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- PDB-9qtj: Structure of Oceanobacillus iheyensis group II intron domains D1-D6 -

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Basic information

Entry
Database: PDB / ID: 9qtj
TitleStructure of Oceanobacillus iheyensis group II intron domains D1-D6
ComponentsRNA (461-MER)
KeywordsRNA / Protein-free RNA cryo-EM / Ribozyme / Metalloenzymes / Splicing
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesOceanobacillus iheyensis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.79 Å
AuthorsJadhav, S.S. / Nigro, M. / Marcia, M.
Funding support Sweden, France, 4items
OrganizationGrant numberCountry
Swedish Research Council2024-04107 Sweden
Other governmentHORIZON-MSCA-2023-DN-01 action (project: TargetRNA, n. 101168667)
Agence Nationale de la Recherche (ANR)ANR-10-INBS-0005-02 France
Agence Nationale de la Recherche (ANR)ANR-17-EURE-0003 France
CitationJournal: Proteins / Year: 2026
Title: Functional Relevance of CASP16 Nucleic Acid Predictions as Evaluated by Structure Providers.
Authors: Rachael C Kretsch / Reinhard Albrecht / Ebbe S Andersen / Hsuan-Ai Chen / Wah Chiu / Rhiju Das / Jeanine G Gezelle / Marcus D Hartmann / Claudia Höbartner / Yimin Hu / Shekhar Jadhav / ...Authors: Rachael C Kretsch / Reinhard Albrecht / Ebbe S Andersen / Hsuan-Ai Chen / Wah Chiu / Rhiju Das / Jeanine G Gezelle / Marcus D Hartmann / Claudia Höbartner / Yimin Hu / Shekhar Jadhav / Philip E Johnson / Christopher P Jones / Deepak Koirala / Emil L Kristoffersen / Eric Largy / Anna Lewicka / Cameron D Mackereth / Marco Marcia / Michela Nigro / Manju Ojha / Joseph A Piccirilli / Phoebe A Rice / Heewhan Shin / Anna-Lena Steckelberg / Zhaoming Su / Yoshita Srivastava / Liu Wang / Yuan Wu / Jiahao Xie / Nikolaj H Zwergius / John Moult / Andriy Kryshtafovych /
Abstract: Accurate biomolecular structure prediction enables the prediction of mutational effects, the speculation of function based on predicted structural homology, the analysis of ligand binding modes, ...Accurate biomolecular structure prediction enables the prediction of mutational effects, the speculation of function based on predicted structural homology, the analysis of ligand binding modes, experimental model building, and many other applications. Such algorithms to predict essential functional and structural features remain out of reach for biomolecular complexes containing nucleic acids. Here, we report a quantitative and qualitative evaluation of nucleic acid structures for the CASP16 blind prediction challenge by 12 of the experimental groups who provided nucleic acid targets. Blind predictions accurately model secondary structure and some aspects of tertiary structure, including reasonable global folds for some complex RNAs; however, predictions often lack accuracy in the regions of highest functional importance. All models have inaccuracies in non-canonical regions where, for example, the nucleic-acid backbone bends, deviating from an A-form helix geometry, or a base forms a non-standard hydrogen bond (not a Watson-Crick base pair). These bends and non-canonical interactions are integral to forming functionally important regions such as RNA enzymatic active sites. Additionally, the modeling of conserved and functional interfaces between nucleic acids and ligands, proteins, or other nucleic acids remains poor. For some targets, the experimental structures may not represent the only structure the biomolecular complex occupies in solution or in its functional life cycle, posing a future challenge for the community.
History
DepositionApr 9, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 18, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 18, 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

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Assembly

Deposited unit
1: RNA (461-MER)


Theoretical massNumber of molelcules
Total (without water)155,8161
Polymers155,8161
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1

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Components

#1: RNA chain RNA (461-MER)


Mass: 155816.406 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Group IIC intron / Source: (synth.) Oceanobacillus iheyensis (bacteria)
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: Group IIC Intron / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightValue: 0.156 MDa / Experimental value: NO
Source (natural)Organism: Oceanobacillus iheyensis (bacteria)
Source (recombinant)Organism: synthetic construct (others)
Buffer solutionpH: 6.5 / Details: 10 mM MgCl2, 150 mM KCl, 5 mM Na-MES pH 6.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 295.15 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 defocus max: 2400 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 36 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
2PHENIXmodel refinement
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.79 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 71128 / Symmetry type: POINT
RefinementCross valid method: NONE

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