9ASH | pdb_00009ash

Cryo-EM structure of the active Lactococcus lactis Csm bound to target in post-cleavage stage

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)
C [auth F]	SCOP2B Superfamily	CRISPR-associated proteins	8106216	3001554	SCOP2B (2022-06-29)
D [auth H]	SCOP2B Superfamily	CRISPR-associated proteins	8106216	3001554	SCOP2B (2022-06-29)
E [auth G]	SCOP2B Superfamily	CRISPR-associated proteins	8106216	3001554	SCOP2B (2022-06-29)
F [auth I]	SCOP2B Superfamily	CRISPR-associated proteins	8106216	3001554	SCOP2B (2022-06-29)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
H [auth D], I [auth E], K [auth C]	PF03750	Csm2 Type III-A (Csm2_III-A)	Csm2 Type III-A	-	Family
L [auth J]	PF03787	RAMP superfamily (RAMPs)	RAMP superfamily	-	Family
C [auth F], D [auth H], E [auth G], F [auth I]	PF03787	RAMP superfamily (RAMPs)	RAMP superfamily	-	Family
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
B	PF03787	RAMP superfamily (RAMPs)	RAMP superfamily	-	Family
A	PF22335	Cas10/Cmr2, second palm domain (Cas10-Cmr2_palm2)	Cas10/Cmr2, second palm domain	This entry represents the second palm domain of Cas10 subunit (named Csm1 in Type III-A and Cmr2 in III-B systems) from type III CRISPR-Cas systems [6]. This domain contains a conserved GGDD motif that is important for DNA polymerase activity [1-5]. ...	This entry represents the second palm domain of Cas10 subunit (named Csm1 in Type III-A and Cmr2 in III-B systems) from type III CRISPR-Cas systems [6]. This domain contains a conserved GGDD motif that is important for DNA polymerase activity [1-5].	Domain
A	PF01966	HD domain (HD)	HD domain	-	Family
A	PF18211	Csm1 subunit domain B (Csm1_B)	Csm1 subunit domain B	This domain is found in the Csm1 subunit of the Csm complex found in Thermococcus onnurineus. Csm is a type III-A CRISPR-Cas system, which is an RNA-guided immune defense mechanism that detects and destroys foreign DNA or RNA. This domain is known as ...	This domain is found in the Csm1 subunit of the Csm complex found in Thermococcus onnurineus. Csm is a type III-A CRISPR-Cas system, which is an RNA-guided immune defense mechanism that detects and destroys foreign DNA or RNA. This domain is known as domain A and is positioned side by side with domain C. Both domain A and domain C adopt the BABBA topology. Domain A interacts primarily with domain B [1].	Domain
A	PF20824	CRISPR RNA silencing complex Cmr2 subunit, second helical domain (Cmr2_hel_dom2)	CRISPR RNA silencing complex Cmr2 subunit, second helical domain	The prokaryotic CRISPR RNA-Cas protein (Cmr) complex provides protection against mobile genetic elements by cleaving foreign RNA. Its largest subunit is Cmr2. This protein shows a N-terminal HD (histidine-aspartate) domain, two RRM domains resembling ...	The prokaryotic CRISPR RNA-Cas protein (Cmr) complex provides protection against mobile genetic elements by cleaving foreign RNA. Its largest subunit is Cmr2. This protein shows a N-terminal HD (histidine-aspartate) domain, two RRM domains resembling adenylate cyclase and two alpha-helical domains. This entry represents the second alpha-helical domain. It is similar to the small subunit Cmr5, which contains six alpha-helices and two helical insertions that fold into a single globular structure [1-5]. This domain is also found in Cas10 proteins from bacteria [6].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G [auth R]	CRISPR RNA	-	-	-
H [auth D], I [auth E], K [auth C]	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	-
M [auth P]	RNA (5'-D((ATP))-R(PAP*A)-3')	-	-	-
L [auth J]	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	-
J [auth T]	Target RNA	-	-	-
C [auth F], D [auth H], E [auth G], F [auth I]	CRISPR system Cms endoribonuclease Csm3	hydrolase activity catalytic activity endonuclease activity nuclease activity catalytic activity, acting on a nucleic acid 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	-
B	CRISPR-associated 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	-
A	CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)	hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on a nucleic acid hydrolase activity exonuclease activity catalytic activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding hydrolase activity, acting on ester bonds nuclease activity catalytic activity, acting on a nucleic acid hydrolase activity exonuclease activity catalytic activity binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding endonuclease activity	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
H [auth D], I [auth E], K [auth C]	IPR010149	CRISPR-associated protein, Csm2 Type III-A	Family
L [auth J]	IPR005537	CRISPR type III-associated protein	Domain
L [auth J]	IPR010173	CRISPR-associated protein Csm5	Family
C [auth F], D [auth H], E [auth G], F [auth I]	IPR052216	CRISPR-associated Csm3 endoribonuclease	Family
C [auth F], D [auth H], E [auth G], F [auth I]	IPR013412	CRISPR-associated RAMP Csm3	Family
C [auth F], D [auth H], E [auth G], F [auth I]	IPR005537	CRISPR type III-associated protein	Domain
B	IPR005537	CRISPR type III-associated protein	Domain
B	IPR005510	CRISPR type III-associated RAMP protein Csm4	Family
B	IPR040932	Csm4, C-terminal	Domain
A	IPR000160	GGDEF domain	Domain
A	IPR013408	CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1	Family
A	IPR048693	CRISPR RNA silencing complex Cmr2-like, C-terminal domain	Domain
A	IPR052117	CRISPR-associated Cas10/Csm1 subtype III-A protein	Family
A	IPR041062	Csm1, subunit domain B	Domain
A	IPR054767	Cas10/Cmr2, second palm domain	Domain
A	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
A	IPR006674	HD domain	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 R01GM157729.