4Z7L

Crystal structure of Cas6b

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD 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 proteins	8103618	3001554	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	CRISPR-associated proteins	8103618	3001554	SCOP2B (2022-06-29)
C [auth D]	SCOP2B Superfamily	CRISPR-associated proteins	8103618	3001554	SCOP2B (2022-06-29)
D [auth G]	SCOP2B Superfamily	CRISPR-associated proteins	8103618	3001554	SCOP2B (2022-06-29)
E	SCOP2 Family	Cas6b C-terminal domain-like	8046733	4005269	SCOP2 (2022-06-29)
E	SCOP2 Superfamily	CRISPR-associated proteins	8103618	3001554	SCOP2 (2022-06-29)
F [auth H]	SCOP2B Superfamily	CRISPR-associated proteins	8103618	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)
A	PF17262	e4z7lA1	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: PF17262	ECOD (1.6)
A	PF17955	e4z7lA2	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: PF17955	ECOD (1.6)
B	PF17262	e4z7lB1	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: PF17262	ECOD (1.6)
B	PF17955	e4z7lB2	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: PF17955	ECOD (1.6)
C [auth D]	PF17262	e4z7lD1	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: PF17262	ECOD (1.6)
C [auth D]	PF17955	e4z7lD2	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: PF17955	ECOD (1.6)
D [auth G]	PF17262	e4z7lG2	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: PF17262	ECOD (1.6)
D [auth G]	PF17955	e4z7lG1	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: PF17955	ECOD (1.6)
E	PF17262	e4z7lE1	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: PF17262	ECOD (1.6)
E	PF17955	e4z7lE2	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: PF17955	ECOD (1.6)
F [auth H]	PF17262	e4z7lH2	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: PF17262	ECOD (1.6)
F [auth H]	PF17955	e4z7lH1	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: PF17955	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C [auth D], D [auth G], E, A, B, C [auth D], D [auth G], E, F [auth H]	PF17262	Cas6b C-terminal domain (Cas6b_C)	Cas6b C-terminal domain	Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci play a pivotal role in the prokaryotic host defense system against invading genetic materials. The CRISPR loci are transcribed to produce CRISPR RNAs (crRNAs), which form interf ...	Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci play a pivotal role in the prokaryotic host defense system against invading genetic materials. The CRISPR loci are transcribed to produce CRISPR RNAs (crRNAs), which form interference complexes with CRISPR-associated (Cas) proteins to target the invading nucleic acid for degradation [1]. Four Cas proteins (Cas5, Cas6b, Cas7 and Cas8b) are proposed to form a Type I-B Cascade complex that mediates the antiviral defense [2]. This is the C-terminal domain found in Cas6b proteins. Cas6b is a member of Cas6 RNA processing endoribonucleases found in bacteria and archaea whose RNA substrates have a wide range of structural features. Cocrystal structures of Cas6 from Methanococcus maripaludis (MmCas6b) bound with its repeat RNA revealed a dual-site binding structure and a cleavage site conformation poised for phosphodiester bond breakage [3].	Domain
A, B, C [auth D], D [auth G], E, A, B, C [auth D], D [auth G], E, F [auth H]	PF17955	Cas6b N-terminal domain (Cas6b_N)	Cas6b N-terminal domain	Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci play a pivotal role in the prokaryotic host defense system against invading genetic materials. The CRISPR loci are transcribed to produce CRISPR RNAs (crRNAs), which form interf ...	Clustered, regularly interspaced, short palindromic repeat (CRISPR) loci play a pivotal role in the prokaryotic host defense system against invading genetic materials. The CRISPR loci are transcribed to produce CRISPR RNAs (crRNAs), which form interference complexes with CRISPR-associated (Cas) proteins to target the invading nucleic acid for degradation [1]. Four Cas proteins (Cas5, Cas6b, Cas7 and Cas8b) are proposed to form a Type I-B Cascade complex that mediates the antiviral defense [2]. This is the N-terminal domain found in Cas6b proteins. Cas6b is a member of Cas6 RNA processing endoribonucleases found in bacteria and archaea whose RNA substrates have a wide range of structural features. Cocrystal structures of Cas6 from Methanococcus maripaludis (MmCas6b) bound with its repeat RNA revealed a dual-site binding structure and a cleavage site conformation poised for phosphodiester bond breakage [3].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C [auth D], D [auth G], E, A, B, C [auth D], D [auth G], E, F [auth H]	Cas6b	identical protein binding protein binding binding	-	-
G [auth C], H [auth F], I	RNA (5'-R(GPCPAPAPAPAPUPAPAPCPAPAPGPC)-3')	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C [auth D], D [auth G], E, A, B, C [auth D], D [auth G], E, F [auth H]	IPR020209	Cas6b, C-terminal domain	Domain
A, B, C [auth D], D [auth G], E, A, B, C [auth D], D [auth G], E, F [auth H]	IPR041528	Cas6b N-terminal	Domain

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.