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- PDB-9qu7: Cryo-EM structure of Oceanobacillus iheyensis group II intron dom... -

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Basic information

Entry
Database: PDB / ID: 9qu7
TitleCryo-EM structure of Oceanobacillus iheyensis group II intron domains D1-D5
ComponentsGroup IIC Intron
KeywordsRNA / Ribozyme / Metalloenzymes / Splicing / Protein-free RNA cryo-EM
Function / homology: / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesOceanobacillus iheyensis (bacteria)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsJadhav, S.S. / Maiorca, M. / Mulvaney, T. / Topf, M. / Marcia, M.
Funding support Sweden, France, 7items
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
Other governmentWellcome Collaborative Award in Science (209250/Z/17/Z)
Other governmentBWFGB Hamburg
Other governmentLeibniz ScienceCampus InterACt
CitationJournal: Bmc Methods / Year: 2025
Title: Cryo-specimen preparation and imaging of highly-structured and dynamic large non-coding RNAs
Authors: Jadhav, S. / Marcia, M.
History
DepositionApr 10, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 25, 2026Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Feb 25, 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
A: Group IIC Intron
B: Group IIC Intron
hetero molecules


Theoretical massNumber of molelcules
Total (without water)257,64921
Polymers257,0982
Non-polymers55119
Water543
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 Group IIC Intron


Mass: 128549.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Oceanobacillus iheyensis (bacteria)
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 13 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: K / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Formula: H2O
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: Group IIC intron / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.133 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
Buffer componentConc.: 5 mM
Name: Sodium Chloride and 4-(2-sulfonatoethyl)morpholin-4-ium
Formula: Na-MES
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
VitrificationCryogen name: ETHANE / Humidity: 100 %

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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: 2200 nm / Nominal defocus min: 800 nm
Image recordingElectron dose: 37.4 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 881868 / Symmetry type: POINT
RefinementCross valid method: NONE
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
Displacement parametersBiso mean: 81.54 Å2
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00917271
ELECTRON MICROSCOPYf_angle_d0.648911317
ELECTRON MICROSCOPYf_chiral_restr0.04411504
ELECTRON MICROSCOPYf_plane_restr0.0058302
ELECTRON MICROSCOPYf_dihedral_angle_d22.20664390

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