4QDL | pdb_00004qdl

Crystal structure of E.coli Cas1-Cas2 complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d4qdld_	Multi-domain proteins (alpha and beta)	CRISPR associated protein Cas1-like	CRISPR associated protein Cas1-like	CRISPR associated protein Cas1-like	Cas1	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C	d4qdlc_	Multi-domain proteins (alpha and beta)	CRISPR associated protein Cas1-like	CRISPR associated protein Cas1-like	CRISPR associated protein Cas1-like	Cas1	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B	d4qdlb_	Multi-domain proteins (alpha and beta)	CRISPR associated protein Cas1-like	CRISPR associated protein Cas1-like	CRISPR associated protein Cas1-like	Cas1	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d4qdla_	Multi-domain proteins (alpha and beta)	CRISPR associated protein Cas1-like	CRISPR associated protein Cas1-like	CRISPR associated protein Cas1-like	Cas1	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
F	d4qdlf1	Alpha and beta proteins (a+b)	Ferredoxin-like	CRISPR associated protein Cas2-like	CRISPR associated protein Cas2-like	Cas2	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
F	d4qdlf2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
E	d4qdle_	Alpha and beta proteins (a+b)	Ferredoxin-like	CRISPR associated protein Cas2-like	CRISPR associated protein Cas2-like	Cas2	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D	SCOP2B Superfamily	CRISPR associated protein Cas1	8053176	3002164	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	CRISPR associated protein Cas1	8053176	3002164	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CRISPR associated protein Cas1	8053176	3002164	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	CRISPR associated protein Cas1	8053176	3002164	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Cas2-like	8090691	3001363	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Cas2-like	8090691	3001363	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)
D	Spermine_synth	e4qdlD1	A: a/b three-layered sandwiches	X: HTH	H: Toll/Interleukin receptor TIR domain	T: Toll/Interleukin receptor TIR domain	F: Spermine_synth	ECOD (v294.1)
C	Spermine_synth	e4qdlC1	A: a/b three-layered sandwiches	X: HTH	H: Toll/Interleukin receptor TIR domain	T: Toll/Interleukin receptor TIR domain	F: Spermine_synth	ECOD (v294.1)
B	Spermine_synth	e4qdlB1	A: a/b three-layered sandwiches	X: HTH	H: Toll/Interleukin receptor TIR domain	T: Toll/Interleukin receptor TIR domain	F: Spermine_synth	ECOD (v294.1)
A	Spermine_synth	e4qdlA1	A: a/b three-layered sandwiches	X: HTH	H: Toll/Interleukin receptor TIR domain	T: Toll/Interleukin receptor TIR domain	F: Spermine_synth	ECOD (v294.1)
F	Spermine_synth	e4qdlF1	A: a/b three-layered sandwiches	X: HTH	H: Toll/Interleukin receptor TIR domain	T: Toll/Interleukin receptor TIR domain	F: Spermine_synth	ECOD (v294.1)
E	Spermine_synth	e4qdlE1	A: a/b three-layered sandwiches	X: HTH	H: Toll/Interleukin receptor TIR domain	T: Toll/Interleukin receptor TIR domain	F: Spermine_synth	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	3.100.10.20	Alpha Beta	Ribosomal Protein L15	Chain: K	domain 2	CATH (4.3.0)
D	1.20.120.920	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	CRISPR-associated endonuclease Cas1, C-terminal domain	CATH (4.3.0)
C	3.100.10.20	Alpha Beta	Ribosomal Protein L15	Chain: K	domain 2	CATH (4.3.0)
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 (4.3.0)
B	3.100.10.20	Alpha Beta	Ribosomal Protein L15	Chain: K	domain 2	CATH (4.3.0)
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 (4.3.0)
A	3.100.10.20	Alpha Beta	Ribosomal Protein L15	Chain: K	domain 2	CATH (4.3.0)
A	1.20.120.920	Mainly Alpha	Up-down Bundle	Four Helix Bundle (Hemerythrin (Met), subunit A)	CRISPR-associated endonuclease Cas1, C-terminal domain	CATH (4.3.0)

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, F	PF09707	CRISPR-associated protein (Cas_Cas2CT1978) (Cas_Cas2CT1978)	CRISPR-associated protein (Cas_Cas2CT1978)	-	Family

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 binding binding nucleic acid binding endonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity crossover junction DNA endonuclease activity DNA nuclease activity DNA endonuclease activity DNA endonuclease activity, producing 3'-phosphomonoesters hydrolase activity, acting on ester bonds catalytic activity, acting on DNA nuclease activity catalytic activity DNA binding binding nucleic acid binding endonuclease activity catalytic activity, acting on a nucleic acid hydrolase activity crossover junction DNA endonuclease activity DNA nuclease activity DNA endonuclease activity DNA endonuclease activity, producing 3'-phosphomonoesters hydrolase activity, acting on ester bonds catalytic activity, acting on DNA nuclease activity catalytic activity identical protein binding protein binding protein homodimerization activity protein dimerization activity 5'-flap endonuclease activity flap endonuclease activity DNA endonuclease activity, producing 5'-phosphomonoesters cation binding ion binding metal ion binding small molecule binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process metabolic process macromolecule metabolic process DNA repair maintenance of CRISPR repeat elements cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process primary metabolic process DNA metabolic process nucleic acid metabolic process nucleobase-containing compound metabolic process metabolic process macromolecule metabolic process DNA repair maintenance of CRISPR repeat elements chromosome organization maintenance of DNA repeat elements cellular component organization organelle organization cellular component organization or biogenesis biological process involved in interspecies interaction between organisms response to other organism defense response defense response to symbiont response to external stimulus clearance of foreign intracellular nucleic acids response to biotic stimulus defense response to other organism CRISPR-cas system response to external biotic stimulus defense response to virus response to virus	cellular anatomical structure intracellular anatomical structure cytoplasm
E, F	CRISPR-associated endoribonuclease Cas2	DNA binding binding nucleic acid binding hydrolase activity catalytic activity endonuclease activity nuclease activity catalytic activity, acting on a nucleic acid	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 clearance of foreign intracellular nucleic acids response to biotic stimulus defense response to other organism response to stress CRISPR-cas system response to external biotic stimulus defense response to virus response to virus 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 clearance of foreign intracellular nucleic acids response to biotic stimulus defense response to other organism response to stress CRISPR-cas system response to external biotic stimulus defense response to virus 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	-

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	IPR033641	CRISPR-associated protein Cas1, type I-E	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	IPR019851	CRISPR-associated protein Cas1, ECOLI subtype	Family
A, B, C, D	IPR050646	CRISPR-associated endonuclease Cas1	Family
E, F	IPR010152	CRISPR-associated protein Cas2 subtype	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.