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- EMDB-48405: CRISPR-associated deaminase Cad1 in cA4 bound in hexamer form ref... -

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Basic information

Entry
Database: EMDB / ID: EMD-48405
TitleCRISPR-associated deaminase Cad1 in cA4 bound in hexamer form refined against the consensus map
Map data
Sample
  • Complex: Binary complex of CRISPR-associated deaminase Cad1 and tetra-adenylate
    • Protein or peptide: CRISPR-associated ring nuclease and adenosine deaminase, subunit A
  • RNA: RNA (5'-R(*AP*(A23))-3')
  • Ligand: ZINC ION
KeywordsCRISPR-associated CARF ring nuclease / Cad1 / CRISPR-associated adenosine deaminase / S-adenosylmethionine / SIGNALING PROTEIN / ANTIVIRAL PROTEIN / ANTIVIRAL PROTEIN-RNA complex
Function / homology
Function and homology information


inosine biosynthetic process / adenosine deaminase / hypoxanthine salvage / adenosine deaminase activity / adenosine catabolic process / cytosol
Similarity search - Function
CRISPR-assoc protein, NE0113/Csx13 / CRISPR-associated protein NE0113 (Cas_NE0113) / Adenosine deaminase domain / Adenosine deaminase / Adenosine/adenine deaminase / Metal-dependent hydrolase
Similarity search - Domain/homology
Biological speciesThermoanaerobaculum aquaticum (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.36 Å
AuthorsLi H / Zhao Y / Whyms C
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM152081 United States
CitationJournal: EMBO J / Year: 2025
Title: The twist-and-squeeze activation of CARF-fused adenosine deaminase by cyclic oligoadenylates.
Authors: Charlisa Whyms / Yu Zhao / Doreen Addo-Yobo / Huan He / Arthur Carl Whittington / Despoina Trasanidou / Carl Raymund P Salazar / Raymond H J Staals / Hong Li /
Abstract: The recently identified CARF (CRISPR-associated Rossman-fold) family of proteins play a critical role in prokaryotic defense, mediating cOA (cyclic oligoadenylate)-stimulated ancillary immune ...The recently identified CARF (CRISPR-associated Rossman-fold) family of proteins play a critical role in prokaryotic defense, mediating cOA (cyclic oligoadenylate)-stimulated ancillary immune responses in the type III CRISPR-Cas systems. Whereas most previously characterized CARF proteins contain nucleic acids or protein degradation effectors, a subset of the family, including the CARF-fused adenosine deaminase (ADA) (Cad1), has recently been shown to convert ATP to ITP. The enzymatic mechanism and the activation process of Cad1, however, remain incompletely understood. Here we present biochemical and structural analyses of a ring nuclease Cad1, revealing its substrate binding specificity and a sequential activation process by cOAs. Despite an overall structural similarity to canonical ADA enzymes, the ADA domain of Cad1 possesses unique structural features that confer a specificity for ATP. Supported by mutational analysis, our structural work demonstrates an allosteric link between the cOA-binding CARF and the ADA domain through a protein network within the hexameric enzyme assembly. Binding of a cA4 molecule to paired CARF domains induces a twisting of the linked ADA domains around one another, which remodels their active sites and alters interactions with neighboring ADA domains, thereby driving a sequential conformational activation mechanism.
History
DepositionDec 20, 2024-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_48405.png

Downloads & links

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Map

FileDownload / File: emd_48405.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å		1.06 Å/pix.
x 320 pix.
= 339.2 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.06 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.329
Minimum - Maximum-4.6396246 - 8.208034
Average (Standard dev.)0.0009307319 (±0.20005436)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 339.19998 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_48405_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_48405_half_map_2.map
Projections & Slices
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Sample components

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Entire : Binary complex of CRISPR-associated deaminase Cad1 and tetra-adenylate

EntireName: Binary complex of CRISPR-associated deaminase Cad1 and tetra-adenylate
Components
  • Complex: Binary complex of CRISPR-associated deaminase Cad1 and tetra-adenylate
    • Protein or peptide: CRISPR-associated ring nuclease and adenosine deaminase, subunit A
  • RNA: RNA (5'-R(*AP*(A23))-3')
  • Ligand: ZINC ION

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Supramolecule #1: Binary complex of CRISPR-associated deaminase Cad1 and tetra-adenylate

SupramoleculeName: Binary complex of CRISPR-associated deaminase Cad1 and tetra-adenylate
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Thermoanaerobaculum aquaticum (bacteria)

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Macromolecule #1: CRISPR-associated ring nuclease and adenosine deaminase, subunit A

MacromoleculeName: CRISPR-associated ring nuclease and adenosine deaminase, subunit A
type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO / EC number: adenosine deaminase
Source (natural)Organism: Thermoanaerobaculum aquaticum (bacteria)
Molecular weightTheoretical: 69.499133 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
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 PR

UniProtKB: adenosine deaminase

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Macromolecule #2: RNA (5'-R(*AP*(A23))-3')

MacromoleculeName: RNA (5'-R(*AP*(A23))-3') / type: rna / ID: 2 / Number of copies: 6
Source (natural)Organism: Thermoanaerobaculum aquaticum (bacteria)
Molecular weightTheoretical: 675.419 Da
SequenceString:
A(A23)

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 6 / 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: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 60.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.8 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: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.36 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 409445
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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