[English] 日本語
Yorodumi- PDB-6s8e: Cryo-EM structure of the type III-B Cmr-beta complex bound to non... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s8e | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | Cryo-EM structure of the type III-B Cmr-beta complex bound to non-cognate target RNA | ||||||||||||
Components |
| ||||||||||||
Keywords | ANTIVIRAL PROTEIN / CRISPR-Cas / Effector complex / nuclease / cyclic oligo-adenylate synthase | ||||||||||||
Function / homology | Function and homology information | ||||||||||||
Biological species | Sulfolobus islandicus REY15A (acidophilic) synthetic construct (others) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||
Authors | Sofos, N. / Montoya, G. / Stella, S. | ||||||||||||
Funding support | Denmark, 3items
| ||||||||||||
Citation | Journal: Mol Cell / Year: 2020 Title: Structures of the Cmr-β Complex Reveal the Regulation of the Immunity Mechanism of Type III-B CRISPR-Cas. Authors: Nicholas Sofos / Mingxia Feng / Stefano Stella / Tillmann Pape / Anders Fuglsang / Jinzhong Lin / Qihong Huang / Yingjun Li / Qunxin She / Guillermo Montoya / Abstract: Cmr-β is a type III-B CRISPR-Cas complex that, upon target RNA recognition, unleashes a multifaceted immune response against invading genetic elements, including single-stranded DNA (ssDNA) ...Cmr-β is a type III-B CRISPR-Cas complex that, upon target RNA recognition, unleashes a multifaceted immune response against invading genetic elements, including single-stranded DNA (ssDNA) cleavage, cyclic oligoadenylate synthesis, and also a unique UA-specific single-stranded RNA (ssRNA) hydrolysis by the Cmr2 subunit. Here, we present the structure-function relationship of Cmr-β, unveiling how binding of the target RNA regulates the Cmr2 activities. Cryoelectron microscopy (cryo-EM) analysis revealed the unique subunit architecture of Cmr-β and captured the complex in different conformational stages of the immune response, including the non-cognate and cognate target-RNA-bound complexes. The binding of the target RNA induces a conformational change of Cmr2, which together with the complementation between the 5' tag in the CRISPR RNAs (crRNA) and the 3' antitag of the target RNA activate different configurations in a unique loop of the Cmr3 subunit, which acts as an allosteric sensor signaling the self- versus non-self-recognition. These findings highlight the diverse defense strategies of type III complexes. #1: Journal: Biorxiv / Year: 2020 Title: Structures of the Cmr-beta Complex Reveal the Regulation of the Immunity Mechanism of Type III-B CRISPR-Cas Authors: Sofos, N. / Feng, M. / Stella, S. / Pape, T. / Fuglsang, A. / Lin, J. / Huang, Q. / Li, Y. / She, Q. / Montoya, G. | ||||||||||||
History |
|
-Structure visualization
Movie |
Movie viewer |
---|---|
Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6s8e.cif.gz | 1.3 MB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6s8e.ent.gz | 1.1 MB | Display | PDB format |
PDBx/mmJSON format | 6s8e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s8/6s8e ftp://data.pdbj.org/pub/pdb/validation_reports/s8/6s8e | HTTPS FTP |
---|
-Related structure data
Related structure data | 10119MC 6s6bC 6s8bC 6s91C 6sh8C 6shbC 6sicC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-CRISPR-associated protein, ... , 3 types, 5 molecules ABCHK
#1: Protein | Mass: 17961.834 Da / Num. of mol.: 3 / Source method: isolated from a natural source Source: (natural) Sulfolobus islandicus REY15A (acidophilic) Strain: REY15A / References: UniProt: F0NDX5 #3: Protein | | Mass: 36008.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Sulfolobus islandicus REY15A (acidophilic) Strain: REY15A / References: UniProt: F0NDX1 #6: Protein | | Mass: 120856.453 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Sulfolobus islandicus REY15A (acidophilic) Strain: REY15A / References: UniProt: F0NDX2 |
---|
-CRISPR-associated RAMP protein, ... , 2 types, 5 molecules DEFGI
#2: Protein | Mass: 32322.359 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: Directed mutation of Asp31 to Ala Source: (gene. exp.) Sulfolobus islandicus REY15A (acidophilic) Strain: REY15A / Gene: SiRe_0602 / Production host: Sulfolobus islandicus REY15A (acidophilic) / References: UniProt: F0NDX6 #4: Protein | | Mass: 33945.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: C-terminal histidine-tag added for co-purification of the complex Source: (gene. exp.) Sulfolobus islandicus REY15A (acidophilic) Strain: REY15A / Gene: SiRe_0599 / Plasmid: pAC / Production host: Sulfolobus islandicus REY15A (acidophilic) / References: UniProt: F0NDX3 |
---|
-Protein , 2 types, 23 molecules JXxTWtwLMOPlmopNnQRSqrs
#5: Protein | Mass: 55388.965 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: The N-terminal "MEEELL" sequence is not part of the annotated sequence (F0NDX4) due to an annotation mistake. Source: (natural) Sulfolobus islandicus REY15A (acidophilic) Strain: REY15A / References: UniProt: F0NDX4 |
---|---|
#9: Protein | Mass: 19705.607 Da / Num. of mol.: 22 / Source method: isolated from a natural source Source: (natural) Sulfolobus islandicus REY15A (acidophilic) Strain: REY15A / References: UniProt: F0NDX7 |
-RNA chain , 2 types, 2 molecules UV
#7: RNA chain | Mass: 15881.327 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) |
---|---|
#8: RNA chain | Mass: 16409.871 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Sulfolobus islandicus REY15A (acidophilic) |
-Non-polymers , 1 types, 1 molecules
#10: Chemical | ChemComp-ZN / |
---|
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Type III-B Cmr-beta complex bound to non-cognate target RNA Type: COMPLEX Details: A non-cognate target RNA is bound, i.e. the 3'-anti-tag is complementary to the 5' tag of the crRNA. Cmr7 is part of the complex. Entity ID: #1-#9 / Source: NATURAL | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Molecular weight | Value: 0.9 MDa / Experimental value: YES | |||||||||||||||||||||||||
Source (natural) | Organism: Sulfolobus islandicus REY15A (acidophilic) | |||||||||||||||||||||||||
Buffer solution | pH: 6 | |||||||||||||||||||||||||
Buffer component |
| |||||||||||||||||||||||||
Specimen | Conc.: 0.8 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Details: 5 mA. Model: Leica EM ACE200 / Grid material: GOLD / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil, UltrAuFoil | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K / Details: 3-4 s blotting before plunging |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
---|---|
Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELDBright-field microscopy / Nominal magnification: 96000 X / Nominal defocus max: 2600 nm / Nominal defocus min: 1700 nm / Cs: 2.1 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 19 sec. / Electron dose: 4.5 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 5190 |
-Processing
EM software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 344000 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 98000 / Num. of class averages: 2 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: AB INITIO MODEL / Space: REAL / Target criteria: Cross-correlation coefficient |