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- PDB-9g54: Group II intron assembly intermediate Domain 1, 2, 3 and 4 "Partl... -

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Basic information

Entry
Database: PDB / ID: 9g54
TitleGroup II intron assembly intermediate Domain 1, 2, 3 and 4 "Partly open" state
ComponentsGROUP IIC INTRON
KeywordsRNA / RNA folding / 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: 6.3 Å
AuthorsJadhav, S.S. / Marcia, M.
Funding support France, 9items
OrganizationGrant numberCountry
Region Auvergne Rhone Alpesproject R21105CC; allocation RPH21004CCA France
Fondation ARCPJA-20191209284 France
Institut National du Cancer (inCA)18CN047-00 France
Other governmentCanceropole CLARA - Oncostarter
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: To Be Published
Title: Sequential assembly of the catalytic structure of a large multidomain RNA visualized by cryo-electron microscopy
Authors: Jadhav, S.S. / Maiorca, M. / Mulvaney, T. / Topf, M. / Marcia, M.
History
DepositionJul 16, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 2025Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Nov 5, 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: GROUP IIC INTRON


Theoretical massNumber of molelcules
Total (without water)117,5741
Polymers117,5741
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 GROUP IIC INTRON


Mass: 117573.617 Da / Num. of mol.: 1 / Source method: obtained synthetically / 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: NATURAL
Molecular weightValue: 0.123 MDa / Experimental value: NO
Source (natural)Organism: Oceanobacillus iheyensis (bacteria)
Buffer solutionpH: 6.5
Buffer componentConc.: 0.5 uM
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
VitrificationInstrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 %

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 105000 X / Nominal defocus max: 2200 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingElectron dose: 40 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k)

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Processing

EM software
IDNameVersionCategory
1cryoSPARC4particle selection
2SerialEMimage acquisition
4cryoSPARCCTF correction
7PHENIX4722model fitting
9cryoSPARCinitial Euler assignment
10cryoSPARCfinal Euler assignment
12cryoSPARC43D reconstruction
19ERRASERmodel refinement
20TEMPymodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 349634
3D reconstructionResolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 41981 / Symmetry type: POINT
Atomic model buildingProtocol: RIGID BODY FIT / Space: REAL
Atomic model buildingPDB-ID: 4FAQ

4faq


Pdb chain-ID: A / Accession code: 4FAQ / Chain residue range: -4-354 / Pdb chain residue range: -4-354 / Source name: PDB / Type: experimental model

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