8DO6 | pdb_00008do6

The structure of S. epidermidis Cas10-Csm bound to target RNA

External Resource: Annotation

Domain Annotation: SCOP2 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 [auth E]	SCOP2B Superfamily	CRISPR-associated proteins	8085903	3001554	SCOP2B (2022-06-29)
B [auth G]	SCOP2B Superfamily	CRISPR-associated proteins	8085903	3001554	SCOP2B (2022-06-29)
C [auth F]	SCOP2B Superfamily	CRISPR-associated proteins	8085903	3001554	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth E], B [auth G], C [auth F]	PF03787	RAMP superfamily (RAMPs)	RAMP superfamily	-	Family
F [auth C], G [auth D]	PF03750	Csm2 Type III-A (Csm2_III-A)	Csm2 Type III-A	-	Family
H [auth B]	PF17953	CRISPR Csm4 C-terminal domain (Csm4_C)	CRISPR Csm4 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. The interference complex of the type III-A CRISPR-Cas system is composed of five Cas proteins (Csm1-Csm5) and a crRNA, and targets invading DNA. This entry represents the C-terminal domain found in Csm4. Csm4 structurally resembles Cmr3, a component of the type III-B CRISPR-Cas interference complex. Studies indicate that Csm3-Csm4 complex binds single-stranded RNA in a non-sequence-specific manner. Structural analysis show , Csm3 and Csm4 have one and two ferredoxin-like folds (also known as an RRM-like fold), respectively. The long beta-hairpin inserted into the C-terminal ferredoxin-like fold of Csm4, is well-conserved in the Cmr3 structure. The corresponding beta-hairpin of Cmr3 binds the D1 domain of Cmr2, as observed in the Cmr2-Cmr3 complex structure. Furthermore, it is suggested that the hairpin of Csm4 is responsible for the interaction with Csm1 (ortholog of Cmr2) [1].	Domain
H [auth B]	PF03787	RAMP superfamily (RAMPs)	RAMP superfamily	-	Family
I [auth H]	PF03787	RAMP superfamily (RAMPs)	RAMP superfamily	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth E], B [auth G], C [auth F]	CRISPR system Cms endoribonuclease Csm3	endonuclease activity nuclease activity catalytic activity, acting on a nucleic acid catalytic activity RNA 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	-
D [auth I]	crRNA	-	-	-
E [auth J]	Target RNA	-	-	-
F [auth C], G [auth D]	CRISPR system Cms protein Csm2	RNA binding binding nucleic acid 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	-
H [auth B]	CRISPR system Cms protein Csm4	RNA binding binding nucleic acid 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	-
I [auth H]	CRISPR system Cms protein Csm5	RNA binding binding nucleic acid 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	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth E], B [auth G], C [auth F]	IPR052216	CRISPR-associated Csm3 endoribonuclease	Family
A [auth E], B [auth G], C [auth F]	IPR013412	CRISPR-associated RAMP Csm3	Family
A [auth E], B [auth G], C [auth F]	IPR005537	CRISPR type III-associated protein	Domain
F [auth C], G [auth D]	IPR010149	CRISPR-associated protein, Csm2 Type III-A	Family
H [auth B]	IPR005537	CRISPR type III-associated protein	Domain
H [auth B]	IPR005510	CRISPR type III-associated RAMP protein Csm4	Family
H [auth B]	IPR040932	Csm4, C-terminal	Domain
I [auth H]	IPR005537	CRISPR type III-associated protein	Domain
I [auth H]	IPR010173	CRISPR-associated protein Csm5	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.