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- EMDB-51080: Group II intron assembly intermediate Domain 1, 2, 3 and 4 "Fully... -

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Basic information

Entry
Database: EMDB / ID: EMD-51080
TitleGroup II intron assembly intermediate Domain 1, 2, 3 and 4 "Fully open" state
Map dataGroup II intron domain assembly intermediate 1 to 4
Sample
  • Complex: GROUP IIC INTRON
    • RNA: GROUP IIC INTRON
KeywordsRNA folding / protein-free RNA cryo-EM / Ribozyme / Metalloenzymes / Splicing / RNA
Biological speciesOceanobacillus iheyensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.54 Å
AuthorsJadhav SS / Marcia M
Funding support France, 9 items
OrganizationGrant numberCountry
Region Auvergne Rhone Alpesproject R21105CC; allocation RPH21004CCA France
Fondation ARCPJA-20191209284 France
Institut National du Cancer (inCA)18CN047-00 France
Other governmentCanceropole CLARA - Oncostarter
Agence Nationale de la Recherche (ANR)ANR-10-INBS-0005-02 France
Agence Nationale de la Recherche (ANR)ANR-17-EURE-0003 France
Other governmentWellcome Collaborative Award in Science (209250/Z/17/Z)
Other governmentBWFGB Hamburg
Other governmentLeibniz ScienceCampus InterACt
CitationJournal: Nat Commun / Year: 2025
Title: Dynamic assembly of a large multidomain ribozyme visualized by cryo-electron microscopy.
Authors: Shekhar Jadhav / Mauro Maiorca / Jacopo Manigrasso / Spandan Saha / Auriane Rakitch / Stefano Muscat / Thomas Mulvaney / Marco De Vivo / Maya Topf / Marco Marcia /
Abstract: Many RNAs rely on their 3D structures for function. While acquiring functional 3D structures, certain RNAs form misfolded, non-functional states ('kinetic traps'). Instead, other RNAs sequentially ...Many RNAs rely on their 3D structures for function. While acquiring functional 3D structures, certain RNAs form misfolded, non-functional states ('kinetic traps'). Instead, other RNAs sequentially assemble into their functional conformations over pre-folded scaffolds. Elucidating the principles of RNA sequential assembly is thus important to understand how RNAs avoid the formation of misfolded, non-functional states. Integrating single-particle electron cryomicroscopy (cryo-EM), image processing, in solution small-angle X-ray scattering (SAXS), EM-driven molecular dynamics (MD) simulations, structure-based mutagenesis, and enzymatic assays, we have visualized the sequential multidomain assembly of a self-splicing ribozyme of biomedical and bioengineering significance. Our work reveals a distinct dynamic interplay of helical subdomains in the ribozyme's 5'-terminal scaffold, which acts as a gate to control the docking of 3'-terminal domains. We identify specific conserved and functionally important secondary structure motifs as the key players for orchestrating the energetically inexpensive conformational changes that lead to the productive formation of the catalytic pocket. Our work provides a near-atomic resolution molecular movie of a large multidomain RNA assembling into its functionally active conformation and establishes a basis for understanding how RNA avoids the formation of non-functional 'kinetic traps'.
History
DepositionJul 16, 2024-
Header (metadata) releaseDec 17, 2025-
Map releaseDec 17, 2025-
UpdateDec 17, 2025-
Current statusDec 17, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51080.png

Downloads & links

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Map

FileDownload / File: emd_51080.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGroup II intron domain assembly intermediate 1 to 4
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.81 Å/pix.
x 300 pix.
= 243. Å		0.81 Å/pix.
x 300 pix.
= 243. Å		0.81 Å/pix.
x 300 pix.
= 243. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.81 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0407
Minimum - Maximum-0.026752248 - 0.1845883
Average (Standard dev.)0.00066348043 (±0.0091375355)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 243.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_51080_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Group II intron domain assembly intermediate 1 to 4

Fileemd_51080_additional_1.map
AnnotationGroup II intron domain assembly intermediate 1 to 4
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Group II intron domain assembly intermediate 1 to 4

Fileemd_51080_half_map_1.map
AnnotationGroup II intron domain assembly intermediate 1 to 4
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Group II intron domain assembly intermediate 1 to 4

Fileemd_51080_half_map_2.map
AnnotationGroup II intron domain assembly intermediate 1 to 4
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : GROUP IIC INTRON

EntireName: GROUP IIC INTRON
Components
  • Complex: GROUP IIC INTRON
    • RNA: GROUP IIC INTRON

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Supramolecule #1: GROUP IIC INTRON

SupramoleculeName: GROUP IIC INTRON / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Oceanobacillus iheyensis (bacteria)
Molecular weightTheoretical: 123 KDa

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Macromolecule #1: GROUP IIC INTRON

MacromoleculeName: GROUP IIC INTRON / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Oceanobacillus iheyensis (bacteria)
Molecular weightTheoretical: 95.439609 KDa
SequenceString: GUUAUGUGUG CCCGGCAUGG GUGCAGUCUA UAGGGUGAGA GUCCCGAACU GUGAAGGCAG AAGUAACAGU UAGCCUAACG CAAGGGUGU CCGUGGCGAC AUGGAAUCUG AAGGAAGCGG ACGGCAAACC UUCGGUCUGA GGAACACGAA CUUCAUAUGA G GCUAGGUA ...String:
GUUAUGUGUG CCCGGCAUGG GUGCAGUCUA UAGGGUGAGA GUCCCGAACU GUGAAGGCAG AAGUAACAGU UAGCCUAACG CAAGGGUGU CCGUGGCGAC AUGGAAUCUG AAGGAAGCGG ACGGCAAACC UUCGGUCUGA GGAACACGAA CUUCAUAUGA G GCUAGGUA UCAAUGGAUG AGUUUGCAUA ACAAAACAAA GUCCUUUCUG CCAAAGUUGG UACAGAGUAA AUGAAGCAGA UU GAUGAAG GGAAAGACUG CAUUCUUACC CGGGGAGGUC UGGAAACAGA AGUCAGC

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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

BufferpH: 6.5 / Component - Concentration: 0.5 uM / Component - Formula: Na-MES
Component - Name: Sodium Chloride and 4-(2-sulfonatoethyl)morpholin-4-ium
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.00045000000000000004 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 105000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 349634
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4faq

Final reconstructionResolution.type: BY AUTHOR / Resolution: 7.54 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 56717
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: RANDOM ASSIGNMENT
Final 3D classificationNumber classes: 2 / Avg.num./class: 50000
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4faq


Chain - Chain ID: A / Chain - Residue range: -4-354 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-9g56:
Group II intron assembly intermediate Domain 1, 2, 3 and 4 "Fully open" state

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