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- PDB-9v7q: Cryo-EM structures of the Azoarcus pre-tRNA(ILE) intron conformat... -

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Basic information

Entry
Database: PDB / ID: 9v7q
TitleCryo-EM structures of the Azoarcus pre-tRNA(ILE) intron conformation after the cyclization
ComponentsRNA (203-MER)
KeywordsRNA / Azoarcus pre-tRNA(ILE) / self-splicing / circular intron / RNA structure
Function / homology: / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesAzoarcus olearius (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.27 Å
AuthorsHong, Y. / Liu, J. / Zhang, X. / Liu, J. / Li, S. / Zhang, K.
Funding support China, 1items
OrganizationGrant numberCountry
Other government China
CitationJournal: Nat Commun / Year: 2026
Title: Pre-splicing conformation and stepwise circularization of a group I intron in Azoarcus pre-tRNA
Authors: Hong, Y. / Liu, J. / Zhang, X. / Liu, J. / Li, S. / Zhang, K.
History
DepositionMay 28, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Mar 25, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 25, 2026Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

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Assembly

Deposited unit
B: RNA (203-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9327
Polymers65,7861
Non-polymers1466
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: RNA chain RNA (203-MER)


Mass: 65786.305 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azoarcus olearius (bacteria)
Production host: in vitro transcription vector pT7-Fluc(deltai) (others)
References: GenBank: 70997234
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg
Has ligand of interestN
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: Cryo-EM structures of the Azoarcus pre-tRNA(ILE) intron conformation after the cyclization
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.067 MDa / Experimental value: YES
Source (natural)Organism: Azoarcus olearius (bacteria)
Source (recombinant)Organism: in vitro transcription vector pT7-Fluc(deltai) (others)
Buffer solutionpH: 7.5
SpecimenConc.: 1 mg/ml / Embedding 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: 3000 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 59.5 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4.7particle selection
2EPUimage acquisition
8PHENIXmodel refinement
12cryoSPARC4.7classification
13cryoSPARC4.73D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 1314171
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.27 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 335306 / Symmetry type: POINT
RefinementStereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0114881
ELECTRON MICROSCOPYf_angle_d1.0557613
ELECTRON MICROSCOPYf_dihedral_angle_d15.5692433
ELECTRON MICROSCOPYf_chiral_restr0.0531015
ELECTRON MICROSCOPYf_plane_restr0.007203

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