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- PDB-9yxa: BtCoV SL5 with SL5c truncated -

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Basic information

Entry
Database: PDB / ID: 9yxa
TitleBtCoV SL5 with SL5c truncated
ComponentsRNA (127-MER)
KeywordsRNA / SL5 / BtCoV
Function / homology: / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesPipistrellus bat coronavirus HKU5
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 9.5 Å
AuthorsKretsch, R.C. / Xu, L. / Chiu, W. / Das, R.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)2330652 United States
CitationJournal: To Be Published
Title: Assessment of nucleic acid structure prediction in CASP16
Authors: Kretsch, R.C. / Hummer, A.M. / He, S. / Yuan, R. / Zhang, J. / Karagianes, T. / Cong, Q. / Kryshtafovych, A. / Das, R.
History
DepositionOct 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2026Provider: repository / Type: Initial release
Revision 1.0Aug 26, 2026Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RNA (127-MER)


Theoretical massNumber of molelcules
Total (without water)40,9081
Polymers40,9081
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Number of models25

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Components

#1: RNA chain RNA (127-MER)


Mass: 40908.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Pipistrellus bat coronavirus HKU5 / References: GenBank: 126030122
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: BtCoV SL5 with SL5c truncated / Type: COMPLEX / Entity ID: all / Source: SYNTHETIC
Source (natural)Organism: Pipistrellus bat coronavirus HKU5
Buffer solutionpH: 8
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: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2600 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 60 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k)

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Processing

EM software
IDNameCategory
1cryoSPARCparticle selection
13cryoSPARC3D reconstruction
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 9.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21246 / Symmetry type: POINT

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