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- PDB-9kgh: Cryo-EM structure of circular intron of thymidylate synthase (td)... -

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Basic information

Entry
Database: PDB / ID: 9kgh
TitleCryo-EM structure of circular intron of thymidylate synthase (td) gene of bacteriophage T4
ComponentsRNA (264-MER)
KeywordsRNA / T4 TD / Group I intron / cryo-EM / circular RNA
Function / homologyRNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesEscherichia phage T4 (virus)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsAn, L. / Li, S. / Zhang, K.
Funding support1items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Mechanistic Insights into Cyclization of the T4 td Group I Intron
Authors: An, L. / Li, S. / Zhang, K.
History
DepositionNov 8, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Nov 12, 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
U: RNA (264-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,0234
Polymers84,9501
Non-polymers733
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: RNA chain RNA (264-MER)


Mass: 84950.125 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia phage T4 (virus)
Production host: in vitro transcription vector pT7-Fluc(deltai) (others)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
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: Cryo-EM structure of circular intron of thymidylate synthase (td) gene of bacteriophage T4
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Molecular weightValue: 0.09 MDa / Experimental value: YES
Source (natural)Organism: Escherichia phage T4 (virus)
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: 2700 nm / Nominal defocus min: 1300 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: FEI FALCON I (4k x 4k)

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Processing

EM software
IDNameVersionCategory
8PHENIXmodel refinement
13cryoSPARC4.5.13D reconstruction
CTF correctionType: NONE
Particle selectionNum. of particles selected: 3600020
SymmetryPoint symmetry: C1 (asymmetric)
3D reconstructionResolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 172889 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.0096287
ELECTRON MICROSCOPYf_angle_d1.1789788
ELECTRON MICROSCOPYf_dihedral_angle_d17.8693159
ELECTRON MICROSCOPYf_chiral_restr0.061320
ELECTRON MICROSCOPYf_plane_restr0.008264

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