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- EMDB-73877: Cryo-EM Structure of the Type III-Bv CRISPR Complex from Dissulfu... -

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Basic information

Entry
Database: EMDB / ID: EMD-73877
TitleCryo-EM Structure of the Type III-Bv CRISPR Complex from Dissulfurispira thermophila bound to a crRNA
Map dataFinal Reconstruction
Sample
  • Complex: Type III-Bv CRISPR Complex from Dissulfurispira thermophila bound to a crRNA
    • Protein or peptide: Type III-B CRISPR-associated protein Cas10/Cmr2
    • Protein or peptide: Type III-B CRISPR module-associated protein Cmr3
    • Protein or peptide: Type III-B CRISPR module RAMP protein Cmr4
    • Protein or peptide: CRISPR type III-B/RAMP module-associated protein Cmr5
    • Protein or peptide: CSD domain-containing protein Cmr6
    • RNA: RNA (38-MER)
    • Protein or peptide: Cmr1-MntA
  • Ligand: ZINC ION
KeywordsCRISPR / complex / crRNA / IMMUNE SYSTEM / IMMUNE SYSTEM-RNA complex
Function / homology
Function and homology information


defense response to virus / nucleic acid binding / nucleotide binding / metal ion binding / cytosol / cytoplasm
Similarity search - Function
Polymerase beta, nucleotidyltransferase / Polymerase beta, Nucleotidyltransferase / CRISPR-associated protein TM1795 / CRISPR-associated protein, TM1793 / CRISPR-associated protein (Cas_Cmr5) / CRISPR-associated protein, TM1791 / CRISPR-associated protein, Cmr3 / CRISPR-associated protein (Cas_Cmr3) / CRISPR-associated protein, Cmr5 / CRISPR-associated RAMP Cmr4 ...Polymerase beta, nucleotidyltransferase / Polymerase beta, Nucleotidyltransferase / CRISPR-associated protein TM1795 / CRISPR-associated protein, TM1793 / CRISPR-associated protein (Cas_Cmr5) / CRISPR-associated protein, TM1791 / CRISPR-associated protein, Cmr3 / CRISPR-associated protein (Cas_Cmr3) / CRISPR-associated protein, Cmr5 / CRISPR-associated RAMP Cmr4 / AF1862-like domain superfamily / CRISPR-associated protein Cmr2 / CRISPR-associated protein Cmr2, N-terminal / CRISPR-Cas system, Cmr2 subunit, D1 domain, cysteine cluster / CRISPR-associated protein Cmr2, N-terminal / Cold-shock (CSD) domain profile. / Cold-shock protein, DNA-binding / 'Cold-shock' DNA-binding domain / : / Cas10/Cmr2, second palm domain / Cold shock domain / Cold shock protein domain / CRISPR type III-associated protein / RAMP superfamily / GGDEF domain profile. / GGDEF domain / Nucleotidyltransferase superfamily / Reverse transcriptase/Diguanylate cyclase domain / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Type III-B CRISPR module-associated protein Cmr3 / Uncharacterized protein / CSD domain-containing protein / CRISPR type III-B/RAMP module-associated protein Cmr5 / Type III-B CRISPR module RAMP protein Cmr4 / Type III-B CRISPR-associated protein Cas10/Cmr2
Similarity search - Component
Biological speciesDissulfurispira thermophila (bacteria) / Escherichia phage MS2 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsBurman N / Pandey S / Wiedenheft B
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM134867 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)F31GM153146 United States
CitationJournal: Structure / Year: 2026
Title: Identification and structure determination of a type III-Bv CRISPR complex that post-translationally modifies an associated toxin.
Authors: Shishir Pandey / Nathaniel Burman / William S Henriques / Tanner Wiegand / Trevor Zahl / Hannah Nyquist / Tanner Spreeuw / Murat Buyukyoruk / Blake Wiedenheft /
Abstract: Cas7-family proteins form the scaffolds of multi-subunit CRISPR RNA-guided surveillance complexes. To explore how Cas7 diversification expands CRISPR function, we identified Cas7 fusion proteins ...Cas7-family proteins form the scaffolds of multi-subunit CRISPR RNA-guided surveillance complexes. To explore how Cas7 diversification expands CRISPR function, we identified Cas7 fusion proteins linked to diverse accessory domains, including a type III-B variant (III-Bv) in which a Cas7 homolog (Cmr1) is fused to the MntA antitoxin and encoded adjacent to a HEPN-family toxin. Structures reveal that the core Cas proteins assemble into a stable surveillance complex in the absence of crRNA, whereas incorporation of the Cmr1-MntA fusion is crRNA-dependent. Target RNA recognition triggers conformational changes that expose the Cas10 cyclase active site and promote cyclic oligoadenylate synthesis. Biochemical analyses show that the CRISPR-associated MntA is enzymatically active and AMPylates the associated HEPN protein. Together, these findings establish the structural basis for assembly of a type III-Bv surveillance complex containing an enzymatically active toxin-antitoxin module.
History
DepositionNov 17, 2025-
Header (metadata) releaseJul 15, 2026-
Map releaseJul 15, 2026-
UpdateJul 15, 2026-
Current statusJul 15, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_73877.png

Downloads & links

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Map

FileDownload / File: emd_73877.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationFinal Reconstruction
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.1 Å/pix.
x 384 pix.
= 423.936 Å		1.1 Å/pix.
x 384 pix.
= 423.936 Å		1.1 Å/pix.
x 384 pix.
= 423.936 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.104 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07
Minimum - Maximum-0.29522923 - 0.72471684
Average (Standard dev.)-0.00003709336 (±0.013565456)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 423.93597 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_73877_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Sharpened map generated by DeepEMHancer

Fileemd_73877_additional_1.map
AnnotationSharpened map generated by DeepEMHancer
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map A of final reconstruction

Fileemd_73877_half_map_1.map
AnnotationHalf Map A of final reconstruction
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Half Map B of final reconstruction

Fileemd_73877_half_map_2.map
AnnotationHalf Map B of final reconstruction
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Type III-Bv CRISPR Complex from Dissulfurispira thermophila bound...

EntireName: Type III-Bv CRISPR Complex from Dissulfurispira thermophila bound to a crRNA
Components
  • Complex: Type III-Bv CRISPR Complex from Dissulfurispira thermophila bound to a crRNA
    • Protein or peptide: Type III-B CRISPR-associated protein Cas10/Cmr2
    • Protein or peptide: Type III-B CRISPR module-associated protein Cmr3
    • Protein or peptide: Type III-B CRISPR module RAMP protein Cmr4
    • Protein or peptide: CRISPR type III-B/RAMP module-associated protein Cmr5
    • Protein or peptide: CSD domain-containing protein Cmr6
    • RNA: RNA (38-MER)
    • Protein or peptide: Cmr1-MntA
  • Ligand: ZINC ION

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Supramolecule #1: Type III-Bv CRISPR Complex from Dissulfurispira thermophila bound...

SupramoleculeName: Type III-Bv CRISPR Complex from Dissulfurispira thermophila bound to a crRNA
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#7
Source (natural)Organism: Dissulfurispira thermophila (bacteria)

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Macromolecule #1: Type III-B CRISPR-associated protein Cas10/Cmr2

MacromoleculeName: Type III-B CRISPR-associated protein Cas10/Cmr2 / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dissulfurispira thermophila (bacteria)
Molecular weightTheoretical: 70.288859 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MGHHHHHHLE VLFQGPMENK FLFLFTITPV QSFINQARKA QDLYAGSFML SHFSKAAANK LKMEFDCEII FPDIANNSIP NRFAAVVNV NENEAQAVGD SLQKAVEAEI KRIGDSVING LKINKPNGFD EQLSSYFTVS YLFVPYNEDD YKQCYSELES L MGAIKSVR ...String:
MGHHHHHHLE VLFQGPMENK FLFLFTITPV QSFINQARKA QDLYAGSFML SHFSKAAANK LKMEFDCEII FPDIANNSIP NRFAAVVNV NENEAQAVGD SLQKAVEAEI KRIGDSVING LKINKPNGFD EQLSSYFTVS YLFVPYNEDD YKQCYSELES L MGAIKSVR AFSQYPDSER GRKCSICGER NVKFYRMAEN EKDIERIKKL KLFSNDVYAV KNSDYRELGP RYLQAGEGLC GV CFTKRGL DRAGIPEYKA KFPSTSKIAL FDAFKQLREK RGDLGTIIDS DNYEPQGIFA LKNNKNLDDF PELSEMEKKN TRE LYEAME DYKISYSPYY AVMLFDGDSM GEWLSGNKIK DEKLKEFHKE LTKKLGEFAN AVRDTIKEPL GVTVYAGGED FLGF FNIKY LLEGMKHLRN KFNELVNLPL KDFYADNTYN MTFSAGAVIA HIKTPLSEVL NWARKVEQEA KDIDDTKDAF AIAVL KHSG EIEKTVFKWR VNDTYTTDLM SKIVTEINND RLSNTFIKKL NQELIKLLDK DGNYRDDNII KAEIKRLLMR SFMKTK DED EDAFKKRKAE TAKELQLHNL LIHSNGVRNF LNFLNITDFI ARQAKGGAA

UniProtKB: Type III-B CRISPR-associated protein Cas10/Cmr2

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Macromolecule #2: Type III-B CRISPR module-associated protein Cmr3

MacromoleculeName: Type III-B CRISPR module-associated protein Cmr3 / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dissulfurispira thermophila (bacteria)
Molecular weightTheoretical: 40.201371 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKRITINALD VLFLRDGKPF TMGSDTWGSG ISLPYPSMIY GVLRSLYFSH NISMLKHAAP IDELNHNDPT RNLKIKGIYL KRASDLLFP VPMDCVVLKN SRDEKLIPLM PVKAQCISNC KTSAVLRPEK GEQIESAEDG WIDKAAMEEY LNGIYENMSY S KLSDFVLS ...String:
MKRITINALD VLFLRDGKPF TMGSDTWGSG ISLPYPSMIY GVLRSLYFSH NISMLKHAAP IDELNHNDPT RNLKIKGIYL KRASDLLFP VPMDCVVLKN SRDEKLIPLM PVKAQCISNC KTSAVLRPEK GEQIESAEDG WIDKAAMEEY LNGIYENMSY S KLSDFVLS EAKIGIARNN KTHIAEDSML YRVGMKRLKD TTIVVDIDGL EIPDAGIIKI GGEGRPASFK AIDIDETSIL QP AINSNKI EKIKLYIATP AIFKKGWLPQ TIDDRDLEGE INGIGLKLIT AAIGRPLYVG GFDIKKGPKP MKRAVPAGSV YYF EIHGQY SNEQIINALH DKAISDREQD RQQGFGIAYV GKWE

UniProtKB: Type III-B CRISPR module-associated protein Cmr3

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Macromolecule #3: Type III-B CRISPR module RAMP protein Cmr4

MacromoleculeName: Type III-B CRISPR module RAMP protein Cmr4 / type: protein_or_peptide / ID: 3 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Dissulfurispira thermophila (bacteria)
Molecular weightTheoretical: 34.96666 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MFKKARPFFI ICETPLHCGS GNDIGNVDLP IQRERHTDFP KIEASSLKGG IREAFEEADK DIKVGSLTIN ISDKSTISLA FGPEQGSDH AGALGFTDAR ILLFPVKSMK GVFAWVTCPQ VLERFKSDLN LCGVNLGFEM PQANTAPKDC SLFINGNKIV L EEYTFEIA ...String:
MFKKARPFFI ICETPLHCGS GNDIGNVDLP IQRERHTDFP KIEASSLKGG IREAFEEADK DIKVGSLTIN ISDKSTISLA FGPEQGSDH AGALGFTDAR ILLFPVKSMK GVFAWVTCPQ VLERFKSDLN LCGVNLGFEM PQANTAPKDC SLFINGNKIV L EEYTFEIA RDRDESGNCT SLANWLSENL FLANSGIQFW KEKIKKDIVV ISDDEFRDFV TLSTEVITRT KINNETGTVQ SG ALFTEEY LPTDTVLYSL ALTTPVFKEK DEEKGIFKQD SANEEDMVME FFTTGLPEII QLGGNATIGK GIARVKIL

UniProtKB: Type III-B CRISPR module RAMP protein Cmr4

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Macromolecule #4: CRISPR type III-B/RAMP module-associated protein Cmr5

MacromoleculeName: CRISPR type III-B/RAMP module-associated protein Cmr5 / type: protein_or_peptide / ID: 4 / Number of copies: 2 / Enantiomer: LEVO
Source (natural)Organism: Dissulfurispira thermophila (bacteria)
Molecular weightTheoretical: 15.953378 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString:
MTDNNLTIQK SIERQRAAFA YKCAEAGKSI TKSKEYKAYV KNIPMLIKTN GIGATFAFVK AKSEADVDKS GYAYKLIYEQ TTEWLKQEP KGLIYEKLNN TDMVKALVEL DSDKYRAVTN EVLALFVWLK RFAEGLIEGE K

UniProtKB: CRISPR type III-B/RAMP module-associated protein Cmr5

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Macromolecule #5: CSD domain-containing protein Cmr6

MacromoleculeName: CSD domain-containing protein Cmr6 / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dissulfurispira thermophila (bacteria)
Molecular weightTheoretical: 42.396605 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MSEKGKIKTF KKAKGFGFIK YSGGEIFFHI NDVIASDSDK IKEGIDVEFE IGKGKEGKPA AKKIKVKSLY RQQNIPINDD ISGINYFLP KDTYAAVKPE QIDNFNLLLN KIPYFDGKKF NFYKKDKKRN EILNLARRFN YNASFIKRLS ERHKNSISQL L GSGSITST ...String:
MSEKGKIKTF KKAKGFGFIK YSGGEIFFHI NDVIASDSDK IKEGIDVEFE IGKGKEGKPA AKKIKVKSLY RQQNIPINDD ISGINYFLP KDTYAAVKPE QIDNFNLLLN KIPYFDGKKF NFYKKDKKRN EILNLARRFN YNASFIKRLS ERHKNSISQL L GSGSITST TLSPDWRFII GIGNESVYET SITLHHIYGI PYIPGQAVKG VVRSWIITEV FGQDEKKALK DALFCHIFGS PK ESAIGEH QGSVIFFDAL PITLPQLEVD VMNPHYGDYY QGKEKSNKPV PPADYLNPNP IPFLTVGKDT KFEFTVGMKK LKQ AREVLK NGSSRLISEC EGLTAEKNLH EIAISWLKKA LTEHGIGAKT AVGYGYFEKT

UniProtKB: CSD domain-containing protein

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Macromolecule #7: Cmr1-MntA

MacromoleculeName: Cmr1-MntA / type: protein_or_peptide / ID: 7 / Number of copies: 1 / Enantiomer: LEVO
Source (natural)Organism: Dissulfurispira thermophila (bacteria)
Molecular weightTheoretical: 49.646605 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MKTVGFTLTT ITPMFLSGID SRTPELRAPS IKGAMRFWWR ALKAEPDIDK LRKKEDQIFG SSDEKIGRAK FSIRVSQIDK KSPSTYKNP DKYDPVGYHF YSVFMEGGRE RYYSPEENRF KIILTSQDEG ILKIASASLW ALVYLGAIGT RARRGAGNMA I ISVDDADK ...String:
MKTVGFTLTT ITPMFLSGID SRTPELRAPS IKGAMRFWWR ALKAEPDIDK LRKKEDQIFG SSDEKIGRAK FSIRVSQIDK KSPSTYKNP DKYDPVGYHF YSVFMEGGRE RYYSPEENRF KIILTSQDEG ILKIASASLW ALVYLGAIGT RARRGAGNMA I ISVDDADK ILDDTGLDFI PKGNNSEEVA KWIRDNCNTA KAIINKDKTT FVSEYSNLCF SRFVIGNQPF KSWKDALGAA GF KAFRDKN KSRILETPSF GFPVRHRTNN INNITVTGRV GKDSFSRRSS PIIFKIIKSG SYYYWMVLRL SGEFLPEGGV IKA NNNTQK PDYSIIDEFW AELKKRGVEH ILSMPDTLMT IIDKLKKDID PQKIILFGSK ARGDFHSRSD TDIAVETDKS LEEL LLNGA VDIVDMNRAN DELKDKIKKE GVVIYERKGE EAS

UniProtKB: Uncharacterized protein

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Macromolecule #6: RNA (38-MER)

MacromoleculeName: RNA (38-MER) / type: rna / ID: 6 / Number of copies: 1
Source (natural)Organism: Escherichia phage MS2 (virus)
Molecular weightTheoretical: 12.24835 KDa
SequenceString:
ACUGAAACGU CUGGAAGUUU GCAGCUGGAU ACGACACA

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Macromolecule #8: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 8 / Number of copies: 1 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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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
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY ARRAY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 45 sec. / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TALOS ARCTICA
SoftwareName: SerialEM (ver. 4.2.0)
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 4871 / Average electron dose: 65.0 e/Å2
Details: Micrographs are the average of 50 subframes with dose of 1.3 electrons per subframe.
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 45000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Talos Arctica / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 1621549
Details: Particles identified using cryoSPARC's template picker. Templates generated from a de novo volume that contained 105809 particles.
CTF correctionSoftware - Name: cryoSPARC (ver. 4.7.1)
Software - details: cryoSPARC's patch CTF estimation was used to determine CTF correction
Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.7.1)
Software - details: non-uniform refinement was used to generate the final reconstruction
Details: cryoSPARC's non-uniform refinement with per particle CTF correction was used to generate the final reconstruction.
Number images used: 194795
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.7.1)
Final 3D classificationNumber classes: 2 / Avg.num./class: 223820 / Software - Name: cryoSPARC (ver. 4.7.1)
Software - details: 3-D classification was used without a focus mask to sort particles in the final stage of classification
Details: Unmasked 3-D classification was used to isolate particles containing the most density for the Cmr1-MntA subunit
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: AlphaFold / Chain - Initial model type: in silico model
Details: Alphafold predicted strucutres of protein subunits were fit into the experimental density using ChimeraX. The crRNA was build de novo using COOT.
SoftwareName: UCSF ChimeraX (ver. 1.10.1)
Details: ChimeraX's Fit in map command was used to dock protein subunits into the experimental density
DetailsInitial fitting was done in ChimeraX, followed by refinement in PHENIX. COOT was used to manually edit the structure to better fit the density before a final refinement in PHENIX
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Target criteria: Cross-correlation coefficient
Output model

PDB-9z7q:
Cryo-EM Structure of the Type III-Bv CRISPR Complex from Dissulfurispira thermophila bound to a crRNA

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