6O1O | pdb_00006o1o

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

• PDB DOI: https://doi.org/10.2210/pdb6O1O/pdb
• EM Map EMD-0454: EMDB EMDataResource
• NAKB: 6O1O

• 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

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Experimental Data Snapshot

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

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

• PubMed: 31278272 
• DOI: https://doi.org/10.1038/s41467-019-10780-2
• Primary Citation 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. 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.

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Organizational Affiliation: 
• Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA.
California Institute for Quantitative Biosciences, Berkeley, CA, 94720, USA.
Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA.
Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA.
Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94720, USA. [e-mail].
California Institute for Quantitative Biosciences, Berkeley, CA, 94720, USA. [e-mail].
Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA. [e-mail].
Howard Hughes Medical Institute, University of California, Berkeley, CA, 94720, USA. [e-mail].
Gladstone Institutes, San Francisco, CA, 94158, USA. [e-mail].
Innovative Genomics Institute, University of California, Berkeley, CA, 94720, USA. [e-mail].
Department of Chemistry, University of California, Berkeley, CA, 94720, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 12-mer - A7B4C1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 12-mer - A6B4C1D1 

Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 4-mer - B4 Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Hetero 6-mer - A3B3 Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 Local Symmetry: Helical - H  (Explore in 3D)
Local Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 278.3 kDa 
• Atom Count: 15,193 
• Modeled Residue Count: 2,823 
• Deposited Residue Count: 2,995 
• Unique protein chains: 4
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Csm1	A	716	Thermus thermophilus	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Csm4	B, G, H	279	Thermus thermophilus	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Csm3	C, D, E, F	218	Thermus thermophilus	Mutation(s): 0

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Csm2	I, J, K, L	118	Thermus thermophilus	Mutation(s): 0

Entity ID: 5
Molecule	Chains	Length	Organism	Image
RNA (36-MER)	M	48	Thermus thermophilus

Entity ID: 6
Molecule	Chains	Length	Organism	Image
RNA (30-MER)	N	50	Thermus thermophilus

Experimental Data & Validation

Experimental Data

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2019-07-10 
Deposition Author(s): Liu, J.J., Liu, T.Y.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P01GM051487
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	F32GM122334
Life Sciences Research Foundation	United States	--

Revision History  

• 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
• Version 1.3: 2024-03-13
  Changes: Data collection, Database references