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Yorodumi- EMDB-0454: Cryo-EM structure of the T. thermophilus Csm complex bound to tar... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0454 | |||||||||||||||
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Title | Cryo-EM structure of the T. thermophilus Csm complex bound to target ssRNA | |||||||||||||||
Map data | RNA-protein complex | |||||||||||||||
Sample |
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Keywords | Csm / RNA substrate / RNA BINDING PROTEIN | |||||||||||||||
Biological species | Thermus thermophilus (bacteria) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||||||||
Authors | Liu JJ / Liu TY | |||||||||||||||
Funding support | United States, 4 items
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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 | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0454.map.gz | 120.8 MB | EMDB map data format | |
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Header (meta data) | emd-0454-v30.xml emd-0454.xml | 8.5 KB 8.5 KB | Display Display | EMDB header |
Images | emd_0454.png | 46.7 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0454 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0454 | HTTPS FTP |
-Related structure data
Related structure data | 6o1oMC 0455C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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-Map
File | Download / File: emd_0454.map.gz / Format: CCP4 / Size: 209.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | RNA-protein complex | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Thermus thermophilus Csm complex bound to target ssRNA
Entire | Name: Thermus thermophilus Csm complex bound to target ssRNA |
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Components |
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-Supramolecule #1: Thermus thermophilus Csm complex bound to target ssRNA
Supramolecule | Name: Thermus thermophilus Csm complex bound to target ssRNA type: complex / ID: 1 / Parent: 0 / Macromolecule list: all |
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Source (natural) | Organism: Thermus thermophilus (bacteria) |
-Macromolecule #1: RNA
Macromolecule | Name: RNA / type: rna / ID: 1 |
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Source (natural) | Organism: Thermus thermophilus (bacteria) |
Sequence | String: GGAUAUGCGC CUUGACGUGG UCGUCCCCGG GCGCCUUAUC UACGGUAUCA |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.9 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy |
Image recording | Film or detector model: DIRECT ELECTRON DE-16 (4k x 4k) / Average electron dose: 45.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: NONE |
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Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 87321 |