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- EMDB-51040: Group II intron assembly intermediate Domain 1 and 2 "Partly open... -

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Basic information

Entry
Database: EMDB / ID: EMD-51040
TitleGroup II intron assembly intermediate Domain 1 and 2 "Partly open" state
Map dataGroup IIC intron assembly intermediate domains 1 and 2
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: 4.61 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: To Be Published
Title: Sequential assembly of the catalytic structure of a large multidomain RNA visualized by cryo-electron microscopy
Authors: Jadhav SS / Maiorca M / Mulvaney T / Topf M / Marcia M
History
DepositionJul 15, 2024-
Header (metadata) releaseNov 5, 2025-
Map releaseNov 5, 2025-
UpdateNov 5, 2025-
Current statusNov 5, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_51040.png

Downloads & links

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Map

FileDownload / File: emd_51040.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationGroup IIC intron assembly intermediate domains 1 and 2
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

Slices (1/3)

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: 0.075
Minimum - Maximum-0.04297601 - 0.28640082
Average (Standard dev.)0.0005412668 (±0.010187471)
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_51040_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Group IIC intron assembly intermediate domains 1 and 2

Fileemd_51040_additional_1.map
AnnotationGroup IIC intron assembly intermediate domains 1 and 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Group IIC intron assembly intermediate domains 1 and 2

Fileemd_51040_half_map_1.map
AnnotationGroup IIC intron assembly intermediate domains 1 and 2
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Group IIC intron assembly intermediate domains 1 and 2

Fileemd_51040_half_map_2.map
AnnotationGroup IIC intron assembly intermediate domains 1 and 2
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: 101 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: 96.130016 KDa
SequenceString: GGGUUAUGUG UGCCCGGCAU GGGUGCAGUC UAUAGGGUGA GAGUCCCGAA CUGUGAAGGC AGAAGUAACA GUUAGCCUAA CGCAAGGGU GUCCGUGGCG ACAUGGAAUC UGAAGGAAGC GGACGGCAAA CCUUCGGUCU GAGGAACACG AACUUCAUAU G AGGCUAGG ...String:
GGGUUAUGUG UGCCCGGCAU GGGUGCAGUC UAUAGGGUGA GAGUCCCGAA CUGUGAAGGC AGAAGUAACA GUUAGCCUAA CGCAAGGGU GUCCGUGGCG ACAUGGAAUC UGAAGGAAGC GGACGGCAAA CCUUCGGUCU GAGGAACACG AACUUCAUAU G AGGCUAGG UAUCAAUGGA UGAGUUUGCA UAACAAAACA AAGUCCUUUC UGCCAAAGUU GGUACAGAGU AAAUGAAGCA GA UUGAUGA AGGGAAAGAC UGCAUUCUUA CCCGGGGAGG UCUGGAAACA GAAGUCAGC

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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

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 38.07 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: 306972
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

4faq

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.61 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 41652
Initial angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final angle assignmentType: RANDOM ASSIGNMENT / Software - Name: cryoSPARC
Final 3D classificationNumber classes: 2 / Avg.num./class: 30000
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

4faq


Chain - Chain ID: A / Chain - Residue range: -4-289 / Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL
Output model

PDB-9g4i:
Group II intron assembly intermediate Domain 1 and 2 "Partly open" state

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