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- EMDB-53353: Structure of Oceanobacillus iheyensis group II intron domains D1-D6 -

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Basic information

Entry
Database: EMDB / ID: EMD-53353
TitleStructure of Oceanobacillus iheyensis group II intron domains D1-D6
Map dataWilt type full length self-splicing group IIC intron from Oceanobacillus iheyensis
Sample
  • Complex: Group IIC Intron
    • RNA: RNA (461-MER)
KeywordsProtein-free RNA cryo-EM / Ribozyme / Metalloenzymes / Splicing / RNA
Biological speciesOceanobacillus iheyensis (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.79 Å
AuthorsJadhav SS / Nigro M / Marcia M
Funding support Sweden, France, 4 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
CitationJournal: Proteins / Year: 2026
Title: Functional Relevance of CASP16 Nucleic Acid Predictions as Evaluated by Structure Providers.
Authors: Rachael C Kretsch / Reinhard Albrecht / Ebbe S Andersen / Hsuan-Ai Chen / Wah Chiu / Rhiju Das / Jeanine G Gezelle / Marcus D Hartmann / Claudia Höbartner / Yimin Hu / Shekhar Jadhav / ...Authors: Rachael C Kretsch / Reinhard Albrecht / Ebbe S Andersen / Hsuan-Ai Chen / Wah Chiu / Rhiju Das / Jeanine G Gezelle / Marcus D Hartmann / Claudia Höbartner / Yimin Hu / Shekhar Jadhav / Philip E Johnson / Christopher P Jones / Deepak Koirala / Emil L Kristoffersen / Eric Largy / Anna Lewicka / Cameron D Mackereth / Marco Marcia / Michela Nigro / Manju Ojha / Joseph A Piccirilli / Phoebe A Rice / Heewhan Shin / Anna-Lena Steckelberg / Zhaoming Su / Yoshita Srivastava / Liu Wang / Yuan Wu / Jiahao Xie / Nikolaj H Zwergius / John Moult / Andriy Kryshtafovych /
Abstract: Accurate biomolecular structure prediction enables the prediction of mutational effects, the speculation of function based on predicted structural homology, the analysis of ligand binding modes, ...Accurate biomolecular structure prediction enables the prediction of mutational effects, the speculation of function based on predicted structural homology, the analysis of ligand binding modes, experimental model building, and many other applications. Such algorithms to predict essential functional and structural features remain out of reach for biomolecular complexes containing nucleic acids. Here, we report a quantitative and qualitative evaluation of nucleic acid structures for the CASP16 blind prediction challenge by 12 of the experimental groups who provided nucleic acid targets. Blind predictions accurately model secondary structure and some aspects of tertiary structure, including reasonable global folds for some complex RNAs; however, predictions often lack accuracy in the regions of highest functional importance. All models have inaccuracies in non-canonical regions where, for example, the nucleic-acid backbone bends, deviating from an A-form helix geometry, or a base forms a non-standard hydrogen bond (not a Watson-Crick base pair). These bends and non-canonical interactions are integral to forming functionally important regions such as RNA enzymatic active sites. Additionally, the modeling of conserved and functional interfaces between nucleic acids and ligands, proteins, or other nucleic acids remains poor. For some targets, the experimental structures may not represent the only structure the biomolecular complex occupies in solution or in its functional life cycle, posing a future challenge for the community.
History
DepositionApr 9, 2025-
Header (metadata) releaseFeb 18, 2026-
Map releaseFeb 18, 2026-
UpdateFeb 18, 2026-
Current statusFeb 18, 2026Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53353.png

Downloads & links

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Map

FileDownload / File: emd_53353.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationWilt type full length self-splicing group IIC intron from Oceanobacillus iheyensis
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.84 Å/pix.
x 300 pix.
= 251.7 Å		0.84 Å/pix.
x 300 pix.
= 251.7 Å		0.84 Å/pix.
x 300 pix.
= 251.7 Å

Surface

Projections

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Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.839 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0847
Minimum - Maximum-0.045260333 - 0.34352267
Average (Standard dev.)0.0013687059 (±0.013608527)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 251.7 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_53353_msk_1.map
Projections & Slices
AxesZYX

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Half map: #2

Fileemd_53353_half_map_1.map
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Half map: #1

Fileemd_53353_half_map_2.map
Projections & Slices
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Sample components

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Entire : Group IIC Intron

EntireName: Group IIC Intron
Components
  • Complex: Group IIC Intron
    • RNA: RNA (461-MER)

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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: 156 KDa

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Macromolecule #1: RNA (461-MER)

MacromoleculeName: RNA (461-MER) / type: rna / ID: 1 / Details: Group IIC intron / Number of copies: 1
Source (natural)Organism: Oceanobacillus iheyensis (bacteria)
Molecular weightTheoretical: 155.816406 KDa
SequenceString: GUGUGCCCGG CAUGGGUGCA GUCUAUAGGG UGAGAGUCCC GAACUGUGAA GGCAGAAGUA ACAGUUAGCC UAACGCAAGG GUGUCCGUG GCGACAUGGA AUCUGAAGGA AGCGGACGGC AAACCUUCGG UCUGAGGAAC ACGAACUUCA UAUGAGGCUA G GUAUCAAU ...String:
GUGUGCCCGG CAUGGGUGCA GUCUAUAGGG UGAGAGUCCC GAACUGUGAA GGCAGAAGUA ACAGUUAGCC UAACGCAAGG GUGUCCGUG GCGACAUGGA AUCUGAAGGA AGCGGACGGC AAACCUUCGG UCUGAGGAAC ACGAACUUCA UAUGAGGCUA G GUAUCAAU GGAUGAGUUU GCAUAACAAA ACAAAGUCCU UUCUGCCAAA GUUGGUACAG AGUAAAUGAA GCAGAUUGAU GA AGGGAAA GACUGCAUUC UUACCCGGGG AGGUCUGAUC GAAACGCCAA GCACUCUUGG UAACCCAUUC AGCAAUGGAU GGC UGAACG GUCAGAAGUC AGCAGAAGUC AUAGUACCCU GCAUACUCGA GAAUGUAAGG GGAAGGACGG AACAAUUAAG UUCG CUUAA UUGAACCGCC GUAUACCGAA CGGUACGUAC GGUGGUGUGA GAGGACGGGG GUUAGUCGCU CCCUUCUACU CUAUU A

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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 / 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 % / Chamber temperature: 295.15 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 36.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.4 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: 3.79 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 71128
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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