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Yorodumi- PDB-6o1o: Cryo-EM structure of the T. thermophilus Csm complex bound to tar... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6o1o | |||||||||||||||
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Title | Cryo-EM structure of the T. thermophilus Csm complex bound to target ssRNA | |||||||||||||||
Components |
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Keywords | RNA BINDING PROTEIN/RNA / Csm / RNA substrate / RNA BINDING PROTEIN / RNA BINDING PROTEIN-RNA complex | |||||||||||||||
Function / homology | RNA / RNA (> 10) Function and homology information | |||||||||||||||
Biological species | Thermus thermophilus (bacteria) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||||||||
Authors | Liu, J.J. / Liu, T.Y. | |||||||||||||||
Funding support | United States, 4items
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Citation | Journal: Nat Commun / Year: 2019 Title: Target preference of Type III-A CRISPR-Cas complexes at the transcription bubble. Authors: Tina Y Liu / Jun-Jie Liu / Abhishek J Aditham / Eva Nogales / Jennifer A Doudna / 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 ...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. | |||||||||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6o1o.cif.gz | 330.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6o1o.ent.gz | 268.3 KB | Display | PDB format |
PDBx/mmJSON format | 6o1o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6o1o_validation.pdf.gz | 725.3 KB | Display | wwPDB validaton report |
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Full document | 6o1o_full_validation.pdf.gz | 747.3 KB | Display | |
Data in XML | 6o1o_validation.xml.gz | 39.2 KB | Display | |
Data in CIF | 6o1o_validation.cif.gz | 76.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/o1/6o1o ftp://data.pdbj.org/pub/pdb/validation_reports/o1/6o1o | HTTPS FTP |
-Related structure data
Related structure data | 0454MC 0455C M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Protein , 4 types, 12 molecules ABGHCDEFIJKL
#1: Protein | Mass: 60953.055 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli) | ||||
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#2: Protein | Mass: 23762.168 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli) #3: Protein | Mass: 18570.826 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli) #4: Protein | Mass: 10060.393 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermus thermophilus (bacteria) / Production host: Escherichia coli (E. coli) |
-RNA chain , 2 types, 2 molecules MN
#5: RNA chain | Mass: 15537.359 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria) |
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#6: RNA chain | Mass: 15995.450 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermus thermophilus (bacteria) |
-Details
Sequence details | The complete sequence of Csm1 is MASMLGDGLSVALAGLLHDVGKLYSRARWGERDDQVPDRTHTAYTAHFVREHAGLFRGAG ...The complete sequence of Csm1 is MASMLGDGLS |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Thermus thermophilus Csm complex bound to target ssRNA Type: COMPLEX / Entity ID: all / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Thermus thermophilus (bacteria) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.9 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 45 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 87321 / Symmetry type: POINT |