9YX9 | pdb_00009yx9

SARS-CoV-2 SL5 rotated junction

• PDB DOI: https://doi.org/10.2210/pdb9YX9/pdb
• EM Map EMD-73600: EMDB EMDataResource

• Classification: RNA
• Organism(s): Severe acute respiratory syndrome coronavirus 2
• Mutation(s): No 


• Deposited: 2025-10-26 Released: 2026-09-02 
• Deposition Author(s): Kretsch, R.C., Xu, L., Chiu, W., Das, R.
• Funding Organization(s): National Science Foundation (NSF, United States)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 6.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

Assessment of Nucleic Acid Structure Prediction in CASP16.

Kretsch, R.C., Hummer, A.M., He, S., Yuan, R., Zhang, J., Karagianes, T., Cong, Q., Kryshtafovych, A., Das, R.

(2026) Proteins 94: 192-217

• PubMed: 41165252 
• DOI: https://doi.org/10.1002/prot.70072
• Primary Citation Related Structures: 
  9YX9, 9YXA


• PubMed 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 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.

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Organizational Affiliation: 
• Biophysics Program, Stanford University School of Medicine, Stanford, California, USA.
Howard Hughes Medical Institute, Stanford University, Stanford, California, USA.
Department of Biochemistry, Stanford University School of Medicine, Stanford, California, USA.
Department of Chemical Engineering, Texas A&M University, College Station, Texas, USA.
Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
Eterna Massive Open Laboratory, Stanford, California, USA.
Harold C. Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas, USA.
Genome Center, University of California, Davis, California, USA.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 39.81 kDa 
• Atom Count: 2,633 
• Modeled Residue Count: 124 
• Deposited Residue Count: 124 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (124-MER)	A	124	Severe acute respiratory syndrome coronavirus 2

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 6.50 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
RECONSTRUCTION	cryoSPARC

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-09-02 
Deposition Author(s): Kretsch, R.C., Xu, L., Chiu, W., Das, R.

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Funding Organization	Location	Grant Number
National Science Foundation (NSF, United States)	United States	2330652

Revision History  

• Version 1.0: 2026-09-02
  Type: Initial release