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- EMDB-39746: The structure of type III CRISPR-associated deaminase in complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-39746
TitleThe structure of type III CRISPR-associated deaminase in complex 2cA6 and 2ATP, partial activated
Map datamerged
Sample
  • Complex: CRISPR-associated adenosine deaminase
    • Protein or peptide: Adenosine deaminase domain-containing protein
    • RNA: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
  • Ligand: ZINC ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Keywordsdefense system / deaminase / IMMUNE SYSTEM
Function / homology
Function and homology information


inosine biosynthetic process / adenosine deaminase / hypoxanthine salvage / adenosine deaminase activity / adenosine catabolic process / cytosol
Similarity search - Function
Adenosine deaminase domain / Adenosine deaminase / Adenosine/adenine deaminase / Metal-dependent hydrolase
Similarity search - Domain/homology
Biological speciesLimisphaera ngatamarikiensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.19 Å
AuthorsChen MR / Li ZX / Xiao YB
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Science / Year: 2025
Title: Antiviral signaling of a type III CRISPR-associated deaminase.
Authors: Yutao Li / Zhaoxing Li / Purui Yan / Chenyang Hua / Jianping Kong / Wanqian Wu / Yurong Cui / Yan Duan / Shunxiang Li / Guanglei Li / Shunli Ji / Yijun Chen / Yucheng Zhao / Peng Yang / ...Authors: Yutao Li / Zhaoxing Li / Purui Yan / Chenyang Hua / Jianping Kong / Wanqian Wu / Yurong Cui / Yan Duan / Shunxiang Li / Guanglei Li / Shunli Ji / Yijun Chen / Yucheng Zhao / Peng Yang / Chunyi Hu / Meiling Lu / Meirong Chen / Yibei Xiao /
Abstract: Prokaryotes have evolved diverse defense strategies against viral infection, including foreign nucleic acid degradation by CRISPR-Cas systems and DNA and RNA synthesis inhibition through nucleotide ...Prokaryotes have evolved diverse defense strategies against viral infection, including foreign nucleic acid degradation by CRISPR-Cas systems and DNA and RNA synthesis inhibition through nucleotide pool depletion. Here, we report an antiviral mechanism of type III CRISPR-Cas-regulated adenosine triphosphate (ATP) depletion in which ATP is converted into inosine triphosphate (ITP) by CRISPR-Cas-associated adenosine deaminase (CAAD) upon activation by either cA or cA, followed by hydrolysis into inosine monophosphate (IMP) by Nudix hydrolase, ultimately resulting in cell growth arrest. The cryo-electron microscopy structures of CAAD in its apo and activated forms, together with biochemical evidence, revealed how cA or cA binds to the CRISPR-associated Rossmann fold (CARF) domain and abrogates CAAD autoinhibition, inducing substantial conformational changes that reshape the structure of CAAD and induce its deaminase activity. Our results reveal the mechanism of a CRISPR-Cas-regulated ATP depletion antiviral strategy.
History
DepositionApr 15, 2024-
Header (metadata) releaseDec 11, 2024-
Map releaseDec 11, 2024-
UpdateJul 16, 2025-
Current statusJul 16, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39746.png

Downloads & links

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Map

FileDownload / File: emd_39746.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmerged
Projections & slices

Image control

Size
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AxesZ (Sec.)Y (Row.)X (Col.)
0.93 Å/pix.
x 512 pix.
= 477.184 Å		0.93 Å/pix.
x 512 pix.
= 477.184 Å		0.93 Å/pix.
x 512 pix.
= 477.184 Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.932 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.043008313 - 0.89031345
Average (Standard dev.)0.0045319316 (±0.013899371)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 477.184 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: raw

Fileemd_39746_additional_1.map
Annotationraw
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Half map: #1

Fileemd_39746_half_map_1.map
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Half map: #2

Fileemd_39746_half_map_2.map
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Sample components

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Entire : CRISPR-associated adenosine deaminase

EntireName: CRISPR-associated adenosine deaminase
Components
  • Complex: CRISPR-associated adenosine deaminase
    • Protein or peptide: Adenosine deaminase domain-containing protein
    • RNA: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
  • Ligand: ZINC ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: CRISPR-associated adenosine deaminase

SupramoleculeName: CRISPR-associated adenosine deaminase / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Limisphaera ngatamarikiensis (bacteria)

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Macromolecule #1: Adenosine deaminase domain-containing protein

MacromoleculeName: Adenosine deaminase domain-containing protein / type: protein_or_peptide / ID: 1 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Limisphaera ngatamarikiensis (bacteria)
Molecular weightTheoretical: 70.859859 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MNVQAHLFVS LGTAPAIVPE AFLLPGARFV SVHVLTTERP DVTLIREFFR RHAPGVNLTI TRVAGFQDLK SEEDHFRFEE VMFRWFLAS RTGPEQRFVC LTGGFKTMSA AMQKAATVLG AAEVFHVLAD DCCVGPQGRL MPPSTLEEIL WARDQGHLHW I RLGPERGW ...String:
MNVQAHLFVS LGTAPAIVPE AFLLPGARFV SVHVLTTERP DVTLIREFFR RHAPGVNLTI TRVAGFQDLK SEEDHFRFEE VMFRWFLAS RTGPEQRFVC LTGGFKTMSA AMQKAATVLG AAEVFHVLAD DCCVGPQGRL MPPSTLEEIL WARDQGHLHW I RLGPERGW PQLRRIAPEQ FPLQVVEEKG DERRVQAEDR AFGTFLQDLL QRASRIAGAW EMLPELPFAD LATWSEGELA WL REPLDPR APADQRWVAG LPKIELHCHL GGFATHGELL RRVRNAAENP GKLPPLEEPR LPEGWPLPAQ PIPLAEYMKL GNA NGTALL RDPGCLREQC RLLYRHLVDQ GVCYAEVRCS PANYAEVRSP WDVLADIRAA FQECMEGART APGGLPACHV NLIL IATRR ASGDYRAAIA RHLALAVTAA EHWRDENACR VVGVDLAGYE DEKTRAHYFR EEFTAVHRCG LAVTVHAGEN DDAEG IWRA VFDLNARRLG HALSLGQSRE LLRSVADRGI GVELCPYANL QIKGFRLDGS DRAGPADPRH EAHAPGPYPL LDYLRE GVR VTVNTDNIGI SAASLTDNLL LAARLCPGLT RLDLLHLQRH ALETAFCTAT QRLTLLRRIS SGIPRPHHHH HH

UniProtKB: adenosine deaminase

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

MacromoleculeName: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3') / type: rna / ID: 2 / Number of copies: 2
Source (natural)Organism: Limisphaera ngatamarikiensis (bacteria)
Molecular weightTheoretical: 1.930277 KDa
SequenceString:
AAAAAA

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Macromolecule #3: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 3 / Number of copies: 2 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 2 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM

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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
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: 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: 3.19 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 67665
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: ANGULAR RECONSTITUTION

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