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- EMDB-75584: MPNN-RFdiff designed RNA molecule -

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Basic information

Entry
Database: EMDB / ID: EMD-75584
TitleMPNN-RFdiff designed RNA molecule
Map dataprimary map
Sample
  • Complex: De novo design of RNA Kissing Multiloops using MPNN-RFdiff
    • RNA: RNA (518-MER)
Keywordspseudoknot / kissing multiloops / RNA
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.8 Å
AuthorsHingey J / Spellmon N / Favor AH / Kubaney A / Baker D / Haack DB / Rudolfs B / Mancino A / Yu Z / Toor N / Das R
Funding support United States, 1 items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Science / Year: 2026
Title: De novo design of RNA pseudoknots with deep learning.
Authors: Jill Townley / Wipapat Kladwang / David Baker / Hamish M Blair / Christian A Choe / Gina El Nesr / Andrew Favor / Eli Fisker / Daniel B Haack / Shujun He / Jason Hingey / Po-Ssu Huang / Rui ...Authors: Jill Townley / Wipapat Kladwang / David Baker / Hamish M Blair / Christian A Choe / Gina El Nesr / Andrew Favor / Eli Fisker / Daniel B Haack / Shujun He / Jason Hingey / Po-Ssu Huang / Rui Huang / Chaitanya K Joshi / Thomas Karagianes / Andrew Kubaney / Pietro Liò / Adamo Mancino / Jonathan Romano / Boris Rudolfs / Nicholas Spellmon / Navtej Toor / Jigyasa Verma / Vivian Wu / Zhiheng Yu / Eterna Participants / Rhiju Das /
Abstract: RNA design has been hindered by the limited accuracy of three-dimensional (3D) structure prediction. In this study, we show that intricate RNA structures can be generated with current deep learning ...RNA design has been hindered by the limited accuracy of three-dimensional (3D) structure prediction. In this study, we show that intricate RNA structures can be generated with current deep learning tools through accurate de novo design of pseudoknot secondary structures. In an Eterna competition involving 57 pseudoknots, generative artificial intelligence (AI) methods matched experienced human designers in solving most blind challenges, evaluated by single nucleotide-resolution chemical mapping, compensatory mutagenesis, and cryo-electron microscopy. AI-generated molecules with accurate secondary structures formed well-ordered 3D folds stabilized by noncanonical tertiary interactions not modeled during design. Success was guided by an RNet foundation model trained on prior chemical mapping data, suggesting that some difficult RNA design tasks may be tractable without first solving RNA 3D structure prediction.
History
DepositionFeb 13, 2026-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateSep 9, 2026-
Current statusSep 9, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75584.png

Downloads & links

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Map

FileDownload / File: emd_75584.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationprimary map
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.73 Å/pix.
x 420 pix.
= 308.112 Å		0.73 Å/pix.
x 420 pix.
= 308.112 Å		0.73 Å/pix.
x 420 pix.
= 308.112 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.7336 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.12743041 - 0.27278176
Average (Standard dev.)0.0002354701 (±0.0036043553)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 308.112 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: full map

Fileemd_75584_additional_1.map
Annotationfull map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map A

Fileemd_75584_half_map_1.map
Annotationhalf map A
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: half map B

Fileemd_75584_half_map_2.map
Annotationhalf map B
Projections & Slices
AxesZYX

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Slices (1/2)
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Histogram

Histogram (log scale)

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Sample components

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Entire : De novo design of RNA Kissing Multiloops using MPNN-RFdiff

EntireName: De novo design of RNA Kissing Multiloops using MPNN-RFdiff
Components
  • Complex: De novo design of RNA Kissing Multiloops using MPNN-RFdiff
    • RNA: RNA (518-MER)

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Supramolecule #1: De novo design of RNA Kissing Multiloops using MPNN-RFdiff

SupramoleculeName: De novo design of RNA Kissing Multiloops using MPNN-RFdiff
type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: synthetic construct (others)

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Macromolecule #1: RNA (518-MER)

MacromoleculeName: RNA (518-MER) / type: rna / ID: 1 / Number of copies: 2
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 167.965844 KDa
SequenceString: GCGCCGGAGG CCCUAAAGGG CCAAGCGAAA GCUUAGGGGG ACCGGCGCAG GGAUAGUACC CCCCACCGGG AGUGAAGGAC GGAACAAGU AUGGCGUUCG CGCCAUGCUU GAACCACCGU AUACCGAACG GUACGUACGG UGGUGAAACA AACAAAUAAA C UAAAUUAU ...String:
GCGCCGGAGG CCCUAAAGGG CCAAGCGAAA GCUUAGGGGG ACCGGCGCAG GGAUAGUACC CCCCACCGGG AGUGAAGGAC GGAACAAGU AUGGCGUUCG CGCCAUGCUU GAACCACCGU AUACCGAACG GUACGUACGG UGGUGAAACA AACAAAUAAA C UAAAUUAU GUGUGCCCGG CAUGGGUGCA GUCUAUAGGG UGAGAGUCCC GAACUGUGAA GGCAGAAGUA ACAGUUAGCC UA ACGCAAG GGUGUCCGUG GCGACAUGGA AUCUGAAGGA AGCGGACGGC AAACCUUCGG UCUGAGGAAC ACGAACUUCA UAU GAGGCU AGGUAUCAAU GGAUGAGUUU GCAUAACAAA ACAAAGUCCU UUCUGCCAAA GUUGGUACAG AGUAAAUGAA GCAG AUUGA UGAAGGGAAA GACUGCAUUC UUACCCGGGG AGGUCUGAGC UUUCGAGCUC AGAAGUCAGC AGAAGUCAUA GUAAC UCCC GGUGCGGGCC UAUAGGCCCG AACUAUCCCG GAUC

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration5 mg/mL
BufferpH: 6.5
VitrificationCryogen name: ETHANE-PROPANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 0.6 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionApplied symmetry - Point group: C2 (2 fold cyclic) / Resolution.type: BY AUTHOR / Resolution: 4.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: cryoSPARC, PHENIX) / Number images used: 115837
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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