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- PDB-9nyi: Structure of HalA in complex with oligodeoxyadenylate -

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Basic information

Entry
Database: PDB / ID: 9nyi
TitleStructure of HalA in complex with oligodeoxyadenylate
Components
  • DNA (5'-D(*AP*AP*AP*AP*AP*A)-3')
  • Structure of HalA in complex with oligodeoxyadenylate
KeywordsANTIVIRAL PROTEIN / Hailong / ion channel / oligodeoxyadenylate / anti-phage defense
Function / homologyDNA
Function and homology information
Biological speciesRhodobacteraceae bacterium QY30 (bacteria)
DNA molecule (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 1.98 Å
AuthorsTan, J.M.J. / Melamed, S. / Cofsky, J.C. / Syangtan, D. / Hobbs, S.J. / Del Marmol, J. / Jost, M. / Kruse, A.C. / Sorek, S. / Kranzusch, P.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)1DP2GM146250 United States
CitationJournal: To Be Published
Title: Structure of Hailong HalA in complex with oligodeoxyadenylate
Authors: Tan, J.M.J. / Melamed, S. / Cofsky, J.C. / Syangtan, D. / Hobbs, S.J. / Del Marmol, J. / Jost, M. / Kruse, A.C. / Sorek, R. / Kranzusch, P.J.
History
DepositionMar 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 7, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Structure of HalA in complex with oligodeoxyadenylate
B: Structure of HalA in complex with oligodeoxyadenylate
C: Structure of HalA in complex with oligodeoxyadenylate
D: Structure of HalA in complex with oligodeoxyadenylate
E: DNA (5'-D(*AP*AP*AP*AP*AP*A)-3')
F: DNA (5'-D(*AP*AP*AP*AP*AP*A)-3')
G: DNA (5'-D(*AP*AP*AP*AP*AP*A)-3')
H: DNA (5'-D(*AP*AP*AP*AP*AP*A)-3')


Theoretical massNumber of molelcules
Total (without water)173,3268
Polymers173,3268
Non-polymers00
Water11,962664
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
Structure of HalA in complex with oligodeoxyadenylate


Mass: 41497.109 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacteraceae bacterium QY30 (bacteria)
Production host: Escherichia coli BL21(DE3) (bacteria)
#2: DNA chain
DNA (5'-D(*AP*AP*AP*AP*AP*A)-3')


Mass: 1834.283 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 664 / Source method: isolated from a natural source / Formula: H2O
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: Structure of Hailong HalA in complex with oligodeoxyadenylate
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Source (natural)Organism: Rhodobacteraceae bacterium QY30 (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
Specimen supportDetails: 30 s glow, 10 s hold. easiGlow (Pelco). Negative. / Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 281 K

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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 magnification: 165000 X / Nominal defocus max: 2000 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 53.8 e/Å2 / Film or detector model: TFS FALCON 4i (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 10951
Image scansWidth: 4096 / Height: 4096

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Processing

EM software
IDNameVersionCategoryDetails
1Topaz0.2.5particle selection
2cryoSPARC4.4.1particle selectionTopaz was run within cryoSPARC
3EPU3.6image acquisition
5cryoSPARC4.4.1CTF correction
10cryoSPARC4.4.1initial Euler assignment
11cryoSPARC4.4.1final Euler assignment
12cryoSPARC4.4.1classification
13cryoSPARC4.4.13D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 1247992
SymmetryPoint symmetry: C4 (4 fold cyclic)
3D reconstructionResolution: 1.98 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 231898 / Symmetry type: POINT
Atomic model buildingSource name: AlphaFold / Type: in silico model

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