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- EMDB-53373: Cryo-EM structure of Oceanobacillus iheyensis group II intron dom... -

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Basic information

Entry
Database: EMDB / ID: EMD-53373
TitleCryo-EM structure of Oceanobacillus iheyensis group II intron domains D1-D5
Map data
Sample
  • Complex: Group IIC intron
    • RNA: Group IIC Intron
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM ION
  • Ligand: water
KeywordsRibozyme / Metalloenzymes / Splicing / Protein-free RNA cryo-EM / RNA
Biological speciesOceanobacillus iheyensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsJadhav SS / Maiorca M / Mulvaney T / Topf M / Marcia M
Funding support Sweden, France, 7 items
OrganizationGrant numberCountry
Swedish Research Council2024-04107 Sweden
Other governmentHORIZON-MSCA-2023-DN-01 action (project: TargetRNA, n. 101168667)
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: Bmc Methods / Year: 2025
Title: Cryo-specimen preparation and imaging of highly-structured and dynamic large non-coding RNAs
Authors: Jadhav S / Marcia M
History
DepositionApr 10, 2025-
Header (metadata) releaseFeb 25, 2026-
Map releaseFeb 25, 2026-
UpdateFeb 25, 2026-
Current statusFeb 25, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53373.png

Downloads & links

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Map

FileDownload / File: emd_53373.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 320 pix.
= 268.8 Å		0.84 Å/pix.
x 320 pix.
= 268.8 Å		0.84 Å/pix.
x 320 pix.
= 268.8 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.84 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.2
Minimum - Maximum-0.22933286 - 0.7285954
Average (Standard dev.)0.0002594507 (±0.015572751)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 268.8 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53373_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_53373_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_53373_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 : Group IIC intron

EntireName: Group IIC intron
Components
  • Complex: Group IIC intron
    • RNA: Group IIC Intron
  • Ligand: MAGNESIUM ION
  • Ligand: POTASSIUM ION
  • Ligand: water

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Supramolecule #1: Group IIC intron

SupramoleculeName: Group IIC intron / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Oceanobacillus iheyensis (bacteria)
Molecular weightTheoretical: 133 KDa

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Macromolecule #1: Group IIC Intron

MacromoleculeName: Group IIC Intron / type: rna / ID: 1 / Number of copies: 2
Source (natural)Organism: Oceanobacillus iheyensis (bacteria)
Molecular weightTheoretical: 128.549094 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 AGUCAGCAGA AGUCAUAGUA CCCUGUUCGC AGG GGAAGG ACGGAACAAG UAUGGCGUUC GCGCCUAAGC UUGAACCGCC GUAUACCGAA CGGUACGUAC GGUGGUGUGG

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 13 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: POTASSIUM ION

MacromoleculeName: POTASSIUM ION / type: ligand / ID: 3 / Number of copies: 6 / Formula: K
Molecular weightTheoretical: 39.098 Da

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Macromolecule #4: water

MacromoleculeName: water / type: ligand / ID: 4 / Number of copies: 3 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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: 5.0 mM / Component - Formula: Na-MES
Component - Name: Sodium Chloride and 4-(2-sulfonatoethyl)morpholin-4-ium
Details: 10 mM MgCl2, 150 mM KCl, 5 mM Na-MES pH-6.5
GridModel: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: AIR / Pretreatment - Pressure: 0.00045000000000000004 kPa
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 37.4 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

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

4faq

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 881868
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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