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- PDB-9ndd: RNA scaffold attached to 8-oxoguanine riboswitch aptamer, combine... -

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Basic information

Entry
Database: PDB / ID: 9ndd
TitleRNA scaffold attached to 8-oxoguanine riboswitch aptamer, combined core plus aptamer
ComponentsRNA (160-MER)
KeywordsRNA / Riboswitch / aptamer / engineering
Function / homology8-OXOGUANINE / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciessynthetic construct (others)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.67 Å
AuthorsJones, C.P. / Ferre-D'Amare, A.R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Heart, Lung, and Blood Institute (NIH/NHLBI) United States
CitationJournal: To Be Published
Title: Symmetric scaffolds enable de novo modelling of RNA by cryoEM
Authors: Jones, C.P. / Ferre-D'Amare, A.R.
History
DepositionFeb 18, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Additional map / Part number: 1 / Data content type: Additional map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 2026Data content type: Mask / Part number: 1 / Data content type: Mask / Provider: repository / Type: Initial release
Revision 1.0Mar 4, 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: RNA (160-MER)
B: RNA (160-MER)
C: RNA (160-MER)
D: RNA (160-MER)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,4428
Polymers205,7824
Non-polymers6604
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: RNA chain
RNA (160-MER)


Mass: 51445.496 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#2: Chemical
ChemComp-OXG / 8-OXOGUANINE


Mass: 165.110 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H3N5O2
Has ligand of interestN
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: RNA scaffold attached to 8-oxoguanine riboswitch aptamer, combined core plus aptamer
Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT
Source (natural)Organism: synthetic construct (others)
Source (recombinant)Organism: in vitro transcription vector pT7-TP(deltai) (others)
Buffer solutionpH: 7.4
SpecimenEmbedding 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: SPOT SCAN
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 1800 nm / Nominal defocus min: 600 nm
Image recordingElectron dose: 39.15 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.19.2_4158 / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 2.67 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 465913 / Symmetry type: POINT
RefinementHighest resolution: 2.67 Å
Stereochemistry target values: REAL-SPACE (WEIGHTED MAP SUM AT ATOM CENTERS)
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00915616
ELECTRON MICROSCOPYf_angle_d0.73324336
ELECTRON MICROSCOPYf_dihedral_angle_d17.2837864
ELECTRON MICROSCOPYf_chiral_restr0.0393276
ELECTRON MICROSCOPYf_plane_restr0.005656

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