6XN3

Structure of the Lactococcus lactis Csm CTR_4:3 CRISPR-Cas Complex


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural and biochemical characterization of in vivo assembled Lactococcus lactis CRISPR-Csm complex.

Sridhara, S.Rai, J.Whyms, C.Goswami, H.He, H.Woodside, W.Terns, M.P.Li, H.

(2022) Commun Biol 5: 279-279

  • DOI: 10.1038/s42003-022-03187-1
  • Primary Citation of Related Structures:  
    6XN3, 6XN4, 6XN5, 6XN7

  • PubMed Abstract: 
  • The small RNA-mediated immunity in bacteria depends on foreign RNA-activated and self RNA-inhibited enzymatic activities. The multi-subunit Type III-A CRISPR-Cas effector complex (Csm) exemplifies this principle and is in addition regulated by cellular metabolites such as divalent metals and ATP ...

    The small RNA-mediated immunity in bacteria depends on foreign RNA-activated and self RNA-inhibited enzymatic activities. The multi-subunit Type III-A CRISPR-Cas effector complex (Csm) exemplifies this principle and is in addition regulated by cellular metabolites such as divalent metals and ATP. Recognition of the foreign or cognate target RNA (CTR) triggers its single-stranded deoxyribonuclease (DNase) and cyclic oligoadenylate (cOA) synthesis activities. The same activities remain dormant in the presence of the self or non-cognate target RNA (NTR) that differs from CTR only in its 3'-protospacer flanking sequence (3'-PFS). Here we employ electron cryomicroscopy (cryoEM), functional assays, and comparative cross-linking to study in vivo assembled mesophilic Lactococcus lactis Csm (LlCsm) at the three functional states: apo, the CTR- and the NTR-bound. Unlike previously studied Csm complexes, we observed binding of 3'-PFS to Csm in absence of bound ATP and analyzed the structures of the four RNA cleavage sites. Interestingly, comparative crosslinking results indicate a tightening of the Csm3-Csm4 interface as a result of CTR but not NTR binding, reflecting a possible role of protein dynamics change during activation.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, 32306, USA. hong.li@fsu.edu.



Macromolecules

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR-associated protein Cas10A756Lactococcus 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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR-associated protein Csm4B296Lactococcus 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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR-associated protein Csm3C [auth F],
E [auth G],
D [auth H],
F [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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR-associated protein Csm5G [auth J]352Lactococcus 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
Protein Feature View
Expand
  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
CRISPR-associated protein Csm2I [auth C],
J [auth D],
K [auth E]
139Lactococcus 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
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 5
MoleculeChainsLengthOrganismImage
Crispr RNAH [auth R]37Lactococcus lactis subsp. lactis
Protein Feature View
Expand
  • Reference Sequence
Find similar nucleic acids by:  (by identity cutoff)  |  3D Structure
Entity ID: 7
MoleculeChainsLengthOrganismImage
target RNAL [auth T]34Lactococcus lactis subsp. lactis
Protein Feature View
Expand
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.00 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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 StatesR01 GM099604

Revision History  (Full details and data files)

  • Version 1.0: 2022-01-12
    Type: Initial release
  • Version 1.1: 2022-04-13
    Changes: Database references