9ASI

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 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

Molecular basis for cA6 synthesis by a type III-A CRISPR-Cas enzyme and its conversion to cA4 production.

Goswami, H.N.Ahmadizadeh, F.Wang, B.Addo-Yobo, D.Zhao, Y.Whittington, A.C.He, H.Terns, M.P.Li, H.

(2024) Nucleic Acids Res 

  • DOI: https://doi.org/10.1093/nar/gkae603
  • Primary Citation of Related Structures:  
    9ASH, 9ASI

  • PubMed Abstract: 

    The type III-A (Csm) CRISPR-Cas systems are multi-subunit and multipronged prokaryotic enzymes in guarding the hosts against viral invaders. Beyond cleaving activator RNA transcripts, Csm confers two additional activities: shredding single-stranded DNA and synthesizing cyclic oligoadenylates (cOAs) by the Cas10 subunit. Known Cas10 enzymes exhibit a fascinating diversity in cOA production. Three major forms-cA3, cA4 and cA6have been identified, each with the potential to trigger unique downstream effects. Whereas the mechanism for cOA-dependent activation is well characterized, the molecular basis for synthesizing different cOA isoforms remains unclear. Here, we present structural characterization of a cA6-producing Csm complex during its activation by an activator RNA. Analysis of the captured intermediates of cA6 synthesis suggests a 3'-to-5' nucleotidyl transferring process. Three primary adenine binding sites can be identified along the chain elongation path, including a unique tyrosine-threonine dyad found only in the cA6-producing Cas10. Consistently, disrupting the tyrosine-threonine dyad specifically impaired cA6 production while promoting cA4 production. These findings suggest that Cas10 utilizes a unique enzymatic mechanism for forming the phosphodiester bond and has evolved distinct strategies to regulate the cOA chain length.


  • Organizational Affiliation

    Institute of Molecular Biophysics, Florida State University, Tallahassee, FL 32306, USA.


Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR-associated protein Csm4A [auth B]297Lactococcus lactis subsp. lactisMutation(s): 0 
Gene Names: csm4
UniProt
Find proteins for L0CFH1 (Lactococcus lactis subsp. lactis)
Explore L0CFH1 
Go to UniProtKB:  L0CFH1
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL0CFH1
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR system Cms endoribonuclease Csm3B [auth F],
C [auth H],
D [auth G],
E [auth I]
214Lactococcus lactis subsp. lactisMutation(s): 0 
Gene Names: csm3
UniProt
Find proteins for L0CEA3 (Lactococcus lactis subsp. lactis)
Explore L0CEA3 
Go to UniProtKB:  L0CEA3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL0CEA3
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR system Cms protein Csm2G [auth D],
H [auth E],
J [auth C]
150Lactococcus lactis subsp. lactisMutation(s): 0 
Gene Names: csm2
UniProt
Find proteins for L0CFW2 (Lactococcus lactis subsp. lactis)
Explore L0CFW2 
Go to UniProtKB:  L0CFW2
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL0CFW2
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR system Cms protein Csm5K [auth J]353Lactococcus lactis subsp. lactisMutation(s): 0 
Gene Names: csm5
UniProt
Find proteins for L0CG31 (Lactococcus lactis subsp. lactis)
Explore L0CG31 
Go to UniProtKB:  L0CG31
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL0CG31
Sequence Annotations
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)L [auth A]757Lactococcus lactis subsp. lactisMutation(s): 0 
Gene Names: cas10
UniProt
Find proteins for L0CEJ3 (Lactococcus lactis subsp. lactis)
Explore L0CEJ3 
Go to UniProtKB:  L0CEJ3
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupL0CEJ3
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChains LengthOrganismImage
CRISPR RNAF [auth R]37Lactococcus lactis subsp. lactis
Sequence Annotations
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChains LengthOrganismImage
Target RNAI [auth T]36Lactococcus lactis subsp. lactis
Sequence Annotations
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.79 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
MODEL REFINEMENTPHENIX1.20.1_4487

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM099604

Revision History  (Full details and data files)

  • Version 1.0: 2024-08-14
    Type: Initial release