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- EMDB-66469: Tetrahymena Ribozyme scaffolded SicX sRNA in complex with C-di-GMP -

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Basic information

Entry
Database: EMDB / ID: EMD-66469
TitleTetrahymena Ribozyme scaffolded SicX sRNA in complex with C-di-GMP
Map data
Sample
  • Complex: Tetrahymena Ribozyme scaffolded SicX sRNA in complex with C-di-GMP
    • RNA: RNA (381-MER)
  • Ligand: 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)
  • Ligand: MAGNESIUM ION
KeywordsRNA / sRNA / C-di-GMP
Biological speciesPseudomonas aeruginosa (bacteria)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.28 Å
AuthorsWang CC
Funding support China, 1 items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: Tetrahymena Ribozyme scaffolded SicX sRNA in complex with C-di-GMP
Authors: Wang CC
History
DepositionOct 3, 2025-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_66469.png

Downloads & links

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Map

FileDownload / File: emd_66469.map.gz / Format: CCP4 / Size: 64 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 256 pix.
= 211.712 Å		0.83 Å/pix.
x 256 pix.
= 211.712 Å		0.83 Å/pix.
x 256 pix.
= 211.712 Å

Surface

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Slices (1/3)

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Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.827 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.164
Minimum - Maximum-1.2268113 - 2.1692443
Average (Standard dev.)0.0020165301 (±0.050696474)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 211.712 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_66469_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_66469_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Tetrahymena Ribozyme scaffolded SicX sRNA in complex with C-di-GMP

EntireName: Tetrahymena Ribozyme scaffolded SicX sRNA in complex with C-di-GMP
Components
  • Complex: Tetrahymena Ribozyme scaffolded SicX sRNA in complex with C-di-GMP
    • RNA: RNA (381-MER)
  • Ligand: 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)
  • Ligand: MAGNESIUM ION

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Supramolecule #1: Tetrahymena Ribozyme scaffolded SicX sRNA in complex with C-di-GMP

SupramoleculeName: Tetrahymena Ribozyme scaffolded SicX sRNA in complex with C-di-GMP
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Pseudomonas aeruginosa (bacteria) / Synthetically produced: Yes

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Macromolecule #1: RNA (381-MER)

MacromoleculeName: RNA (381-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Pseudomonas aeruginosa (bacteria)
Molecular weightTheoretical: 123.342852 KDa
SequenceString: GGGUCUGUUG AUAUGGAUGC AGUUCACAGA CUAAAUGUCG GUCGGGGAAG AUGUAUUCUU CUCAUAAGAU AUAGUCGGAC CUCUCCUUA AUGGGAGCUA GCGGAUGAAG UGAUGCAACA CUGGAGCCGC UGGGGCGGAG AGUGGGACGC CUUGGAGUAC U CGUUGGAG ...String:
GGGUCUGUUG AUAUGGAUGC AGUUCACAGA CUAAAUGUCG GUCGGGGAAG AUGUAUUCUU CUCAUAAGAU AUAGUCGGAC CUCUCCUUA AUGGGAGCUA GCGGAUGAAG UGAUGCAACA CUGGAGCCGC UGGGGCGGAG AGUGGGACGC CUUGGAGUAC U CGUUGGAG GGAAAAGUUA UCAGGCAUGC ACCUGGUAGC UAGUCUUUAA ACCAAUAGAU UGCAUCGGUU UAAAAGGCAA GA CCGUCAA AUUGCGGGAA AGGGGUCAAC AGCCGUUCAG UACCAAGUCU CAGGGGAAAC UUUGAGAUGG CCUUGCAAAG GGU AUGGUA AUAAGCUGAC GGACAUGGUC CUAACCACGC AGCCAAGUCC UAAGUCAACA GACCC

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Macromolecule #2: 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydr...

MacromoleculeName: 9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)
type: ligand / ID: 2 / Number of copies: 1 / Formula: C2E
Molecular weightTheoretical: 690.411 Da
Chemical component information

ChemComp-C2E:
9,9'-[(2R,3R,3aS,5S,7aR,9R,10R,10aS,12S,14aR)-3,5,10,12-tetrahydroxy-5,12-dioxidooctahydro-2H,7H-difuro[3,2-d:3',2'-j][1,3,7,9,2,8]tetraoxadiphosphacyclododecine-2,9-diyl]bis(2-amino-1,9-dihydro-6H-purin-6-one)

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 22 / 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

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 1.5625 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.2 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: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.28 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 173332
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
FSC plot (resolution estimation)

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