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- EMDB-74675: S. marcescens Cas10-Csm unbound to target RNA -

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Basic information

Entry
Database: EMDB / ID: EMD-74675
TitleS. marcescens Cas10-Csm unbound to target RNA
Map dataS. marcescens Cas10-Csm unbound to target RNA
Sample
  • Complex: Cas10-Csm
    • Protein or peptide: CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)
    • Protein or peptide: CRISPR system Cms endoribonuclease Csm3
    • Protein or peptide: CRISPR system Cms protein Csm4
    • Protein or peptide: CRISPR system Cms protein Csm5
    • RNA: RNA (30-MER)
KeywordsCRISPR / crRNA / Cas10 / type III / RNA BINDING PROTEIN
Function / homology
Function and homology information


exonuclease activity / transferase activity / endonuclease activity / defense response to virus / hydrolase activity / RNA binding / ATP binding
Similarity search - Function
CRISPR-associated protein Csm5 / CRISPR-associated RAMP Csm3 / CRISPR type III-associated RAMP protein Csm4 / CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 / Csm1, subunit domain B / Csm1 subunit domain B / : / : / Cas10/Cmr2, second palm domain / : ...CRISPR-associated protein Csm5 / CRISPR-associated RAMP Csm3 / CRISPR type III-associated RAMP protein Csm4 / CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 / Csm1, subunit domain B / Csm1 subunit domain B / : / : / Cas10/Cmr2, second palm domain / : / CRISPR type III-associated protein / RAMP superfamily / GGDEF domain profile. / GGDEF domain / Reverse transcriptase/Diguanylate cyclase domain
Similarity search - Domain/homology
CRISPR system Cms protein Csm5 / CRISPR system Cms endoribonuclease Csm3 / CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A) / CRISPR system Cms protein Csm4
Similarity search - Component
Biological speciesSerratia (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsPerdigao CC / Dokland T / Dunkle JA
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM142966 United States
National Institutes of Health/Office of the DirectorS10OD024978 United States
CitationJournal: bioRxiv / Year: 2026
Title: Structural insights into target detection by the type III CRISPR complex and its deployment in SNP identification.
Authors: Calvin C Perdigao / Luqman O Ajisafe / Anju T Sunny / Si Wu / Terje Dokland / Jack A Dunkle /
Abstract: Type III CRISPR systems utilize a complex containing Cas10, additional Cas proteins and a crRNA to detect foreign transcripts. Upon detection, Cas10 synthesizes cyclic oligoadenylates (cOA), ...Type III CRISPR systems utilize a complex containing Cas10, additional Cas proteins and a crRNA to detect foreign transcripts. Upon detection, Cas10 synthesizes cyclic oligoadenylates (cOA), signaling molecules that coordinate interference by stimulating downstream enzymes with DNase, RNase, protease or other activities. Type III systems are among the most abundant CRISPR systems in prokaryotes and understanding the structure-function relationships that control transcript detection and cOA synthesis will advance the understanding of the broader physiological roles of these systems. Type III systems possess properties well-suited to their deployment as molecule diagnostics: specific detection and activation of a cascade of multi-turnover enzymatic reactions that can be harnessed for signal generation. We determined that Cas10-Csm (SmCas10-Csm) synthesizes predominantly cA molecules and this synthesis is sensitive to mismatches in the crRNA-target RNA duplex adjacent to Cas10. We determined the structure of SmCas10-Csm unbound and bound to target RNA identifying conformational changes associated with target binding. We demonstrate that SmCas10-Csm can distinguish between single nucleotide polymorphisms that occur in the human transcript that are associated with sickle cell disease indicating an additional role for type III CRISPR systems in point-of-care diagnostics in low-resource settings.
History
DepositionDec 22, 2025-
Header (metadata) releaseApr 22, 2026-
Map releaseApr 22, 2026-
UpdateApr 22, 2026-
Current statusApr 22, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74675.png

Downloads & links

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Map

FileDownload / File: emd_74675.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationS. marcescens Cas10-Csm unbound to target RNA
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.94 Å/pix.
x 420 pix.
= 394.8 Å		0.94 Å/pix.
x 420 pix.
= 394.8 Å		0.94 Å/pix.
x 420 pix.
= 394.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.94 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.08105521 - 0.23969333
Average (Standard dev.)-0.00012227178 (±0.007007664)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 394.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: S. marcescens Cas10-Csm unbound to target RNA, half map A

Fileemd_74675_half_map_1.map
AnnotationS. marcescens Cas10-Csm unbound to target RNA, half map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: S. marcescens Cas10-Csm unbound to target RNA, half map B

Fileemd_74675_half_map_2.map
AnnotationS. marcescens Cas10-Csm unbound to target RNA, half map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Cas10-Csm

EntireName: Cas10-Csm
Components
  • Complex: Cas10-Csm
    • Protein or peptide: CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)
    • Protein or peptide: CRISPR system Cms endoribonuclease Csm3
    • Protein or peptide: CRISPR system Cms protein Csm4
    • Protein or peptide: CRISPR system Cms protein Csm5
    • RNA: RNA (30-MER)

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Supramolecule #1: Cas10-Csm

SupramoleculeName: Cas10-Csm / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Serratia (bacteria)

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Macromolecule #1: CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1...

MacromoleculeName: CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)
type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Serratia (bacteria)
Molecular weightTheoretical: 90.390656 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNWLAASCHV AAFALLHNLK PLAQRAGIQD FPSPALANKL FAPLPESLSA RADLHENTLT LLLDFAARLA RGLPETPVSR GETGLIPLT HLLADDNHSA PAERCYSPLA PLGVDSLMPV TAALPTGERQ AAYRQVYQAL IEGLEAIPAA HRLQPSLWLD H LDSLWMTT ...String:
MNWLAASCHV AAFALLHNLK PLAQRAGIQD FPSPALANKL FAPLPESLSA RADLHENTLT LLLDFAARLA RGLPETPVSR GETGLIPLT HLLADDNHSA PAERCYSPLA PLGVDSLMPV TAALPTGERQ AAYRQVYQAL IEGLEAIPAA HRLQPSLWLD H LDSLWMTT CHALPDGDGA SGISLYDQGK TTAALAVALW QHHARQATPE KEISLTPGDD ARLLLIQADV FGIQELIFAQ GN QTQKMAA KLLRGRSFQV SLLAETAALR VLETFDLPPV CQLINAAGKS LIVAPNLPDA AERLAGLRQR LDEWFLTHTY AQT GIGLCS TVAGSAEFLG EQAYGRLQNR LAQAMEQQKY QRFSLCAGDA PPPVFEGYLD QIAQGAGGEP CPMNGLHPVE TTLN GLGCS RLAADQITLG HWINHGHWIS HGERYARLLI LRDSTATFSD DRCLHLTLFG YQVVAVSLKE DSGEFGELAC NGSLR RCWD VSLPPEGTSL FQGYARRFIN GWMPLAQGEY QPECYPGIEE ALANGDIKTF DHLSCEDLYQ DADQSLRGTC ALGVLK GDI DNLGHLFRSG LPQPGFAKTI GLSRQIHLFF TLWLPHLCRK DPRFANTYTV FAGGDDFFLI GPWRSQQTLA LTMAQDF AR YSGHNPALHF SLGLVQAKPG YPVRALAAQA EAALKQAKQH PGKNAICLYN EVMGWPEYDA LLACSEELAR WREHDGYP L SSGLLYRLLA LSEQSAEESE KPQAALWRSR LAYFLRRNLV DNVKVPTKEN PAAFRHQLHL ELFEKLEQHL KRHRQRYRV ALQRHLYHYR TVPRGE

UniProtKB: CRISPR system single-strand-specific deoxyribonuclease Cas10/Csm1 (subtype III-A)

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Macromolecule #2: CRISPR system Cms endoribonuclease Csm3

MacromoleculeName: CRISPR system Cms endoribonuclease Csm3 / type: protein_or_peptide / ID: 2 / Number of copies: 4 / Enantiomer: LEVO
Source (natural)Organism: Serratia (bacteria)
Molecular weightTheoretical: 27.185859 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MQLNNIQTLR ATLVCETGLH IGGGDTALQI GGIASAVVRH PLTQQPYIPG SSLKGKLRSL LEWRAGVVGD TEGKVLSHQV YQQLIDDKK QAQALQALKI LQLFGVSGGD KLSAEQAQQI GPTRLSFWDC EFDEHWLAQQ GGRVQTEEKA ENCIDRISGV A LHPRFIER ...String:
MQLNNIQTLR ATLVCETGLH IGGGDTALQI GGIASAVVRH PLTQQPYIPG SSLKGKLRSL LEWRAGVVGD TEGKVLSHQV YQQLIDDKK QAQALQALKI LQLFGVSGGD KLSAEQAQQI GPTRLSFWDC EFDEHWLAQQ GGRVQTEEKA ENCIDRISGV A LHPRFIER VPAGSRFDFR LTVRQLDGDS PDLLDTLLAG LKMLELDGLG GSISRGYGKV RFEALTLDGK DLQPRFEQLQ PF KHTTQGA G

UniProtKB: CRISPR system Cms endoribonuclease Csm3

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Macromolecule #3: CRISPR system Cms protein Csm4

MacromoleculeName: CRISPR system Cms protein Csm4 / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Serratia (bacteria)
Molecular weightTheoretical: 35.770551 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MPSPVAPAAA WQWLRLRLLP DSAFATALRG DTLFGQLCWY LRESLGEAGL NALLAGYHDQ RPFAVISDPM LADHLPRPHL PEHRLGFAA ADARARKQRK QQCWLPLAFA HQPLAEWGAH LTAAPEHHQH RSDVQMHNSI NRQTLTTGGD DAFAPFGSEQ H WFDVDTAW ...String:
MPSPVAPAAA WQWLRLRLLP DSAFATALRG DTLFGQLCWY LRESLGEAGL NALLAGYHDQ RPFAVISDPM LADHLPRPHL PEHRLGFAA ADARARKQRK QQCWLPLAFA HQPLAEWGAH LTAAPEHHQH RSDVQMHNSI NRQTLTTGGD DAFAPFGSEQ H WFDVDTAW DLYLLHDKRL SAAQLTDALR AIGLLGYGKD ASIGKGRFHL TPQPMPELPT PDGNPLRLTL APCAPQQGHW HS ADSFFSP LVRVGRHGAA LVVQGHPFKN PLLLADSAAV LAPVTPDNRP FVGQGLGGNG RLSTALPQTV HQGYAPVIPV RFH HKAQPQ

UniProtKB: CRISPR system Cms protein Csm4

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Macromolecule #4: CRISPR system Cms protein Csm5

MacromoleculeName: CRISPR system Cms protein Csm5 / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Serratia (bacteria)
Molecular weightTheoretical: 63.148707 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MTRDQTPRRH TACDSDNMQY FTLTCLSPVH VATGDSLNPG EYLIDENALY ELGQGGLSPA LTATQRSELL TILESNDPAL PLTVQRFLA REAGKLKYAA RRMCPLLPGI SRYYQSRLGQ VMQNDTKNKK QMINQLELMR HVGAALGAPY IPGSTLKGAI R TALVSALN ...String:
MTRDQTPRRH TACDSDNMQY FTLTCLSPVH VATGDSLNPG EYLIDENALY ELGQGGLSPA LTATQRSELL TILESNDPAL PLTVQRFLA REAGKLKYAA RRMCPLLPGI SRYYQSRLGQ VMQNDTKNKK QMINQLELMR HVGAALGAPY IPGSTLKGAI R TALVSALN QGQPLQAERR ETDKLSSKVA QDAERQLLGF DTRRDSPRYR IEHDPFHWLQ VGDAVSPAEH PPMLDYWLVR RQ PFKRTEK QDNKADNMEL SPVECLKPRQ SPLHCQITVK TPPTALAIKN PRLKQWLGKV SQLAQQVNRI TLPQCHHELA WLA EKHIGT DDVYAPGQNW VAQMQQLLRQ LDDPLQRGEA LLLRVGKYGG AISKTVAGWR HIARLGRQGT RTTYHPDVTT CTLA LPQAD ALTQALPFGW VLLHQPDQPE VTEFVASHHD WCQQQQQRLD AHQQQQHTHR QQRQQLAQAR EEEAQRLADK ARQSK ARQS IMSLAEQLAS EQTFQHKNPN GPLRGQLATC VGCVATEGSA EEKAELCTLF DDILNYWGIK PGKDKKLTAL RNKLL

UniProtKB: CRISPR system Cms protein Csm5

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Macromolecule #5: RNA (30-MER)

MacromoleculeName: RNA (30-MER) / type: rna / ID: 5 / Number of copies: 1
Source (natural)Organism: Serratia (bacteria)
Molecular weightTheoretical: 13.361948 KDa
SequenceString:
AUUAAGACCA UUUACAGAAC CUGUUCCACU UAAUGAAGUU GC

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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: 8
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS GLACIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.1 µm

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Image processing

CTF correctionSoftware - Name: cryoSPARC (ver. 4) / Type: PHASE FLIPPING ONLY
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4) / Number images used: 42471
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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