4QYZ | pdb_00004qyz

Crystal structure of a CRISPR RNA-guided surveillance complex, Cascade, bound to a ssDNA target

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
J	SCOP2B Superfamily	CRISPR-associated proteins	8052154	3001554	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cse1 C-terminal domain-like	8053925	3002248	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cse1 N-terminal domain-like	8053924	3002247	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Cse2-like	8053946	3002252	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Cse2-like	8053946	3002252	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	CRISPR-associated proteins	8052153	3001554	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	CRISPR-associated proteins	8052153	3001554	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	CRISPR-associated proteins	8052153	3001554	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	CRISPR-associated proteins	8052153	3001554	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	CRISPR-associated proteins	8052153	3001554	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	CRISPR-associated proteins	8052153	3001554	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)
J	Cas_Cas5d	e4qyzJ1	A: a+b two layers	X: Alpha-beta plaits	H: CRISPR system Cas5 homologs (From Topology)	T: CRISPR system Cas5 homologs	F: Cas_Cas5d	ECOD (1.6)
A	CRISPR_Cse1	e4qyzA1	A: a+b complex topology	X: Cas8-like	H: Cascade subunit CasA/Cse1/Cas8 (From Topology)	T: Cascade subunit CasA/Cse1/Cas8	F: CRISPR_Cse1	ECOD (1.6)
B	CRISPR_Cse2	e4qyzB1	A: alpha bundles	X: CRISPR-associated protein Cse2 (From Topology)	H: CRISPR-associated protein Cse2 (From Topology)	T: CRISPR-associated protein Cse2	F: CRISPR_Cse2	ECOD (1.6)
C	CRISPR_Cse2	e4qyzC1	A: alpha bundles	X: CRISPR-associated protein Cse2 (From Topology)	H: CRISPR-associated protein Cse2 (From Topology)	T: CRISPR-associated protein Cse2	F: CRISPR_Cse2	ECOD (1.6)
D	Cas_CT1975	e4qyzD1	A: a+b two layers	X: Alpha-beta plaits	H: Cas7-related	T: CRISPR-associated protein Cas7/Csa2-related	F: Cas_CT1975	ECOD (1.6)
E	Cas_CT1975	e4qyzE1	A: a+b two layers	X: Alpha-beta plaits	H: Cas7-related	T: CRISPR-associated protein Cas7/Csa2-related	F: Cas_CT1975	ECOD (1.6)
F	Cas_CT1975	e4qyzF1	A: a+b two layers	X: Alpha-beta plaits	H: Cas7-related	T: CRISPR-associated protein Cas7/Csa2-related	F: Cas_CT1975	ECOD (1.6)
G	Cas_CT1975	e4qyzG1	A: a+b two layers	X: Alpha-beta plaits	H: Cas7-related	T: CRISPR-associated protein Cas7/Csa2-related	F: Cas_CT1975	ECOD (1.6)
H	Cas_CT1975	e4qyzH1	A: a+b two layers	X: Alpha-beta plaits	H: Cas7-related	T: CRISPR-associated protein Cas7/Csa2-related	F: Cas_CT1975	ECOD (1.6)
I	Cas_CT1975	e4qyzI1	A: a+b two layers	X: Alpha-beta plaits	H: Cas7-related	T: CRISPR-associated protein Cas7/Csa2-related	F: Cas_CT1975	ECOD (1.6)
K	CRISPR_assoc_C	e4qyzK1	A: a+b two layers	X: Alpha-beta plaits	H: CRISPR transcript (pre-crRNA) processing endoribonuclease-related (From Topology)	T: CRISPR transcript (pre-crRNA) processing endoribonuclease-related	F: CRISPR_assoc_C	ECOD (1.6)
K	CRISPR_assoc_N	e4qyzK2	A: a+b two layers	X: Alpha-beta plaits	H: CRISPR transcript (pre-crRNA) processing endoribonuclease-related (From Topology)	T: CRISPR transcript (pre-crRNA) processing endoribonuclease-related	F: CRISPR_assoc_N	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
J	3.30.70.2660	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits		CATH (4.3.0)
B	1.10.520.40	Mainly Alpha	Orthogonal Bundle	Peroxidase	domain 1	CATH (4.3.0)
C	1.10.520.40	Mainly Alpha	Orthogonal Bundle	Peroxidase	domain 1	CATH (4.3.0)
K	3.30.70.1200	Alpha Beta	2-Layer Sandwich	Alpha-Beta Plaits	Crispr-associated protein	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
J	PF09704	CRISPR-associated protein (Cas_Cas5) (Cas_Cas5d)	CRISPR-associated protein (Cas_Cas5)	-	Family
A	PF09481	CRISPR-associated protein Cse1 (CRISPR_cse1) (CRISPR_Cse1)	CRISPR-associated protein Cse1 (CRISPR_cse1)	-	Family
B, C	PF09485	CRISPR-associated protein Cse2 (CRISPR_cse2) (CRISPR_Cse2)	CRISPR-associated protein Cse2 (CRISPR_cse2)	-	Family
D, E, F, G, H D, E, F, G, H, I	PF09344	CT1975-like protein (Cas_CT1975)	CT1975-like protein	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
J	CRISPR system Cascade subunit CasD	RNA binding binding nucleic acid binding DNA/RNA hybrid 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 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	protein-containing complex
L	RNA (55-MER)	-	-	-
A	CRISPR system Cascade subunit CasA	DNA binding binding nucleic acid binding cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding RNA 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 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	protein-containing complex
B, C	CRISPR system Cascade subunit CasB	DNA binding binding nucleic acid binding RNA 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 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	protein-containing complex
D, E, F, G, H D, E, F, G, H, I	CRISPR system Cascade subunit CasC	RNA binding binding nucleic acid binding DNA/RNA hybrid 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 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	protein-containing complex
K	CRISPR system Cascade subunit CasE	endonuclease activity nuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on RNA RNA endonuclease activity catalytic activity, acting on a nucleic acid RNA nuclease activity hydrolase activity catalytic activity RNA binding binding nucleic acid 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 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 RNA metabolic process primary 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 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 RNA metabolic process primary metabolic process gene expression nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process biosynthetic process metabolic process cellular process RNA processing macromolecule metabolic process defense response to virus response to virus	protein-containing complex
M	DNA (33-MER)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
J	IPR010147	CRISPR-associated protein, CasD	Family
J	IPR021124	CRISPR-associated protein, Cas5	Family
J	IPR013422	CRISPR-associated protein Cas5, N-terminal	Domain
A	IPR013381	CRISPR-associated protein Cse1	Family
B, C	IPR013382	CRISPR-associated protein Cse2	Family
B, C	IPR038287	Cse2 superfamily	Homologous Superfamily
D, E, F, G, H D, E, F, G, H, I	IPR010148	CRISPR-associated protein, CT1975	Family
K	IPR010179	CRISPR-associated protein Cse3	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.