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- PDB-8z3p: The structure of type III CRISPR-associated deaminase in complex ... -

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Basic information

Entry
Database: PDB / ID: 8z3p
TitleThe structure of type III CRISPR-associated deaminase in complex cA6 and ATP, fully activated
Components
  • Adenosine deaminase domain-containing protein
  • RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
KeywordsIMMUNE SYSTEM / defense system / deaminase
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
ADENOSINE-5'-TRIPHOSPHATE / RNA / adenosine deaminase
Similarity search - Component
Biological speciesLimisphaera ngatamarikiensis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsChen, M.R. / Li, Z.X. / Xiao, Y.B.
Funding support China, 1items
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, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Dec 25, 2024Provider: repository / Type: Initial release
Revision 1.0Dec 25, 2024Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Dec 25, 2024Data content type: Additional map / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Dec 25, 2024Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
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Revision 1.0Dec 25, 2024Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Dec 25, 2024Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Mar 5, 2025Group: Data collection / Database references / Category: citation / em_admin
Item: _citation.journal_volume / _citation.year / _em_admin.last_update
Revision 1.1Mar 5, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Database references / Experimental summary / Data content type: EM metadata / EM metadata / Category: citation / em_admin / Data content type: EM metadata / EM metadata / EM metadata
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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
Y: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
Z: RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
A: Adenosine deaminase domain-containing protein
B: Adenosine deaminase domain-containing protein
C: Adenosine deaminase domain-containing protein
D: Adenosine deaminase domain-containing protein
E: Adenosine deaminase domain-containing protein
F: Adenosine deaminase domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)428,67423
Polymers425,1899
Non-polymers3,48414
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: RNA chain RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')


Mass: 1930.277 Da / Num. of mol.: 3 / Source method: obtained synthetically / Source: (synth.) Limisphaera ngatamarikiensis (bacteria)
#2: Protein
Adenosine deaminase domain-containing protein


Mass: 69899.766 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Limisphaera ngatamarikiensis (bacteria)
Gene: G4L39_03315 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A6M1RED6
#3: Chemical
ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: CAAD:CA6:ATP 6:3:6 / Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Limisphaera ngatamarikiensis (bacteria)
Source (recombinant)Organism: Escherichia coli (E. coli)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: TFS KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2400 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 40 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21_5207 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 55742 / Symmetry type: POINT
RefinementHighest resolution: 3.4 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00330244
ELECTRON MICROSCOPYf_angle_d0.67441249
ELECTRON MICROSCOPYf_dihedral_angle_d8.6934512
ELECTRON MICROSCOPYf_chiral_restr0.0474522
ELECTRON MICROSCOPYf_plane_restr0.0065365

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