11AG | pdb_000011ag

MPNN-RFdiff designed RNA molecule

• PDB DOI: https://doi.org/10.2210/pdb11AG/pdb
• EM Map EMD-75584: EMDB EMDataResource

• Classification: RNA
• Organism(s): synthetic construct
• Expression System: Escherichia phage T7
• Mutation(s): No 


• Deposited: 2026-02-13 Released: 2026-05-27 
• Deposition Author(s): Hingey, J., Spellmon, N., Favor, A.H., Kubaney, A., Baker, D., Haack, D.B., Rudolfs, B., Mancino, A., Yu, Z., Toor, N., Das, R.
• Funding Organization(s): Howard Hughes Medical Institute (HHMI)

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Experimental Data Snapshot

• Method: ELECTRON MICROSCOPY
• Resolution: 4.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

Literature

De novo design of RNA pseudoknots with deep learning

Joshi, C.K., Spellmon, N., Haack, D.B., Das, R.

To be published.

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: electron microscopy

Macromolecule Content 

• Total Structure Weight: 335.93 kDa 
• Atom Count: 4,338 
• Modeled Residue Count: 202 
• Deposited Residue Count: 1,036 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (518-MER)	A, B [auth C]	518	synthetic construct

Experimental Data & Validation

Experimental Data

• Method: ELECTRON MICROSCOPY
• Resolution: 4.80 Å
• Aggregation State: PARTICLE 
• Reconstruction Method: SINGLE PARTICLE 

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.21.1_5286
RECONSTRUCTION	cryoSPARC
RECONSTRUCTION	PHENIX

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2026-05-27 
Deposition Author(s): Hingey, J., Spellmon, N., Favor, A.H., Kubaney, A., Baker, D., Haack, D.B., Rudolfs, B., Mancino, A., Yu, Z., Toor, N., Das, R.

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Funding Organization	Location	Grant Number
Howard Hughes Medical Institute (HHMI)	United States	--

Revision History  

• Version 1.0: 2026-05-27
  Type: Initial release