8DO6

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


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

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Literature

The structure of a Type III-A CRISPR-Cas effector complex reveals conserved and idiosyncratic contacts to target RNA and crRNA among Type III-A systems.

Paraan, M.Nasef, M.Chou-Zheng, L.Khweis, S.A.Schoeffler, A.J.Hatoum-Aslan, A.Stagg, S.M.Dunkle, J.A.

(2023) PLoS One 18: e0287461-e0287461

  • DOI: https://doi.org/10.1371/journal.pone.0287461
  • Primary Citation of Related Structures:  
    8DO6

  • PubMed Abstract: 

    Type III CRISPR-Cas systems employ multiprotein effector complexes bound to small CRISPR RNAs (crRNAs) to detect foreign RNA transcripts and elicit a complex immune response that leads to the destruction of invading RNA and DNA. Type III systems are among the most widespread in nature, and emerging interest in harnessing these systems for biotechnology applications highlights the need for detailed structural analyses of representatives from diverse organisms. We performed cryo-EM reconstructions of the Type III-A Cas10-Csm effector complex from S. epidermidis bound to an intact, cognate target RNA and identified two oligomeric states, a 276 kDa complex and a 318 kDa complex. 3.1 Å density for the well-ordered 276 kDa complex allowed construction of atomic models for the Csm2, Csm3, Csm4 and Csm5 subunits within the complex along with the crRNA and target RNA. We also collected small-angle X-ray scattering data which was consistent with the 276 kDa Cas10-Csm architecture we identified. Detailed comparisons between the S. epidermidis Cas10-Csm structure and the well-resolved bacterial (S. thermophilus) and archaeal (T. onnurineus) Cas10-Csm structures reveal differences in how the complexes interact with target RNA and crRNA which are likely to have functional ramifications. These structural comparisons shed light on the unique features of Type III-A systems from diverse organisms and will assist in improving biotechnologies derived from Type III-A effector complexes.


  • Organizational Affiliation

    National Center for In-situ Tomographic Ultramicroscopy, Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, United States of America.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR system Cms endoribonuclease Csm3A [auth E],
B [auth G],
C [auth F]
214Staphylococcus epidermidis RP62AMutation(s): 0 
Gene Names: SERP2459
UniProt
Find proteins for Q5HK91 (Staphylococcus epidermidis (strain ATCC 35984 / RP62A))
Explore Q5HK91 
Go to UniProtKB:  Q5HK91
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5HK91
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  • Reference Sequence
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR system Cms protein Csm2F [auth C],
G [auth D]
141Staphylococcus epidermidis RP62AMutation(s): 0 
Gene Names: csm2E1M97_06325E1M99_06625
UniProt
Find proteins for A0A2R3SZR9 (Staphylococcus epidermidis)
Explore A0A2R3SZR9 
Go to UniProtKB:  A0A2R3SZR9
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Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA0A2R3SZR9
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  • Reference Sequence
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR system Cms protein Csm4H [auth B]304Staphylococcus epidermidis RP62AMutation(s): 0 
Gene Names: SERP2458
UniProt
Find proteins for Q5HK92 (Staphylococcus epidermidis (strain ATCC 35984 / RP62A))
Explore Q5HK92 
Go to UniProtKB:  Q5HK92
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ5HK92
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  • Reference Sequence
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Entity ID: 6
MoleculeChains Sequence LengthOrganismDetailsImage
CRISPR system Cms protein Csm5I [auth H]340Staphylococcus epidermidis RP62AMutation(s): 0 
Gene Names: SERP2457
UniProt
Find proteins for Q5HK93 (Staphylococcus epidermidis (strain ATCC 35984 / RP62A))
Explore Q5HK93 
Go to UniProtKB:  Q5HK93
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UniProt GroupQ5HK93
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  • Reference Sequence
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Entity ID: 2
MoleculeChains LengthOrganismImage
crRNAD [auth I]37Staphylococcus epidermidis RP62A
Sequence Annotations
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Entity ID: 3
MoleculeChains LengthOrganismImage
Target RNAE [auth J]43Staphylococcus epidermidis RP62A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.10 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 
EM Software:
TaskSoftware PackageVersion
RECONSTRUCTIONcryoSPARC

Structure Validation

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Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesR35GM142966

Revision History  (Full details and data files)

  • Version 1.0: 2023-06-21
    Type: Initial release
  • Version 1.1: 2023-07-05
    Changes: Database references