9QU6 | pdb_00009qu6

Cryo-EM structure of Oceanobacillus iheyensis group II intron domains D1-D5

• PDB DOI: https://doi.org/10.2210/pdb9QU6/pdb
• EM Map EMD-53372: EMDB EMDataResource

• Classification: RNA
• Organism(s): Oceanobacillus iheyensis
• Mutation(s): No 


• Deposited: 2025-04-10 Released: 2026-02-25 
• Deposition Author(s): Jadhav, S.S., Maiorca, M., Mulvaney, T., Topf, M., Marcia, M.
• Funding Organization(s): Swedish Research Council, Other government, Agence Nationale de la Recherche (ANR)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Cryo-specimen preparation and imaging of highly-structured and dynamic large non-coding RNAs

Jadhav, S., Marcia, M.

(2025) BMC Methods 2: 26

• DOI: https://doi.org/10.1186/s44330-025-00045-4

Biological Assembly 1  

Biological assembly 1 assigned by authors and generated by (software)

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 130.26 kDa 
• Atom Count: 6,835 
• Modeled Residue Count: 317 
• Deposited Residue Count: 401 
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
Group IIC Intron	A	396	Oceanobacillus iheyensis

Entity ID: 2
Molecule	Chains	Length	Organism	Image
Group IIC Intron 5'-exon	B	5	Oceanobacillus iheyensis

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
K (Subject of Investigation/LOI)	H [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 3.20 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2026-02-25 
Deposition Author(s): Jadhav, S.S., Maiorca, M., Mulvaney, T., Topf, M., Marcia, M.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2024-04107
Other government		HORIZON-MSCA-2023-DN-01 action (project: TargetRNA, n. 101168667)
Agence Nationale de la Recherche (ANR)	France	ANR-10-INBS-0005-02
Agence Nationale de la Recherche (ANR)	France	ANR-17-EURE-0003
Other government		Wellcome Collaborative Award in Science (209250/Z/17/Z)
Other government		BWFGB Hamburg
Other government		Leibniz ScienceCampus InterACt

Revision History  

• Version 1.0: 2026-02-25
  Type: Initial release