombination DNA metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol
F, H	Integration host factor subunit beta	DNA binding binding nucleic acid binding structural molecule activity structural constituent of chromatin	regulation of biosynthetic process regulation of biological process regulation of cellular process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of gene expression biosynthetic process regulation of translation regulation of biosynthetic process regulation of biological process regulation of cellular process regulation of protein metabolic process biological regulation primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression regulation of gene expression biosynthetic process regulation of translation regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule metabolic process protein metabolic process regulation of metabolic process RNA metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process nucleobase-containing compound biosynthetic process nucleic acid metabolic process regulation of DNA-templated transcription DNA recombination DNA metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol intracellular organelle organelle membraneless organelle intracellular membraneless organelle chromosome
I	CRISPR leader, sense strand of DNA	-	-	-
J	CRISPR leader and repeat, anti-sense strand of DNA	-	-	-
K	CRISPR repeat and prespacer, sense strand of DNA	-	-	-
L	Prespacer, anti-sense strand of DNA	-	-	-
M, N	CRISPR-associated nuclease/helicase Cas3 subtype I-F/YPEST	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding catalytic activity, acting on a nucleic acid helicase activity catalytic activity ATP-dependent activity hydrolase activity cation binding metal ion binding	biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response 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	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR002729	CRISPR-associated protein Cas1	Family
A, B, C, D	IPR042206	CRISPR-associated endonuclease Cas1, C-terminal domain	Homologous Superfamily
A, B, C, D	IPR042211	CRISPR-associated endonuclease Cas1, N-terminal domain	Homologous Superfamily
A, B, C, D	IPR050646	CRISPR-associated endonuclease Cas1	Family
A, B, C, D	IPR019857	CRISPR-associated protein Cas1, YPEST subtype	Family
E, G	IPR020816	Histone-like DNA-binding protein, conserved site	Conserved Site
E, G	IPR010992	Integration host factor (IHF)-like DNA-binding domain superfamily	Homologous Superfamily
E, G	IPR005684	Integration host factor, alpha subunit	Family
E, G	IPR000119	Histone-like DNA-binding protein	Family
F, H	IPR020816	Histone-like DNA-binding protein, conserved site	Conserved Site
F, H	IPR010992	Integration host factor (IHF)-like DNA-binding domain superfamily	Homologous Superfamily
F, H	IPR005685	Integration host factor, beta subunit	Family
F, H	IPR000119	Histone-like DNA-binding protein	Family
M, N	IPR054712	CRISPR-associated nuclease/helicase Cas3 domain	Domain
M, N	IPR048824	CRISPR-associated Cas3 subtype I-F/YPEST-like, C-terminal domain	Domain
M, N	IPR048823	CRISPR-associated nuclease/helicase Cas3, I-F/YPEST, Cas2 domain	Domain
M, N	IPR013395	CRISPR-associated Cas3, Yersinia-type	Family
M, N	IPR038257	CRISPR-associated Cas3-type HD domain superfamily	Homologous Superfamily
M, N	IPR006483	CRISPR-associated Cas3-type, HD domain	Domain
M, N	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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.

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8FLJ

Cas1-Cas2/3 integrase and IHF bound to CRISPR leader, repeat and foreign DNA

External Resource: Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage