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- EMDB-35223: The Tet-S1 state of G264A mutated Tetrahymena group I intron with... -

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Basic information

Entry
Database: EMDB / ID: EMD-35223
TitleThe Tet-S1 state of G264A mutated Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleoside
Map data
Sample
  • Complex: Co-transcriptional folded G264A mutated Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleoside
    • RNA: The Tet-S1 state molecule of co-transcriptional folded G264A mutated Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleoside
  • Ligand: MAGNESIUM ION
  • Ligand: SPERMIDINE
  • Ligand: (2R,3R,4S,5R)-2-(2-azanylpurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol
KeywordsCatalytic RNA / G264A mutated Tetrahymena group I intron / RNA
Biological speciesTetrahymena thermophila (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.98 Å
AuthorsLuo B / Zhang C / Ling X / Mukherjee S / Jia G / Xie J / Jia X / Liu L / Baulin EF / Luo Y ...Luo B / Zhang C / Ling X / Mukherjee S / Jia G / Xie J / Jia X / Liu L / Baulin EF / Luo Y / Jiang L / Dong H / Wei X / Bujnicki JM / Su Z
Funding support China, Poland, European Union, 7 items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2021YFA1301900 China
Ministry of Science and Technology (MoST, China)2022YFC2303700 China
National Natural Science Foundation of China (NSFC)32070049 China
National Natural Science Foundation of China (NSFC)32222040 China
Polish National Science Centre2017/26/A/NZ1/01083 Poland
Polish National Science Centre2021/43/D/NZ1/03360 Poland
European Molecular Biology Organization (EMBO)ALTF 525-2022European Union
CitationJournal: Nat Catal / Year: 2023
Title: Cryo-EM reveals dynamics of Tetrahymena group I intron self-splicing
Authors: Luo B / Zhang C / Ling X / Mukherjee S / Jia G / Xie J / Jia X / Liu L / Baulin EF / Luo Y / Jiang L / Dong H / Wei X / Bujnicki JM / Su Z
History
DepositionFeb 1, 2023-
Header (metadata) releaseMar 29, 2023-
Map releaseMar 29, 2023-
UpdateJul 3, 2024-
Current statusJul 3, 2024Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_35223.png

Downloads & links

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Map

FileDownload / File: emd_35223.map.gz / Format: CCP4 / Size: 42.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.85 Å/pix.
x 224 pix.
= 190.4 Å		0.85 Å/pix.
x 224 pix.
= 190.4 Å		0.85 Å/pix.
x 224 pix.
= 190.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.85 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02
Minimum - Maximum-0.16064787 - 0.4473657
Average (Standard dev.)0.00047802483 (±0.008229675)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions224224224
Spacing224224224
CellA=B=C: 190.40001 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_35223_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_35223_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 : Co-transcriptional folded G264A mutated Tetrahymena group I intro...

EntireName: Co-transcriptional folded G264A mutated Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleoside
Components
  • Complex: Co-transcriptional folded G264A mutated Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleoside
    • RNA: The Tet-S1 state molecule of co-transcriptional folded G264A mutated Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleoside
  • Ligand: MAGNESIUM ION
  • Ligand: SPERMIDINE
  • Ligand: (2R,3R,4S,5R)-2-(2-azanylpurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol

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Supramolecule #1: Co-transcriptional folded G264A mutated Tetrahymena group I intro...

SupramoleculeName: Co-transcriptional folded G264A mutated Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleoside
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Tetrahymena thermophila (eukaryote)

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Macromolecule #1: The Tet-S1 state molecule of co-transcriptional folded G264A muta...

MacromoleculeName: The Tet-S1 state molecule of co-transcriptional folded G264A mutated Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleoside
type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 134.810516 KDa
SequenceString: CUCUCUAAAU AGCAAUAUUU ACCUUUGGAG GGAAAAGUUA UCAGGCAUGC ACCUGGUAGC UAGUCUUUAA ACCAAUAGAU UGCAUCGGU UUAAAAGGCA AGACCGUCAA AUUGCGGGAA AGGGGUCAAC AGCCGUUCAG UACCAAGUCU CAGGGGAAAC U UUGAGAUG ...String:
CUCUCUAAAU AGCAAUAUUU ACCUUUGGAG GGAAAAGUUA UCAGGCAUGC ACCUGGUAGC UAGUCUUUAA ACCAAUAGAU UGCAUCGGU UUAAAAGGCA AGACCGUCAA AUUGCGGGAA AGGGGUCAAC AGCCGUUCAG UACCAAGUCU CAGGGGAAAC U UUGAGAUG GCCUUGCAAA GGGUAUGGUA AUAAGCUGAC GGACAUGGUC CUAACCACGC AGCCAAGUCC UAAGUCAACA GA UCUUCUG UUGAUAUGGA UGCAGUUCAC AAACUAAAUG UCGGUCGGGG AAGAUGUAUU CUUCUCAUAA GAUAUAGUCG GAC CUCUCC UUAAUGGGAG CUAGCGGAUG AAGUGAUGCA ACACUGGAGC CGCUGGGAAC UAAUUUGUAU GCGAAAGUAU AUUG AUUAG UUUUGGAGUA CUC

GENBANK: GENBANK: JN547815.1

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 27 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: SPERMIDINE

MacromoleculeName: SPERMIDINE / type: ligand / ID: 3 / Number of copies: 1 / Formula: SPD
Molecular weightTheoretical: 145.246 Da
Chemical component information

ChemComp-SPD:
SPERMIDINE

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Macromolecule #4: (2R,3R,4S,5R)-2-(2-azanylpurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol

MacromoleculeName: (2R,3R,4S,5R)-2-(2-azanylpurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol
type: ligand / ID: 4 / Number of copies: 1 / Formula: OJI
Molecular weightTheoretical: 267.241 Da
Chemical component information

ChemComp-OJI:
(2R,3R,4S,5R)-2-(2-azanylpurin-9-yl)-5-(hydroxymethyl)oxolane-3,4-diol

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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: 7
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 K

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Electron microscopy

MicroscopeFEI TITAN KRIOS
TemperatureMin: 79.3 K
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-30 / Average electron dose: 55.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 50.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.7 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 165000
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: 4012136
Startup modelType of model: PDB ENTRY
PDB model - PDB ID:

7xd4

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.98 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 953401
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1)
Final 3D classificationNumber classes: 6 / Software - Name: RELION (ver. 3.1)

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Atomic model buiding 1

RefinementSpace: REAL / Protocol: AB INITIO MODEL
Output model

PDB-8i7n:
The Tet-S1 state of G264A mutated Tetrahymena group I intron with 6nt 3'/5'-exon and 2-aminopurine nucleoside

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