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- EMDB-39750: The structure of type III CRISPR-associated deaminase in complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-39750
TitleThe structure of type III CRISPR-associated deaminase in complex cA6 and ATP, fully activated
Map data
Sample
  • Complex: CAAD:CA6:ATP 6:3:6
    • RNA: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
    • Protein or peptide: Adenosine deaminase domain-containing protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION
Keywordsdefense system / deaminase / IMMUNE SYSTEM
Function / homology
Function and homology information


inosine biosynthetic process / adenosine deaminase / hypoxanthine salvage / adenosine catabolic process / adenosine deaminase activity / 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: 3.4 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 25, 2024-
Map releaseDec 25, 2024-
UpdateMar 5, 2025-
Current statusMar 5, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_39750.png

Downloads & links

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Map

FileDownload / File: emd_39750.map.gz / Format: CCP4 / Size: 512 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 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: 0.1
Minimum - Maximum-0.024852645 - 0.68628323
Average (Standard dev.)0.0053423047 (±0.015413953)
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: #1

Fileemd_39750_additional_1.map
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Half map: #2

Fileemd_39750_half_map_1.map
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Half map: #1

Fileemd_39750_half_map_2.map
Projections & Slices
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Sample components

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Entire : CAAD:CA6:ATP 6:3:6

EntireName: CAAD:CA6:ATP 6:3:6
Components
  • Complex: CAAD:CA6:ATP 6:3:6
    • RNA: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
    • Protein or peptide: Adenosine deaminase domain-containing protein
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
  • Ligand: ZINC ION
  • Ligand: MAGNESIUM ION

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Supramolecule #1: CAAD:CA6:ATP 6:3:6

SupramoleculeName: CAAD:CA6:ATP 6:3:6 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Source (natural)Organism: Limisphaera ngatamarikiensis (bacteria)

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Macromolecule #1: 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: 1 / Number of copies: 3
Source (natural)Organism: Limisphaera ngatamarikiensis (bacteria)
Molecular weightTheoretical: 1.930277 KDa
SequenceString:
AAAAAA

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Macromolecule #2: Adenosine deaminase domain-containing protein

MacromoleculeName: Adenosine deaminase domain-containing protein / type: protein_or_peptide / ID: 2 / Number of copies: 6 / Enantiomer: LEVO
Source (natural)Organism: Limisphaera ngatamarikiensis (bacteria)
Molecular weightTheoretical: 69.899766 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: NVQAHLFVSL GTAPAIVPEA FLLPGARFVS VHVLTTERPD VTLIREFFRR HAPGVNLTIT RVAGFQDLKS EEDHFRFEEV MFRWFLASR TGPEQRFVCL TGGFKTMSAA MQKAATVLGA AEVFHVLADD CCVGPQGRLM PPSTLEEILW ARDQGHLHWI R LGPERGWP ...String:
NVQAHLFVSL GTAPAIVPEA FLLPGARFVS VHVLTTERPD VTLIREFFRR HAPGVNLTIT RVAGFQDLKS EEDHFRFEEV MFRWFLASR TGPEQRFVCL TGGFKTMSAA MQKAATVLGA AEVFHVLADD CCVGPQGRLM PPSTLEEILW ARDQGHLHWI R LGPERGWP QLRRIAPEQF PLQVVEEKGD ERRVQAEDRA FGTFLQDLLQ RASRIAGAWE MLPELPFADL ATWSEGELAW LR EPLDPRA PADQRWVAGL PKIELHCHLG GFATHGELLR RVRNAAENPG KLPPLEEPRL PEGWPLPAQP IPLAEYMKLG NAN GTALLR DPGCLREQCR LLYRHLVDQG VCYAEVRCSP ANYAEVRSPW DVLADIRAAF QECMEGARTA PGGLPACHVN LILI ATRRA SGDYRAAIAR HLALAVTAAE HWRDENACRV VGVDLAGYED EKTRAHYFRE EFTAVHRCGL AVTVHAGEND DAEGI WRAV FDLNARRLGH ALSLGQSREL LRSVADRGIG VELCPYANLQ IKGFRLDGSD RAGPADPRHE AHAPGPYPLL DYLREG VRV TVNTDNIGIS AASLTDNLLL AARLCPGLTR LDLLHLQRHA LETAFCTATQ RLTLLRRISS GIPRP

UniProtKB: adenosine deaminase

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Macromolecule #3: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 6 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

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

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Macromolecule #4: ZINC ION

MacromoleculeName: ZINC ION / type: ligand / ID: 4 / Number of copies: 6 / Formula: ZN
Molecular weightTheoretical: 65.409 Da

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Macromolecule #5: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 5 / Number of copies: 2 / Formula: MG
Molecular weightTheoretical: 24.305 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: 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

Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 55742
Initial angle assignmentType: ANGULAR RECONSTITUTION
Final angle assignmentType: RANDOM ASSIGNMENT

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