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- EMDB-75575: MPNN-fixbb designed RNA molecule -

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Open data


ID or keywords:

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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: To Be Published
Title: De novo design of RNA pseudoknots with deep learning
Authors: Joshi CK / Spellmon N / Haack DB / Das R
History
DepositionFeb 13, 2026-
Header (metadata) releaseMay 27, 2026-
Map releaseMay 27, 2026-
UpdateMay 27, 2026-
Current statusMay 27, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_75575.png

Downloads & links

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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 °

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Supplemental data

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Additional map: full map

Fileemd_75575_additional_1.map
Annotationfull map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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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)

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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)

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Sample components

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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)

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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)

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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

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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 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)

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