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- PDB-9yx9: SARS-CoV-2 SL5 rotated junction -

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Basic information

Entry
Database: PDB / ID: 9yx9
TitleSARS-CoV-2 SL5 rotated junction
ComponentsRNA (124-MER)
KeywordsRNA / SL5 / SARS-CoV-2
Function / homology: / RNA / RNA (> 10) / RNA (> 100)
Function and homology information
Biological speciesSevere acute respiratory syndrome coronavirus 2
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 6.5 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
Citation
Journal: Proteins / Year: 2026
Title: Assessment of Nucleic Acid Structure Prediction in CASP16.
Authors: Rachael C Kretsch / Alissa M Hummer / Shujun He / Rongqing Yuan / Jing Zhang / Thomas Karagianes / Qian Cong / Andriy Kryshtafovych / Rhiju Das /
Abstract: Consistently accurate 3D nucleic acid structure prediction would facilitate studies of the diverse RNA and DNA molecules underlying life. In CASP16, blind predictions for 42 targets canvassing a full ...Consistently accurate 3D nucleic acid structure prediction would facilitate studies of the diverse RNA and DNA molecules underlying life. In CASP16, blind predictions for 42 targets canvassing a full array of nucleic acid functions, from dopamine binding by DNA to formation of elaborate RNA nanocages, were submitted by 65 groups from 46 different labs worldwide. In contrast to concurrent protein structure predictions, performance on nucleic acids was generally poor, with no predictions of previously unseen natural RNA structures achieving TM-scores above 0.8. Even though automated server performance has improved, all top-performing groups were human expert predictors: Vfold, GuangzhouRNA-human, and KiharaLab. Good performance on one template-free modeling target (OLE RNA) and accurate global secondary structure prediction suggested that structural information can be extracted from multiple sequence alignments. However, 3D accuracy generally appeared to depend on the availability of closely related 3D structure templates, and predictions still did not achieve consistent recovery of pseudoknots, singlet Watson-Crick-Franklin pairs, non-canonical pairs, or tertiary motifs like A-minor interactions. For the first time, blind predictions of nucleic acid interactions with small molecules, proteins, and other nucleic acids could be assessed in CASP16. As with nucleic acid monomers, prediction accuracy for nucleic acid complexes was generally poor unless 3D templates were available. Accounting for template availability, there has not been a notable increase in nucleic acid modeling accuracy between previous blind challenges and CASP16.
#1: Journal: bioRxiv / Year: 2025
Title: Assessment of nucleic acid structure prediction in CASP16.
Authors: Rachael C Kretsch / Alissa M Hummer / Shujun He / Rongqing Yuan / Jing Zhang / Thomas Karagianes / Qian Cong / Andriy Kryshtafovych / Rhiju Das /
Abstract: Consistently accurate 3D nucleic acid structure prediction would facilitate studies of the diverse RNA and DNA molecules underlying life. In CASP16, blind predictions for 42 targets canvassing a full ...Consistently accurate 3D nucleic acid structure prediction would facilitate studies of the diverse RNA and DNA molecules underlying life. In CASP16, blind predictions for 42 targets canvassing a full array of nucleic acid functions, from dopamine binding by DNA to formation of elaborate RNA nanocages, were submitted by 65 groups from 46 different labs worldwide. In contrast to concurrent protein structure predictions, performance on nucleic acids was generally poor, with no predictions of previously unseen natural RNA structures achieving TM-scores above 0.8. Even though automated server performance has improved, all top-performing groups were human expert predictors: Vfold, GuangzhouRNA-human, and KiharaLab. Good performance on one template-free modeling target (OLE RNA) and accurate global secondary structure prediction suggested that structural information can be extracted from multiple sequence alignments. However, 3D accuracy generally appeared to depend on the availability of closely related 3D structures, and predictions still did not achieve consistent recovery of pseudoknots, singlet Watson-Crick-Franklin pairs, non-canonical pairs, or tertiary motifs like A-minor interactions. For the first time, blind predictions of nucleic acid interactions with small molecules, proteins, and other nucleic acids could be assessed in CASP16. As with nucleic acid monomers, prediction accuracy for nucleic acid complexes was generally poor unless 3D templates were available. Accounting for template availability, there has not been a notable increase in nucleic acid modeling accuracy between previous blind challenges and CASP16.
History
DepositionOct 26, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 2, 2026Provider: repository / Type: Initial release
Revision 1.0Sep 2, 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 (124-MER)


Theoretical massNumber of molelcules
Total (without water)39,8071
Polymers39,8071
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551
Number of models10

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Components

#1: RNA chain RNA (124-MER)


Mass: 39807.484 Da / Num. of mol.: 1 / Source method: obtained synthetically
Source: (synth.) Severe acute respiratory syndrome coronavirus 2
References: GenBank: 2168080771
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: SARS-CoV-2 SL5 junction rotated / Type: COMPLEX / Entity ID: all / Source: SYNTHETIC
Source (natural)Organism: Severe acute respiratory syndrome coronavirus 2
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: 6.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 446097 / Symmetry type: POINT

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