RCSB PDB - 9G9A: CryoEM structure of Enterococcus italicus Csm-crRNA (3.2 complex)

 9G9A

CryoEM structure of Enterococcus italicus Csm-crRNA (3.2 complex)


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Mechanistic determinants and dynamics of cA6 synthesis in type III CRISPR-Cas effector complexes.

Jungfer, K.Moravcik, S.Garcia-Doval, C.Knorlein, A.Hall, J.Jinek, M.

(2025) Nucleic Acids Res 53

  • DOI: https://doi.org/10.1093/nar/gkae1277
  • Primary Citation of Related Structures:  
    9G9A, 9G9B, 9G9E, 9G9F, 9G9G, 9G9H, 9G9I, 9G9J, 9G9K

  • PubMed Abstract: 

    Type III clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems (type III CRISPR-Cas systems) use guide RNAs to recognize RNA transcripts of foreign genetic elements, which triggers the generation of cyclic oligoadenylate (cOA) second messengers by the Cas10 subunit of the type III effector complex. In turn, cOAs bind and activate ancillary effector proteins to reinforce the host immune response. Type III systems utilize distinct cOAs, including cyclic tri- (cA3), tetra- (cA4) and hexa-adenylates (cA6). However, the molecular mechanisms dictating cOA product identity are poorly understood. Here we used cryoelectron microscopy to visualize the mechanism of cA6 biosynthesis by the Csm effector complex from Enterococcus italicus (EiCsm). We show that EiCsm synthesizes oligoadenylate nucleotides in 3'-5' direction using a set of conserved binding sites in the Cas10 Palm domains to determine the size of the nascent oligoadenylate chain. Our data also reveal that conformational dynamics induced by target RNA binding results in allosteric activation of Cas10 to trigger oligoadenylate synthesis. Mutations of a key structural element in Cas10 perturb cOA synthesis to favor cA3 and cA4 formation. Together, these results provide comprehensive insights into the dynamics of cOA synthesis in type III CRISPR-Cas systems and reveal key determinants of second messenger product selectivity, thereby illuminating potential avenues for their engineering.


  • Organizational Affiliation

    Department of Biochemistry, University of Zurich, Winterthurerstrass 190, 8057 Zurich, Switzerland.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)774Enterococcus italicus DSM 15952Mutation(s): 0 
Gene Names: cas10csm1HMPREF9088_1947
EC: 3.1 (PDB Primary Data), 2.7.7 (PDB Primary Data)
UniProt
Find proteins for E6LHV7 (Enterococcus italicus (strain DSM 15952 / CCUG 50447 / LMG 22039 / TP 1.5))
Explore E6LHV7 
Go to UniProtKB:  E6LHV7
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE6LHV7
Sequence Annotations
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR system Cms protein Csm2B,
G [auth C]
140Enterococcus italicus DSM 15952Mutation(s): 0 
Gene Names: csm2HMPREF9088_1946
UniProt
Find proteins for E6LHV6 (Enterococcus italicus (strain DSM 15952 / CCUG 50447 / LMG 22039 / TP 1.5))
Explore E6LHV6 
Go to UniProtKB:  E6LHV6
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE6LHV6
Sequence Annotations
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  • Reference Sequence
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR system Cms endoribonuclease Csm3C [auth D],
D [auth E],
E [auth F]
214Enterococcus italicus DSM 15952Mutation(s): 1 
Gene Names: csm3HMPREF9088_1945
EC: 3.1
UniProt
Find proteins for E6LHV5 (Enterococcus italicus (strain DSM 15952 / CCUG 50447 / LMG 22039 / TP 1.5))
Explore E6LHV5 
Go to UniProtKB:  E6LHV5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE6LHV5
Sequence Annotations
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR system Cms protein Csm4F [auth G]307Enterococcus italicus DSM 15952Mutation(s): 0 
Gene Names: csm4HMPREF9088_1944
UniProt
Find proteins for E6LHV4 (Enterococcus italicus (strain DSM 15952 / CCUG 50447 / LMG 22039 / TP 1.5))
Explore E6LHV4 
Go to UniProtKB:  E6LHV4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE6LHV4
Sequence Annotations
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR system Cms protein Csm5379Enterococcus italicus DSM 15952Mutation(s): 0 
Gene Names: csm5HMPREF9088_1943
UniProt
Find proteins for E6LHV3 (Enterococcus italicus (strain DSM 15952 / CCUG 50447 / LMG 22039 / TP 1.5))
Explore E6LHV3 
Go to UniProtKB:  E6LHV3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupE6LHV3
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.83 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC4.4.1

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Research Council (ERC)European Union820152

Revision History  (Full details and data files)

  • Version 1.0: 2025-01-29
    Type: Initial release