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- PDB-9ofe: CryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two... -

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Basic information

Entry
Database: PDB / ID: 9ofe
TitleCryoEM structure of Cad1 bound with cA4 and ATP, hexamer with two intact dimers
Components
  • CRISPR-associated ring nuclease and adenosine deaminase, subunit A
  • cA4 cleavage product, A2>P
KeywordsIMMUNE SYSTEM / HYDROLASE / CRISPR-associated Rossman-fold (CARF) / ATP deaminase / CRISPR immunity / cooperative activation
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
ADENOSINE-5'-TRIPHOSPHATE / RNA / adenosine deaminase
Similarity search - Component
Biological speciesThermoanaerobaculum aquaticum (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.68 Å
AuthorsZhao, Y. / Li, H.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM152081 United States
CitationJournal: To Be Published
Title: Sequential Conformational Activation of a CARF-Fused Adenosine Deaminase by Cyclic Oligoadenylates
Authors: Zhao, Y. / Li, H.
History
DepositionApr 29, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 20, 2025Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Aug 20, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CRISPR-associated ring nuclease and adenosine deaminase, subunit A
B: CRISPR-associated ring nuclease and adenosine deaminase, subunit A
C: cA4 cleavage product, A2>P
D: cA4 cleavage product, A2>P
G: CRISPR-associated ring nuclease and adenosine deaminase, subunit A
H: CRISPR-associated ring nuclease and adenosine deaminase, subunit A
K: CRISPR-associated ring nuclease and adenosine deaminase, subunit A
L: CRISPR-associated ring nuclease and adenosine deaminase, subunit A
J: cA4 cleavage product, A2>P
I: cA4 cleavage product, A2>P
hetero molecules


Theoretical massNumber of molelcules
Total (without water)423,15623
Polymers419,69610
Non-polymers3,46013
Water1448
1


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

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Components

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Protein / RNA chain , 2 types, 10 molecules ABGHKLCDJI

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


Mass: 69499.133 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 (E. coli) / References: UniProt: A0A062XY19, adenosine deaminase
#2: RNA chain
cA4 cleavage product, A2>P


Mass: 675.419 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Thermoanaerobaculum aquaticum (bacteria)

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Non-polymers , 4 types, 21 molecules

#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.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Formula: H2O

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Details

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: Cad1 / Type: COMPLEX / Entity ID: #1-#2 / Source: MULTIPLE SOURCES
Source (natural)Organism: Thermoanaerobaculum aquaticum (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: 2500 nm / Nominal defocus min: 820 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: GATAN K2 QUANTUM (4k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.20.1_4487 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.68 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 257900 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 59.67 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.002126206
ELECTRON MICROSCOPYf_angle_d0.456135814
ELECTRON MICROSCOPYf_chiral_restr0.04233950
ELECTRON MICROSCOPYf_plane_restr0.00364654
ELECTRON MICROSCOPYf_dihedral_angle_d7.50143587

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