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- EMDB-62319: Cryo-EM structure of circular intron of thymidylate synthase (td)... -

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Basic information

Entry
Database: EMDB / ID: EMD-62319
TitleCryo-EM structure of circular intron of thymidylate synthase (td) gene of bacteriophage T4
Map dataCryo-EM structure of circular intron of thymidylate synthase (td) gene of bacteriophage T4 (unsharpen map)
Sample
  • Complex: Cryo-EM structure of circular intron of thymidylate synthase (td) gene of bacteriophage T4
    • RNA: RNA (264-MER)
  • Ligand: MAGNESIUM ION
KeywordsT4 TD / Group I intron / cryo-EM / circular RNA / RNA
Biological speciesEscherichia phage T4 (virus)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsAn L / Li S / Zhang K
Funding support1 items
OrganizationGrant numberCountry
Other government
CitationJournal: To Be Published
Title: Mechanistic Insights into Cyclization of the T4 td Group I Intron
Authors: An L / Li S / Zhang K
History
DepositionNov 8, 2024-
Header (metadata) releaseNov 12, 2025-
Map releaseNov 12, 2025-
UpdateNov 12, 2025-
Current statusNov 12, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_62319.png

Downloads & links

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Map

FileDownload / File: emd_62319.map.gz / Format: CCP4 / Size: 144.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM structure of circular intron of thymidylate synthase (td) gene of bacteriophage T4 (unsharpen map)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.96 Å/pix.
x 336 pix.
= 322.56 Å		0.96 Å/pix.
x 336 pix.
= 322.56 Å		0.96 Å/pix.
x 336 pix.
= 322.56 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.96 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.08
Minimum - Maximum-0.17828372 - 0.7138857
Average (Standard dev.)0.00037303226 (±0.010323951)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions336336336
Spacing336336336
CellA=B=C: 322.56 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: Cryo-EM structure of circular intron of thymidylate synthase...

Fileemd_62319_additional_1.map
AnnotationCryo-EM structure of circular intron of thymidylate synthase (td) gene of bacteriophage T4 (sharpen map)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of circular intron of thymidylate synthase...

Fileemd_62319_half_map_1.map
AnnotationCryo-EM structure of circular intron of thymidylate synthase (td) gene of bacteriophage T4 (half map 1)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Cryo-EM structure of circular intron of thymidylate synthase...

Fileemd_62319_half_map_2.map
AnnotationCryo-EM structure of circular intron of thymidylate synthase (td) gene of bacteriophage T4 (half map 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 : Cryo-EM structure of circular intron of thymidylate synthase (td)...

EntireName: Cryo-EM structure of circular intron of thymidylate synthase (td) gene of bacteriophage T4
Components
  • Complex: Cryo-EM structure of circular intron of thymidylate synthase (td) gene of bacteriophage T4
    • RNA: RNA (264-MER)
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Cryo-EM structure of circular intron of thymidylate synthase (td)...

SupramoleculeName: Cryo-EM structure of circular intron of thymidylate synthase (td) gene of bacteriophage T4
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 90 KDa

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Macromolecule #1: RNA (264-MER)

MacromoleculeName: RNA (264-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Escherichia phage T4 (virus)
Molecular weightTheoretical: 84.950125 KDa
SequenceString: AAUUGAGGCC UGAGUAUAAG GUGACUUAUA CUUGUAAUCU AUCUAAACGG GGAACCUCUC UAGUAGACAA UCCCGUGCUA AAUUGUAGG ACUGCCCGGG UUCUACAUAA AUGCCUAACG ACUAUCCCUU UGGGGAGUAG GGUCAAGUGA CUCGAAACGA U AGACAACU ...String:
AAUUGAGGCC UGAGUAUAAG GUGACUUAUA CUUGUAAUCU AUCUAAACGG GGAACCUCUC UAGUAGACAA UCCCGUGCUA AAUUGUAGG ACUGCCCGGG UUCUACAUAA AUGCCUAACG ACUAUCCCUU UGGGGAGUAG GGUCAAGUGA CUCGAAACGA U AGACAACU UGCUUUAACA AGUUGGAGAU AUAGUCUGCU CUGCAUGGUG ACAUGCAGCU GGAUAUAAUU CCGGGGUAAG AU UAACGAC CUUAUCUGAA CAUAAUG

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 3 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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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

Concentration1 mg/mL
BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: FEI FALCON I (4k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.3 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 3600020
CTF correctionType: NONE
Startup modelType of model: NONE
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.5.1) / Number images used: 172889
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD

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