8FLJ

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

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
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)
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)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
C	PF01867	e8fljC1	A: alpha complex topology	X: Cas1 (From Topology)	H: Cas1 (From Topology)	T: Cas1	F: PF01867	ECOD (1.6)
D	PF01867	e8fljD1	A: alpha complex topology	X: Cas1 (From Topology)	H: Cas1 (From Topology)	T: Cas1	F: PF01867	ECOD (1.6)
A	PF01867	e8fljA1	A: alpha complex topology	X: Cas1 (From Topology)	H: Cas1 (From Topology)	T: Cas1	F: PF01867	ECOD (1.6)
B	PF01867	e8fljB1	A: alpha complex topology	X: Cas1 (From Topology)	H: Cas1 (From Topology)	T: Cas1	F: PF01867	ECOD (1.6)
E	PF00216	e8fljE1	A: alpha arrays	X: HTH	H: IHF-like DNA-binding proteins (From Topology)	T: IHF-like DNA-binding proteins	F: PF00216	ECOD (1.6)
G	PF00216	e8fljG1	A: alpha arrays	X: HTH	H: IHF-like DNA-binding proteins (From Topology)	T: IHF-like DNA-binding proteins	F: PF00216	ECOD (1.6)
H	PF00216	e8fljH1	A: alpha arrays	X: HTH	H: IHF-like DNA-binding proteins (From Topology)	T: IHF-like DNA-binding proteins	F: PF00216	ECOD (1.6)
F	PF00216	e8fljF1	A: alpha arrays	X: HTH	H: IHF-like DNA-binding proteins (From Topology)	T: IHF-like DNA-binding proteins	F: PF00216	ECOD (1.6)
N	PF18019	e8fljN3	A: alpha complex topology	X: PDEase-like	H: HD-domain/PDEase-like (From Topology)	T: HD-domain/PDEase-like	F: PF18019	ECOD (1.6)
N	PF21384	e8fljN5	A: a+b two layers	X: Alpha-beta plaits	H: CRISPR associated protein Cas2-like (From Topology)	T: CRISPR associated protein Cas2-like	F: PF21384	ECOD (1.6)
N	PF21802	e8fljN1	A: a+b two layers	X: Cas3 C-terminal domain	H: Cas3 subtype I-F/YPEST C-terminal domain (From Topology)	T: Cas3 subtype I-F/YPEST C-terminal domain	F: PF21802	ECOD (1.6)
N	F_UNCLASSIFIED	e8fljN4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: F_UNCLASSIFIED	ECOD (1.6)
N	PF22590	e8fljN2	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF22590	ECOD (1.6)
M	PF18019	e8fljM3	A: alpha complex topology	X: PDEase-like	H: HD-domain/PDEase-like (From Topology)	T: HD-domain/PDEase-like	F: PF18019	ECOD (1.6)
M	PF21384	e8fljM2	A: a+b two layers	X: Alpha-beta plaits	H: CRISPR associated protein Cas2-like (From Topology)	T: CRISPR associated protein Cas2-like	F: PF21384	ECOD (1.6)
M	PF21802	e8fljM1	A: a+b two layers	X: Cas3 C-terminal domain	H: Cas3 subtype I-F/YPEST C-terminal domain (From Topology)	T: Cas3 subtype I-F/YPEST C-terminal domain	F: PF21802	ECOD (1.6)
M	F_UNCLASSIFIED	e8fljM5	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: F_UNCLASSIFIED	ECOD (1.6)
M	PF22590	e8fljM4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: P-loop domains-related	T: P-loop containing nucleoside triphosphate hydrolases	F: PF22590	ECOD (1.6)

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 organic cyclic compound binding nucleic acid binding cation 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 organic cyclic compound 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 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 maintenance of CRISPR repeat elements chromosome organization 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 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 organic cyclic compound metabolic process organelle organization organic substance metabolic process cellular process metabolic process cellular component organization or biogenesis macromolecule metabolic process	-
E, G	Integration host factor subunit alpha	DNA binding binding organic cyclic compound binding nucleic acid binding structural molecule activity structural constituent of chromatin	regulation of cellular process cellular biosynthetic process organonitrogen compound biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression organic substance metabolic process organic substance biosynthetic process protein metabolic process regulation of biosynthetic process regulation of biological process organonitrogen compound metabolic process cellular metabolic process regulation of protein metabolic process biological regulation regulation of cellular process cellular biosynthetic process organonitrogen compound biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression organic substance metabolic process organic substance biosynthetic process protein metabolic process regulation of biosynthetic process regulation of biological process organonitrogen compound metabolic process cellular metabolic process regulation of protein metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process regulation of translation regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule 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 organic cyclic compound metabolic process organic cyclic compound biosynthetic process regulation of DNA-templated transcription DNA recombination DNA metabolic process	-
F, H	Integration host factor subunit beta	DNA binding binding organic cyclic compound binding nucleic acid binding structural molecule activity structural constituent of chromatin	regulation of cellular process cellular biosynthetic process organonitrogen compound biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression organic substance metabolic process organic substance biosynthetic process protein metabolic process regulation of biosynthetic process regulation of biological process organonitrogen compound metabolic process cellular metabolic process regulation of protein metabolic process biological regulation regulation of cellular process cellular biosynthetic process organonitrogen compound biosynthetic process regulation of primary metabolic process post-transcriptional regulation of gene expression organic substance metabolic process organic substance biosynthetic process protein metabolic process regulation of biosynthetic process regulation of biological process organonitrogen compound metabolic process cellular metabolic process regulation of protein metabolic process biological regulation regulation of cellular metabolic process primary metabolic process regulation of macromolecule metabolic process gene expression translation macromolecule biosynthetic process regulation of cellular biosynthetic process regulation of gene expression biosynthetic process regulation of translation regulation of macromolecule biosynthetic process metabolic process cellular process macromolecule 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 organic cyclic compound metabolic process organic cyclic compound biosynthetic process regulation of DNA-templated transcription DNA recombination DNA metabolic process	intracellular organelle intracellular anatomical structure organelle intracellular non-membrane-bounded organelle chromosome cellular anatomical entity non-membrane-bounded organelle
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 organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound 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 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	-

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	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	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 R01GM133198.