+Open data
-Basic information
Entry | Database: PDB / ID: 8bmw | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | SsoCsm | |||||||||
Components |
| |||||||||
Keywords | RNA BINDING PROTEIN / Sulfolobus / Type III CRISPR | |||||||||
Function / homology | Function and homology information | |||||||||
Biological species | Saccharolobus solfataricus (archaea) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | |||||||||
Authors | Spagnolo, L. / White, M.F. | |||||||||
Funding support | United Kingdom, European Union, 2items
| |||||||||
Citation | Journal: Curr Res Struct Biol / Year: 2023 Title: Structure of the type III-D CRISPR effector. Authors: Giuseppe Cannone / Dmytro Kompaniiets / Shirley Graham / Malcolm F White / Laura Spagnolo / Abstract: CRISPR-Cas is a prokaryotic adaptive immune system, classified into six different types, each characterised by a signature protein. Type III systems, classified based on the presence of a Cas10 ...CRISPR-Cas is a prokaryotic adaptive immune system, classified into six different types, each characterised by a signature protein. Type III systems, classified based on the presence of a Cas10 subunit, are rather diverse multi-subunit assemblies with a range of enzymatic activities and downstream ancillary effectors. The broad array of current biotechnological CRISPR applications is mainly based on proteins classified as Type II, however recent developments established the feasibility and efficacy of multi-protein Type III CRISPR-Cas effector complexes as RNA-targeting tools in eukaryotes. The crenarchaeon has two type III system subtypes (III-B and III-D). Here, we report the cryo-EM structure of the Csm Type III-D complex from (SsoCsm), which uses CRISPR RNA to bind target RNA molecules, activating the Cas10 subunit for antiviral defence. The structure reveals the complex organisation, subunit/subunit connectivity and protein/guide RNA interactions of the SsoCsm complex, one of the largest CRISPR effectors known. | |||||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8bmw.cif.gz | 620 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8bmw.ent.gz | 513 KB | Display | PDB format |
PDBx/mmJSON format | 8bmw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bmw_validation.pdf.gz | 840.2 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 8bmw_full_validation.pdf.gz | 899.3 KB | Display | |
Data in XML | 8bmw_validation.xml.gz | 91.9 KB | Display | |
Data in CIF | 8bmw_validation.cif.gz | 143.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/8bmw ftp://data.pdbj.org/pub/pdb/validation_reports/bm/8bmw | HTTPS FTP |
-Related structure data
Related structure data | 16126MC M: map data used to model this data C: citing same article (ref.) |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
Other databases |
|
-Links
-Assembly
Deposited unit |
|
---|---|
1 |
|
-Components
-CRISPR-associated Cas7 paralog (Type III- ... , 5 types, 7 molecules JLNGFHI
#2: Protein | Mass: 30536.256 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus (archaea) / References: UniProt: A0A157T1A2 | ||
---|---|---|---|
#3: Protein | Mass: 22781.088 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus (archaea) / References: UniProt: A0A157T2I3 | ||
#4: Protein | Mass: 28961.107 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus (archaea) / References: UniProt: A0A157T1J6 | ||
#6: Protein | Mass: 27715.232 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus (archaea) / References: UniProt: A0A157T0X8 #7: Protein | Mass: 31226.941 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus (archaea) / References: UniProt: A0A157T120 |
-CRISPR-associated protein ... , 2 types, 2 molecules KM
#8: Protein | Mass: 94935.594 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus (archaea) / References: UniProt: A0A157T112 |
---|---|
#9: Protein | Mass: 34497.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus (archaea) / References: UniProt: A0A157T1I2 |
-Protein / RNA chain , 2 types, 6 molecules ABCDER
#1: Protein | Mass: 15971.459 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus (archaea) / References: UniProt: A0A157T170 #5: RNA chain | | Mass: 14821.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus (archaea) |
---|
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
---|---|
EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: SsoCsm / Type: COMPLEX / Details: Type III-D CRISPR system / Entity ID: all / Source: NATURAL |
---|---|
Source (natural) | Organism: Saccharolobus solfataricus (archaea) |
Buffer solution | pH: 7.5 |
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 |
---|---|
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 / Nominal defocus max: 0 nm / Nominal defocus min: 0 nm |
Image recording | Electron dose: 34 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k) |
-Processing
Software | Name: PHENIX / Version: 1.20.1_4487: / Classification: refinement | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 192787 / Symmetry type: POINT | ||||||||||||||||||||||||
Refine LS restraints |
|