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- PDB-8bmw: SsoCsm -

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Basic information

Entry
Database: PDB / ID: 8bmw
TitleSsoCsm
Components
  • (CRISPR-associated Cas7 paralog (Type III- ...) x 5
  • (CRISPR-associated protein ...) x 2
  • CRISPR-associated small subunit protein (Type III-D)
  • RNA (48-MER)
KeywordsRNA BINDING PROTEIN / Sulfolobus / Type III CRISPR
Function / homology
Function and homology information


defense response to virus
Similarity search - Function
CRISPR-associated RAMP TM1809 / Uncharacterised conserved protein UCP032748 / CRISPR type III-associated protein / RAMP superfamily / HD domain / HD domain / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
RNA / RNA (> 10) / CRISPR-associated Cas7 paralog (Type III-D) / CRISPR-associated protein Cas10 (Type III-D) / CRISPR-associated Cas7 paralog (Type III-D) / CRISPR-associated small subunit protein (Type III-D) / CRISPR-associated Cas7 paralog (Type III-D) / CRISPR-associated protein Cas5 (Type III-D) / CRISPR-associated Cas7 paralog (Type III-D) / CRISPR-associated Cas7 paralog (Type III-D)
Similarity search - Component
Biological speciesSaccharolobus solfataricus (archaea)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSpagnolo, L. / White, M.F.
Funding support United Kingdom, European Union, 2items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/J005673/1 United Kingdom
European Research Council (ERC)101018608European Union
CitationJournal: 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
DepositionNov 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Mar 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CRISPR-associated small subunit protein (Type III-D)
B: CRISPR-associated small subunit protein (Type III-D)
C: CRISPR-associated small subunit protein (Type III-D)
D: CRISPR-associated small subunit protein (Type III-D)
E: CRISPR-associated small subunit protein (Type III-D)
J: CRISPR-associated Cas7 paralog (Type III-D)
L: CRISPR-associated Cas7 paralog (Type III-D)
N: CRISPR-associated Cas7 paralog (Type III-D)
R: RNA (48-MER)
G: CRISPR-associated Cas7 paralog (Type III-D)
F: CRISPR-associated Cas7 paralog (Type III-D)
H: CRISPR-associated Cas7 paralog (Type III-D)
I: CRISPR-associated Cas7 paralog (Type III-D)
K: CRISPR-associated protein Cas10 (Type III-D)
M: CRISPR-associated protein Cas5 (Type III-D)


Theoretical massNumber of molelcules
Total (without water)424,27515
Polymers424,27515
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: mass spectrometry
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

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CRISPR-associated Cas7 paralog (Type III- ... , 5 types, 7 molecules JLNGFHI

#2: Protein CRISPR-associated Cas7 paralog (Type III-D)


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 CRISPR-associated Cas7 paralog (Type III-D)


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 CRISPR-associated Cas7 paralog (Type III-D)


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 CRISPR-associated Cas7 paralog (Type III-D) / CRISPR-associated RAMP 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 CRISPR-associated Cas7 paralog (Type III-D) / CRISPR-associated RAMP protein


Mass: 31226.941 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus (archaea) / References: UniProt: A0A157T120

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CRISPR-associated protein ... , 2 types, 2 molecules KM

#8: Protein CRISPR-associated protein Cas10 (Type III-D)


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 CRISPR-associated protein Cas5 (Type III-D)


Mass: 34497.805 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus (archaea) / References: UniProt: A0A157T1I2

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Protein / RNA chain , 2 types, 6 molecules ABCDER

#1: Protein
CRISPR-associated small subunit protein (Type III-D)


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 RNA (48-MER)


Mass: 14821.234 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Saccharolobus solfataricus (archaea)

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: SsoCsm / Type: COMPLEX / Details: Type III-D CRISPR system / Entity ID: all / Source: NATURAL
Source (natural)Organism: Saccharolobus solfataricus (archaea)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 0 nm / Nominal defocus min: 0 nm
Image recordingElectron dose: 34 e/Å2 / Film or detector model: GATAN K2 BASE (4k x 4k)

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Processing

SoftwareName: PHENIX / Version: 1.20.1_4487: / Classification: refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 192787 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00329237
ELECTRON MICROSCOPYf_angle_d0.42739593
ELECTRON MICROSCOPYf_dihedral_angle_d11.2194386
ELECTRON MICROSCOPYf_chiral_restr0.0384524
ELECTRON MICROSCOPYf_plane_restr0.0024852

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