8FYD | pdb_00008fyd

Cryo-EM structure of Cas1:Cas2-DEDDh:half-site integration complex bent CRISPR repeat conformation

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
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)
B [auth A]	F_UNCLASSIFIED	e8fydA1	A: a+b two layers	X: Alpha-beta plaits	H: CRISPR associated protein Cas2-like (From Topology)	T: CRISPR associated protein Cas2-like	F: F_UNCLASSIFIED	ECOD (1.6)
E [auth D]	F_UNCLASSIFIED	e8fydD1	A: a+b two layers	X: Alpha-beta plaits	H: CRISPR associated protein Cas2-like (From Topology)	T: CRISPR associated protein Cas2-like	F: F_UNCLASSIFIED	ECOD (1.6)
C [auth B]	F_UNCLASSIFIED	e8fydB1	A: alpha complex topology	X: Cas1 (From Topology)	H: Cas1 (From Topology)	T: Cas1	F: F_UNCLASSIFIED	ECOD (1.6)
D [auth C]	F_UNCLASSIFIED	e8fydC1	A: alpha complex topology	X: Cas1 (From Topology)	H: Cas1 (From Topology)	T: Cas1	F: F_UNCLASSIFIED	ECOD (1.6)
F [auth E]	F_UNCLASSIFIED	e8fydE1	A: alpha complex topology	X: Cas1 (From Topology)	H: Cas1 (From Topology)	T: Cas1	F: F_UNCLASSIFIED	ECOD (1.6)
G [auth F]	F_UNCLASSIFIED	e8fydF1	A: alpha complex topology	X: Cas1 (From Topology)	H: Cas1 (From Topology)	T: Cas1	F: F_UNCLASSIFIED	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
C [auth B]	1.20.120.920	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	CRISPR-associated endonuclease Cas1, C-terminal domain	CATH (utative)
D [auth C]	3.100.10.20	Alpha Beta	Ribosomal Protein L15	Chain: K	domain 2	CATH (utative)
D [auth C]	1.20.120.920	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	CRISPR-associated endonuclease Cas1, C-terminal domain	CATH (utative)
F [auth E]	1.20.120.920	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	CRISPR-associated endonuclease Cas1, C-terminal domain	CATH (utative)
G [auth F]	3.100.10.20	Alpha Beta	Ribosomal Protein L15	Chain: K	domain 2	CATH (utative)
G [auth F]	1.20.120.920	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	CRISPR-associated endonuclease Cas1, C-terminal domain	CATH (utative)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth J]	DNA (49-MER)	-	-	-
B [auth A], E [auth D]	Cas2-DEDDh	binding nucleic acid binding hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on a nucleic acid 3'-5' exonuclease activity hydrolase activity exonuclease activity catalytic activity	cellular response to stimulus DNA-templated DNA replication response to stimulus DNA-templated DNA replication maintenance of fidelity DNA replication proofreading primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA replication cellular response to stress DNA damage response response to stress metabolic process cellular response to stimulus DNA-templated DNA replication response to stimulus DNA-templated DNA replication maintenance of fidelity DNA replication proofreading primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process DNA replication cellular response to stress DNA damage response response to stress metabolic process cellular process macromolecule metabolic process DNA repair	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol
C [auth B], D [auth C], F [auth E], G [auth F]	Cas1	DNA endonuclease activity endonuclease activity catalytic activity, acting on DNA nuclease activity catalytic activity, acting on a nucleic acid catalytic activity DNA nuclease activity DNA binding binding nucleic acid binding cation binding ion binding metal ion binding small molecule binding	biological process involved in interspecies interaction between organisms defense response to virus response to stimulus defense response response to other organism response to stress response to external stimulus response to external biotic stimulus response to virus response to biotic stimulus maintenance of CRISPR repeat elements chromosome organization primary metabolic process DNA metabolic process biological process involved in interspecies interaction between organisms defense response to virus response to stimulus defense response response to other organism response to stress response to external stimulus response to external biotic stimulus response to virus response to biotic stimulus 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	-
H [auth G]	DNA (64-MER)	-	-	-
I [auth H]	DNA (30-MER)	-	-	-
J [auth I]	DNA (13-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth A], E [auth D]	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
B [auth A], E [auth D]	IPR010152	CRISPR-associated protein Cas2 subtype	Family
B [auth A], E [auth D]	IPR013520	Ribonuclease H-like domain	Domain
B [auth A], E [auth D]	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
C [auth B], D [auth C], F [auth E], G [auth F]	IPR019851	CRISPR-associated protein Cas1, ECOLI subtype	Family
C [auth B], D [auth C], F [auth E], G [auth F]	IPR002729	CRISPR-associated protein Cas1	Family
C [auth B], D [auth C], F [auth E], G [auth F]	IPR033641	CRISPR-associated protein Cas1, type I-E	Family
C [auth B], D [auth C], F [auth E], G [auth F]	IPR042206	CRISPR-associated endonuclease Cas1, C-terminal domain	Homologous Superfamily
C [auth B], D [auth C], F [auth E], G [auth F]	IPR042211	CRISPR-associated endonuclease Cas1, N-terminal domain	Homologous Superfamily
C [auth B], D [auth C], F [auth E], G [auth F]	IPR050646	CRISPR-associated endonuclease Cas1	Family

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.