[English] 日本語
Yorodumi
- EMDB-75575: MPNN-fixbb designed RNA molecule -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-75575
TitleMPNN-fixbb designed RNA molecule
Map dataprimary map
Sample
  • Complex: De novo design of RNA Kissing Multiloops using gRNAde
    • RNA: RNA (518-MER)
Keywordssynthetic / pseudoknot / kissing multiloops / RNA
Biological speciesEscherichia phage T7 (virus) / synthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.0 Å
AuthorsHaack DB / Spellmon N / Favor AH / Kubaney A / Baker D / Rudolfs B / Hingey J / 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

-
Structure visualization

Supplemental images

emd_75575.png

Downloads & links

-
Map

FileDownload / File: emd_75575.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
Contrast
Others
AxesX (Sec.)Y (Row.)Z (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-0.113671124 - 0.22955163
Average (Standard dev.)0.00004642061 (±0.0023411545)
SymmetrySpace group: 1
Details

EMDB XML:

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

-
Supplemental data

-
Additional map: full map

Fileemd_75575_additional_1.map
Annotationfull map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map B

Fileemd_75575_half_map_1.map
Annotationhalf map B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: half map A

Fileemd_75575_half_map_2.map
Annotationhalf map A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : De novo design of RNA Kissing Multiloops using gRNAde

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

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

SupramoleculeName: De novo design of RNA Kissing Multiloops using gRNAde / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Escherichia phage T7 (virus)

-
Macromolecule #1: RNA (518-MER)

MacromoleculeName: RNA (518-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 168.048891 KDa
SequenceString: GGACGCCCGG CGCUGUAGCG CCGGCCGAAA GGCCACGCCC AGGCGUCCUG GCGGGCCAGG GCGGUCGGGG AGUGAAGGAC GGAACAAGU AUGGCGUUCG CGCCAUGCUU GAACCACCGU AUACCGAACG GUACGUACGG UGGUGAAACA AACAAAUAAA C UAAAUUAU ...String:
GGACGCCCGG CGCUGUAGCG CCGGCCGAAA GGCCACGCCC AGGCGUCCUG GCGGGCCAGG GCGGUCGGGG 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 CGACGGGCCC GAAAGGGCCC AGGCCCGCCG GAUC

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

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

-
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

+
Image processing

CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: cryoSPARC, PHENIX) / Number images used: 113234
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more