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- PDB-9ubo: The structure of type III CRISPR-associated deaminase in complex ... -

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Basic information

Entry
Database: PDB / ID: 9ubo
TitleThe structure of type III CRISPR-associated deaminase in complex cA6 and ATP, state 5
Components
  • RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')
  • adenosine deaminase
KeywordsHYDROLASE/RNA / deaminase / complex / ATP / HYDROLASE-RNA complex
Function / homology
Function and homology information


inosine biosynthetic process / adenosine deaminase / adenosine catabolic process / hypoxanthine salvage / adenosine deaminase activity / metal ion binding / 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
ADENOSINE-5'-TRIPHOSPHATE / RNA / adenosine deaminase
Similarity search - Component
Biological speciesThermoanaerobaculum aquaticum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsKong, J.P. / Wu, W.Q. / Li, Z.X. / Xiao, Y.B.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)82473977 China
CitationJournal: To Be Published
Title: The structure of type III CRISPR-associated deaminase
Authors: Kong, J.P. / Wu, W.Q. / Li, Z.X. / Xiao, Y.B.
History
DepositionApr 3, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 15, 2026Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 15, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: adenosine deaminase
D: adenosine deaminase
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')
B: adenosine deaminase
C: adenosine deaminase
E: adenosine deaminase
F: adenosine deaminase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)431,34027
Polymers427,7599
Non-polymers3,58118
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
adenosine deaminase / type III CRISPR-associated deaminase CAAD


Mass: 70328.023 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobaculum aquaticum (bacteria)
Gene: EG19_07865 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A062XY19, adenosine deaminase
#2: RNA chain RNA (5'-R(P*AP*AP*AP*AP*AP*A)-3')


Mass: 1930.277 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoanaerobaculum aquaticum (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)
#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.: 6 / 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: The structure of type III CRISPR-associated deaminase in complex cA6 and ATP, state 1
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: Thermoanaerobaculum aquaticum (bacteria)
Source (recombinant)Organism: Escherichia coli BL21(DE3) (bacteria)
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: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 106481 / Symmetry type: POINT
RefinementHighest resolution: 2.84 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)

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