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- EMDB-65542: Focused map of area 1 of the type III CRISPR-associated deaminase... -

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Basic information

Entry
Database: EMDB / ID: EMD-65542
TitleFocused map of area 1 of the type III CRISPR-associated deaminase in complex cA6 and ATP, State 4
Map data
Sample
  • Complex: type III CRISPR-associated deaminase in complex cA6 and ATP
    • Protein or peptide: adenosine deaminase
Keywordsdeaminase / complex / ATP / HYDROLASE
Biological speciesThermoanaerobaculum aquaticum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.07 Å
AuthorsLi ZX / Kong JP / Wu WQ / Xiao YB
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Nucleic Acids Res / Year: 2026
Title: Structural and functional insights into the adenosine deaminase of the type III-B CRISPR-Cas system.
Authors: Zhaoxing Li / Jianping Kong / Wanqian Wu / Yan Duan / Ziyi Zhu / Chenyang Hua / Purui Yan / Chen Cao / Xu Cao / Yibei Xiao / Meiling Lu / Meirong Chen /
Abstract: Type III CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated proteins) systems confer antiviral immunity via cyclic oligoadenylate (cOA) signaling. Here, we ...Type III CRISPR-Cas (Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR-associated proteins) systems confer antiviral immunity via cyclic oligoadenylate (cOA) signaling. Here, we elucidate a cooperative bacterial defense strategy involving two cOA-activated CRISPR-associated Rossmann fold (CARF)-containing effectors, adenosine deaminase CAAD and ribonuclease Csx1, in Thermoanaerobaculum aquaticum. Genomic analyses indicate widespread co-occurrence of CRISPR-associated adenosine deaminase (CAAD) with ancillary CARF-containing effectors in type III CRISPR systems, suggesting that multiple CARF-containing proteins may contribute to a coordinated cOA-dependent defense. Biochemical and structural studies reveal the intrinsic dynamics of CAAD hexamer, and demonstrate that cA4/cA6 binding stabilizes CAAD hexamers, triggering metal-ion-dependent conversion of ATP into inosine triphosphate. Concurrently, the downstream Csx1 is exclusively activated by cA4 to cleave single-stranded RNA. Strikingly, we found that both effectors are capable of degrading cA4, suggesting that this CAAD-Csx1 pair may be cross-regulated and achieve immunity through a dual-targeting mechanism: in response to infection, Csx1 degrades viral RNA while CAAD disrupts nucleotide metabolism via ATP deamination, which can be relieved via cA4 degradation when infection has been eliminated. This study proposes an enhanced defense mechanism through coordinated activation and regulation of multiple CRISPR effectors by a single signaling molecule, unveiling unprecedented complexity in CRISPR immunoregulation.
History
DepositionJul 25, 2025-
Header (metadata) releaseMay 13, 2026-
Map releaseMay 13, 2026-
UpdateMay 13, 2026-
Current statusMay 13, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_65542.png

Downloads & links

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Map

FileDownload / File: emd_65542.map.gz / Format: CCP4 / Size: 216 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 384 pix.
= 357.888 Å		0.93 Å/pix.
x 384 pix.
= 357.888 Å		0.93 Å/pix.
x 384 pix.
= 357.888 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.15
Minimum - Maximum-0.006045068 - 2.3783627
Average (Standard dev.)0.00028318242 (±0.013555415)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 357.888 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_65542_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_65542_half_map_2.map
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 CRISPR-associated deaminase in complex cA6 and ATP

EntireName: type III CRISPR-associated deaminase in complex cA6 and ATP
Components
  • Complex: type III CRISPR-associated deaminase in complex cA6 and ATP
    • Protein or peptide: adenosine deaminase

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Supramolecule #1: type III CRISPR-associated deaminase in complex cA6 and ATP

SupramoleculeName: type III CRISPR-associated deaminase in complex cA6 and ATP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Thermoanaerobaculum aquaticum (bacteria)

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Macromolecule #1: adenosine deaminase

MacromoleculeName: adenosine deaminase / type: protein_or_peptide / ID: 1 / Enantiomer: LEVO
Source (natural)Organism: Thermoanaerobaculum aquaticum (bacteria)
Recombinant expressionOrganism: Escherichia coli BL21(DE3) (bacteria)
SequenceString: MRILLCSVGT SWAVVPEAMQ LLGSQGFDEV HVLTTASSKI SPGVEQLLRY FEMHPGPRFS ISRVQDFEDL RSEQDHMLFE EVLWRWLLQ RAPQAAHRYI CLAGGYKTIS AAMQRAAALF GACEVFHVLC EPRFGPQGNR EASTLEEVEQ AIATNALRFV R LGPEPGWP ...String:
MRILLCSVGT SWAVVPEAMQ LLGSQGFDEV HVLTTASSKI SPGVEQLLRY FEMHPGPRFS ISRVQDFEDL RSEQDHMLFE EVLWRWLLQ RAPQAAHRYI CLAGGYKTIS AAMQRAAALF GACEVFHVLC EPRFGPQGNR EASTLEEVEQ AIATNALRFV R LGPEPGWP QLRLLSAPSF PLESTLQGPV HWVRASDMRL RQHVEGVLER SRHILAAWEG ISELPIPALA AWPPSHLRWL HE PLDPVQD KAWVQALPKV ELHCHLGGFA THGELLHKVR QEAANPESLP PVRAIPLPPG WPIPEEPIGL ERYMRLGDNN GSA LLKDPG CLRAQCRLLY EALLADHVAY AEIRCSPANY ASASRSPWVV LQEIRNHFQQ AMEETPEDRR CHVNLLLTAT REEG GDRSR IARHLALAIT AAEHWKNGCR VVGVDLAGFE DRTTRAAMFA TDFEPVHRVG LAVTVHAGEN DDVEGIWQAV FKLSA RRLG HALHLSRSPD LLRVVAERGI AVELCPYANL QIKGFPLDEE QEGSETYPLR GYLAAGVAVT LNTDNLGISQ ASLTDN LLL TARLCPGITR LEVLKTQVFA AQAAFANQAE RKALWARLAQ VPVPTDTEQK NGNDAKASHQ PRHHHHHH

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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

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON IV (4k x 4k) / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 µm / Nominal defocus min: 1.0 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.07 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 80058
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION
FSC plot (resolution estimation)

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