6O1O

Cryo-EM structure of the T. thermophilus Csm complex bound to target ssRNA

  • Classification: RNA BINDING PROTEIN/RNA
  • Organism(s): Thermus thermophilus
  • Expression System: Escherichia coli
  • Mutation(s): No 

  • Deposited: 2019-02-21 Released: 2019-07-10 
  • Deposition Author(s): Liu, J.J., Liu, T.Y.
  • Funding Organization(s): Howard Hughes Medical Institute (HHMI), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), Life Sciences Research Foundation

Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Target preference of Type III-A CRISPR-Cas complexes at the transcription bubble.

Liu, T.Y., Liu, J.J., Aditham, A.J., Nogales, E., Doudna, J.A.

(2019) Nat Commun 10: 3001-3001

  • DOI: 10.1038/s41467-019-10780-2
  • Primary Citation of Related Structures:  
    6O1O

  • PubMed Abstract: 

    • Type III-A CRISPR-Cas systems are prokaryotic RNA-guided adaptive immune systems that use a protein-RNA complex, Csm, for transcription-dependent immunity against foreign DNA. Csm can cleave RNA and single-stranded DNA (ssDNA), but whether it targets one or both nucleic acids during transcription elongation is unknown ...

    Type III-A CRISPR-Cas systems are prokaryotic RNA-guided adaptive immune systems that use a protein-RNA complex, Csm, for transcription-dependent immunity against foreign DNA. Csm can cleave RNA and single-stranded DNA (ssDNA), but whether it targets one or both nucleic acids during transcription elongation is unknown. Here, we show that binding of a Thermus thermophilus (T. thermophilus) Csm (TthCsm) to a nascent transcript in a transcription elongation complex (TEC) promotes tethering but not direct contact of TthCsm with RNA polymerase (RNAP). Biochemical experiments show that both TthCsm and Staphylococcus epidermidis (S. epidermidis) Csm (SepCsm) cleave RNA transcripts, but not ssDNA, at the transcription bubble. Taken together, these results suggest that Type III systems primarily target transcripts, instead of unwound ssDNA in TECs, for immunity against double-stranded DNA (dsDNA) phages and plasmids. This reveals similarities between Csm and eukaryotic RNA interference, which also uses RNA-guided RNA targeting to silence actively transcribed genes.

    Organizational Affiliation: 

    Department of Chemistry, University of California, Berkeley, CA, 94720, USA. doudna@berkeley.edu.



Macromolecules

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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Csm1A716Thermus thermophilusMutation(s): 0 
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Csm4B, G, H279Thermus thermophilusMutation(s): 0 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Csm3C, D, E, F218Thermus thermophilusMutation(s): 0 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Csm2I, J, K, L118Thermus thermophilusMutation(s): 0 
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Entity ID: 5
MoleculeChainsLengthOrganismImage
RNA (36-MER)M48Thermus thermophilus
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Entity ID: 6
MoleculeChainsLengthOrganismImage
RNA (30-MER)N50Thermus thermophilus
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Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 3.80 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Howard Hughes Medical Institute (HHMI)United States--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesP01GM051487
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesF32GM122334
Life Sciences Research FoundationUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2019-07-10
    Type: Initial release
  • Version 1.1: 2019-07-17
    Changes: Data collection, Database references
  • Version 1.2: 2019-11-20
    Changes: Author supporting evidence