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- EMDB-16126: SsoCsm -

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Basic information

Entry
Database: EMDB / ID: EMD-16126
TitleSsoCsm
Map datacombined EM map
Sample
  • Complex: SsoCsm
    • Protein or peptide: CRISPR-associated small subunit protein (Type III-D)
    • Protein or peptide: CRISPR-associated Cas7 paralog (Type III-D)
    • Protein or peptide: CRISPR-associated Cas7 paralog (Type III-D)
    • Protein or peptide: CRISPR-associated Cas7 paralog (Type III-D)
    • RNA: RNA (48-MER)
    • Protein or peptide: CRISPR-associated Cas7 paralog (Type III-D)
    • Protein or peptide: CRISPR-associated Cas7 paralog (Type III-D)
    • Protein or peptide: CRISPR-associated protein Cas10 (Type III-D)
    • Protein or peptide: CRISPR-associated protein Cas5 (Type III-D)
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
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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.5 Å
AuthorsSpagnolo L / White MF
Funding support United Kingdom, European Union, 2 items
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, 2022-
Header (metadata) releaseMar 1, 2023-
Map releaseMar 1, 2023-
UpdateMar 22, 2023-
Current statusMar 22, 2023Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_16126.png

Downloads & links

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Map

FileDownload / File: emd_16126.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationcombined EM map
Voxel sizeX=Y=Z: 1.046 Å
Density
Contour LevelBy AUTHOR: 0.008
Minimum - Maximum-0.0036102654 - 0.06897931
Average (Standard dev.)0.000310444 (±0.0018546397)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 313.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Sample components

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Entire : SsoCsm

EntireName: SsoCsm
Components
  • Complex: SsoCsm
    • Protein or peptide: CRISPR-associated small subunit protein (Type III-D)
    • Protein or peptide: CRISPR-associated Cas7 paralog (Type III-D)
    • Protein or peptide: CRISPR-associated Cas7 paralog (Type III-D)
    • Protein or peptide: CRISPR-associated Cas7 paralog (Type III-D)
    • RNA: RNA (48-MER)
    • Protein or peptide: CRISPR-associated Cas7 paralog (Type III-D)
    • Protein or peptide: CRISPR-associated Cas7 paralog (Type III-D)
    • Protein or peptide: CRISPR-associated protein Cas10 (Type III-D)
    • Protein or peptide: CRISPR-associated protein Cas5 (Type III-D)

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Supramolecule #1: SsoCsm

SupramoleculeName: SsoCsm / type: complex / ID: 1 / Chimera: Yes / Parent: 0 / Macromolecule list: #1-#9 / Details: Type III-D CRISPR system
Source (natural)Organism: Saccharolobus solfataricus (archaea)

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

MacromoleculeName: CRISPR-associated small subunit protein (Type III-D) / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus (archaea)
Molecular weightTheoretical: 15.971459 KDa
SequenceString:
MRVKHYIQRE FNYSVSSQDL LDIATRIAIS AIKPKPKSNK PEPYVDSSTI NSLLSFLQSR RNVNELLLYI MRQAGRDEID EETGKLLLA SLKDRELKDA VNLLGYVKWV YDTLTGLKVN YNNVKGVKTF KELVNILSKV

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

MacromoleculeName: CRISPR-associated Cas7 paralog (Type III-D) / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus (archaea)
Molecular weightTheoretical: 30.536256 KDa
SequenceString: RSPIRRSNYT PRNEKGLEGV IELQLNVVSD YLHVGSGKYD VEVMRSVSDV KRLVEDYLSG GNKRIPNNVD QYFSMVAFLM VRNKDNVVI PGSTIKGMVR SRLELSVPGS CYIVTGHSTS SSAVYKRIFN PDPNRGSDRF DVNKFPQVCP VCDLLGNMGL A SRVSLSDF ...String:
RSPIRRSNYT PRNEKGLEGV IELQLNVVSD YLHVGSGKYD VEVMRSVSDV KRLVEDYLSG GNKRIPNNVD QYFSMVAFLM VRNKDNVVI PGSTIKGMVR SRLELSVPGS CYIVTGHSTS SSAVYKRIFN PDPNRGSDRF DVNKFPQVCP VCDLLGNMGL A SRVSLSDF VMTSGKVDYV NVKGRDYEVV TKGSIFAGKV LYKSLKPVEI GMLLYGFGFV KDCNGSKVML LGRFKFSDKR FG RVKFSLK TPIADCNKLV SDFVKQFNPR YINEE

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Macromolecule #3: CRISPR-associated Cas7 paralog (Type III-D)

MacromoleculeName: CRISPR-associated Cas7 paralog (Type III-D) / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus (archaea)
Molecular weightTheoretical: 22.781088 KDa
SequenceString: MIPIKVSMRN LSSLTIAGGS TISSIDIPLN PLGVPPSTIK GTMRTAVHNL LPNGYTSCGE VEPESIREAH KNGVCDVCKL FGYPDSLTG CFTIDVSKTD YRTSYITRVS IDDKTQRAKE GSLFTQQIIL PNSDISFTVY YNCNDERLFK LLLYSILDLR Y WRLGRNTM ...String:
MIPIKVSMRN LSSLTIAGGS TISSIDIPLN PLGVPPSTIK GTMRTAVHNL LPNGYTSCGE VEPESIREAH KNGVCDVCKL FGYPDSLTG CFTIDVSKTD YRTSYITRVS IDDKTQRAKE GSLFTQQIIL PNSDISFTVY YNCNDERLFK LLLYSILDLR Y WRLGRNTM IDVKVNNVEE ICKSVKCDEE INGILNQLSR YLWE

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Macromolecule #4: CRISPR-associated Cas7 paralog (Type III-D)

MacromoleculeName: CRISPR-associated Cas7 paralog (Type III-D) / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus (archaea)
Molecular weightTheoretical: 28.961107 KDa
SequenceString: MVIQVFRLNF RLRTGFRVGG GQEVGDNVIR QLRIGVEGVM IPASSWKGMF RRVSEIVLNS EDHFEEHSKK EVDTRTINAL LKSDEKFRR IAISKVGKEV ITQNGINVDK LDSESLSDLR RIYNEYNCPI ERLYGSNYFA GGITISDSVI PNASIMERTH V TIERKSKK ...String:
MVIQVFRLNF RLRTGFRVGG GQEVGDNVIR QLRIGVEGVM IPASSWKGMF RRVSEIVLNS EDHFEEHSKK EVDTRTINAL LKSDEKFRR IAISKVGKEV ITQNGINVDK LDSESLSDLR RIYNEYNCPI ERLYGSNYFA GGITISDSVI PNASIMERTH V TIERKSKK ASEKHLFSEE IIDAEKIEVK VIVRNEFELW KNSLKLLREI GYFIGGSKSR GIGYIVLDEK ESEYAVINNF SE TPKFSEL KRYLS

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Macromolecule #6: CRISPR-associated Cas7 paralog (Type III-D)

MacromoleculeName: CRISPR-associated Cas7 paralog (Type III-D) / type: protein_or_peptide / ID: 6 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus (archaea)
Molecular weightTheoretical: 27.715232 KDa
SequenceString: MSCMDLDVIT TVVKIEGKLR NETLLRVGKG KTQDFAEATD NPIIKYRDRP LIPGSSLKGA FRSLVESYTK SLNDSKYYVC DLDDNSCVS CEEKKKDNGI VEGRYCIPCI LFGFKDLASR VYILDAIAEK YSISQRTMVA INRVFGGQMP GHLYTLDYVD P GSEFSFMM ...String:
MSCMDLDVIT TVVKIEGKLR NETLLRVGKG KTQDFAEATD NPIIKYRDRP LIPGSSLKGA FRSLVESYTK SLNDSKYYVC DLDDNSCVS CEEKKKDNGI VEGRYCIPCI LFGFKDLASR VYILDAIAEK YSISQRTMVA INRVFGGQMP GHLYTLDYVD P GSEFSFMM MIYNLNLIEG EKDWKAKSVE ALKFLLATLV REGIFVGARK SVGYGLIKLV DAKVSLYKAP DHLVSPVIVK KL EEVIGTN G

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Macromolecule #7: CRISPR-associated Cas7 paralog (Type III-D)

MacromoleculeName: CRISPR-associated Cas7 paralog (Type III-D) / type: protein_or_peptide / ID: 7 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus (archaea)
Molecular weightTheoretical: 31.226941 KDa
SequenceString: MVNYTFIDKR VIKRTTMIEG DVETVSPLKI GGGKDNFDPS SLAKDSILKD VEGRPIIPGS SWKGIFRSTG ERILRLRNIE VCSGIGKDY CLNNNRKERD FNSALKENVD QALEIFWDYT CLNCKVFGTM SVIGAVRFLD SLPISYSLNT RSMIAISRTE G AVARRALV ...String:
MVNYTFIDKR VIKRTTMIEG DVETVSPLKI GGGKDNFDPS SLAKDSILKD VEGRPIIPGS SWKGIFRSTG ERILRLRNIE VCSGIGKDY CLNNNRKERD FNSALKENVD QALEIFWDYT CLNCKVFGTM SVIGAVRFLD SLPISYSLNT RSMIAISRTE G AVARRALV TVEYVDVGSK FSFKMMGYNL PNYAIGYLIT IMKNIHDGFT QVGGHKSRGF GFVKFGKVKF TDLGEKRIGD ED IQVKDVG DLVEGNGDEF FGRMKPFMEA FNNAKIPYPK K

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

MacromoleculeName: CRISPR-associated protein Cas10 (Type III-D) / type: protein_or_peptide / ID: 8 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus (archaea)
Molecular weightTheoretical: 94.935594 KDa
SequenceString: MIRGKLLLPE KKVVFINESE VQSLRKDVVD ALKVFSSLAC ELADNNETKA TNIFADLISM IYKLPMLISY VPSDKLSTPH EYFFAYIVF RHLVEDSMPS NDIAKLLEIL EEKKRDEIKE VLDYARTLRK IYEKLLYVPA DTRPGYNFTS LASHLQLSSI L VWLLQKGS ...String:
MIRGKLLLPE KKVVFINESE VQSLRKDVVD ALKVFSSLAC ELADNNETKA TNIFADLISM IYKLPMLISY VPSDKLSTPH EYFFAYIVF RHLVEDSMPS NDIAKLLEIL EEKKRDEIKE VLDYARTLRK IYEKLLYVPA DTRPGYNFTS LASHLQLSSI L VWLLQKGS VDLNYLRISA LLHDIGKLFN PTNHVSESIK ILDEVIEGSE CLKTNLSRVK SLVEQHHAPL ETILNDADRL AA STDRFSE IVKGALNNTK IGECYSLCYG RDVRTKECME CLEEYGEETY SEESKRLYDV ISNSVVSQKV EGNAIGYLVY IDF PGIQRF ITSFPKLREM SFASFLVDFV TSIYSFIVLD QAYYERTGKK SRIPAEALLS GYGGHSYIIV RSDFGSKDEV KAWL ESVSS SALSKLGIRL DVKVADFAYE NYVRNYKEVY EDMMSKSYER YLIRDEGKVY SYGLHRVCDN CGIRPAVNRS DDGEY LCET CNLVRDLSKN RGFIAKYKSK YTLYEEQRIE ISPKEDIKFK LDKNQDPTSY AMEIIAGYRT TSDSRYIALI KADGNN AGK IFGNTVTFSE YVDKSFRLDF GVKKMFYDTL LDIMRASSDE SIKKDLVSRI LLGVLYLGGD DIMLLSPSAI AVPFAVK MF KRSLEYTGFT FKVGIISVKP DHPVQFAYGA VNALMEESKI HTGEKSSIGV LVFSSTLASE GVVKSDLKNY RKEKESFL V VSNDVDDVER LLNLMELDDF GKLMELYWNP EEGRKVIRDK IRSLERFVNY ADTHDFYNTL AYLIRSKAKS EENSLIKRI IDLTIKGRDD FVFPLYDYYF ILKSIRVGI

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Macromolecule #9: CRISPR-associated protein Cas5 (Type III-D)

MacromoleculeName: CRISPR-associated protein Cas5 (Type III-D) / type: protein_or_peptide / ID: 9 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Saccharolobus solfataricus (archaea)
Molecular weightTheoretical: 34.497805 KDa
SequenceString: MILIKLKVKG YITTQMRRIR NYYFSITNYI PSTTLRGAIL AEYYNQTGKI DENFYVSPAY PIKTAPAHYF SPAKERKGDE FIEVKRILE KKEKEFEANK PIEEIMKLEI DGKHPKPKIG SLITYEGETD KENKYREFSS KSIIQMHVAI DKTSISSYKG M LFAYEYKE ...String:
MILIKLKVKG YITTQMRRIR NYYFSITNYI PSTTLRGAIL AEYYNQTGKI DENFYVSPAY PIKTAPAHYF SPAKERKGDE FIEVKRILE KKEKEFEANK PIEEIMKLEI DGKHPKPKIG SLITYEGETD KENKYREFSS KSIIQMHVAI DKTSISSYKG M LFAYEYKE FDEMWAIASD SEVIDTVKRI KIGRGKNRGN KVVDVEKVRE VSLDQSKGLL YCLSPCIGSL FGKTFFKAKY II GDKSIYS GWFTVDSFSG QKPVFETLRE GSLVYVESFS NEKSLMPAGL NFMLRISDLS SIL

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Macromolecule #5: RNA (48-MER)

MacromoleculeName: RNA (48-MER) / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Saccharolobus solfataricus (archaea)
Molecular weightTheoretical: 14.821234 KDa
SequenceString:
AUUGAAAGUU UUUUUUUUUU UUUUUUUUUU UUUUUUUUUU UUUUUUUU

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 0.0 µm / Nominal defocus min: 0.0 µm
Image recordingFilm or detector model: GATAN K2 BASE (4k x 4k) / Average electron dose: 34.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.5 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 192787

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