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- EMDB-75574: gRNAde designed RNA molecule -

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Open data


ID or keywords:

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Basic information

Entry
Database: EMDB / ID: EMD-75574
TitlegRNAde designed RNA molecule
Map dataprimary map
Sample
  • Complex: De novo design of RNA Kissing Multiloops using gRNAde
    • RNA: RNA (519-MER)
Keywordspseudoknot / kissing multiloops / RNA
Biological speciessynthetic construct (others)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.9 Å
AuthorsSpellmon N / Haack DB / Joshi CK / Hingey J / Rudolfs B / Mancino A / Toor N / Yu Z / 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_75574.png

Downloads & links

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Map

FileDownload / File: emd_75574.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: 0.04
Minimum - Maximum-0.15210989 - 0.30026066
Average (Standard dev.)-0.000061069506 (±0.0025275494)
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: #1

Fileemd_75574_additional_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_75574_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_75574_half_map_2.map
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 (519-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: synthetic construct (others)

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Macromolecule #1: RNA (519-MER)

MacromoleculeName: RNA (519-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: synthetic construct (others)
Molecular weightTheoretical: 168.281969 KDa
SequenceString: GUGCCACGGG GAGCGAUAGC UCCGGGUGAA AACCCUGGGG GCCGUGGCUA GGCUGGAGGC CCCCGGCAGG GAGUGAAGGA CGGAACAAG UAUGGCGUUC GCGCCAUGCU UGAACCACCG UAUACCGAAC GGUACGUACG GUGGUGAAAC AAACAAAUAA A CUAAAUUA ...String:
GUGCCACGGG GAGCGAUAGC UCCGGGUGAA AACCCUGGGG GCCGUGGCUA GGCUGGAGGC CCCCGGCAGG GAGUGAAGGA CGGAACAAG UAUGGCGUUC GCGCCAUGCU UGAACCACCG UAUACCGAAC GGUACGUACG GUGGUGAAAC AAACAAAUAA A CUAAAUUA UGUGUGCCCG GCAUGGGUGC AGUCUAUAGG GUGAGAGUCC CGAACUGUGA AGGCAGAAGU AACAGUUAGC CU AACGCAA GGGUGUCCGU GGCGACAUGG AAUCUGAAGG AAGCGGACGG CAAACCUUCG GUCUGAGGAA CACGAACUUC AUA UGAGGC UAGGUAUCAA UGGAUGAGUU UGCAUAACAA AACAAAGUCC UUUCUGCCAA AGUUGGUACA GAGUAAAUGA AGCA GAUUG AUGAAGGGAA AGACUGCAUU CUUACCCGGG GAGGUCUGAG CUUUCGAGCU CAGAAGUCAG CAGAAGUCAU AGUAA CUCC CUGCCGUACA CGAAAGUGUA CCCUCCAGCC GGAUC

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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: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.9 Å / Resolution method: FSC 0.143 CUT-OFF / Software: (Name: cryoSPARC, PHENIX) / Number images used: 479673
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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