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- EMDB-42498: Tetrahymena ribozyme with water and magnesium ions -

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Basic information

Entry
Database: EMDB / ID: EMD-42498
TitleTetrahymena ribozyme with water and magnesium ions
Map data
Sample
  • Complex: Apo L-21 ScaI Tetrahymena ribozyme with water and metal ions.
    • RNA: RNA (387-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: water
KeywordsRibozyme / Magnesium ions / Water / RNA
Biological speciesTetrahymena thermophila (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.31 Å
AuthorsKretsch RC / Li S / Pintilie G / Palo MZ / Case DA / Das R / Zhang K / Chiu W
Funding support United States, China, 10 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM122579 United States
Howard Hughes Medical Institute (HHMI) United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)U24GM129541 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM079429 United States
Chinese Academy of SciencesXDB0490000 China
Other governmentCenter for Advanced Interdisciplinary Science and Biomedicine of IHM QYPY20220019
Other governmentNational Key R&D Program of China 2022YFC2303700
Other governmentNational Key R&D Program of China 2022YFA1302700
Other governmentFundamental Research Funds for the Central Universities WK9100000032
Other governmentFundamental Research Funds for the Central Universities WK9100000044
CitationJournal: Nature / Year: 2025
Title: Complex water networks visualized by cryogenic electron microscopy of RNA.
Authors: Rachael C Kretsch / Shanshan Li / Grigore Pintilie / Michael Z Palo / David A Case / Rhiju Das / Kaiming Zhang / Wah Chiu /
Abstract: The stability and function of biomolecules are directly influenced by their myriad interactions with water. Here we investigated water through cryogenic electron microscopy (cryo-EM) on a highly ...The stability and function of biomolecules are directly influenced by their myriad interactions with water. Here we investigated water through cryogenic electron microscopy (cryo-EM) on a highly solvated molecule: the Tetrahymena ribozyme. By using segmentation-guided water and ion modelling (SWIM), an approach combining resolvability and chemical parameters, we automatically modelled and cross-validated water molecules and Mg ions in the ribozyme core, revealing the extensive involvement of water in mediating RNA non-canonical interactions. Unexpectedly, in regions where SWIM does not model ordered water, we observed highly similar densities in both cryo-EM maps. In many of these regions, the cryo-EM densities superimpose with complex water networks predicted by molecular dynamics, supporting their assignment as water and suggesting a biophysical explanation for their elusiveness to conventional atomic coordinate modelling. Our study demonstrates an approach to unveil both rigid and flexible waters that surround biomolecules through cryo-EM map densities, statistical and chemical metrics, and molecular dynamics simulations.
History
DepositionOct 26, 2023-
Header (metadata) releaseNov 20, 2024-
Map releaseNov 20, 2024-
UpdateApr 9, 2025-
Current statusApr 9, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_42498.png

Downloads & links

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Map

FileDownload / File: emd_42498.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.)
0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å		0.82 Å/pix.
x 256 pix.
= 209.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.82 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 3.0
Minimum - Maximum-43.521366 - 65.479479999999995
Average (Standard dev.)-0.000000000010969 (±1.0)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions256256256
Spacing256256256
CellA=B=C: 209.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #1

Fileemd_42498_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_42498_half_map_2.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Apo L-21 ScaI Tetrahymena ribozyme with water and metal ions.

EntireName: Apo L-21 ScaI Tetrahymena ribozyme with water and metal ions.
Components
  • Complex: Apo L-21 ScaI Tetrahymena ribozyme with water and metal ions.
    • RNA: RNA (387-MER)
  • Ligand: MAGNESIUM ION
  • Ligand: water

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Supramolecule #1: Apo L-21 ScaI Tetrahymena ribozyme with water and metal ions.

SupramoleculeName: Apo L-21 ScaI Tetrahymena ribozyme with water and metal ions.
type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Tetrahymena thermophila (eukaryote) / Synthetically produced: Yes
Molecular weightTheoretical: 125 KDa

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Macromolecule #1: RNA (387-MER)

MacromoleculeName: RNA (387-MER) / type: rna / ID: 1 / Number of copies: 1
Source (natural)Organism: Tetrahymena thermophila (eukaryote)
Molecular weightTheoretical: 125.096773 KDa
SequenceString: GGAGGGAAAA GUUAUCAGGC AUGCACCUGG UAGCUAGUCU UUAAACCAAU AGAUUGCAUC GGUUUAAAAG GCAAGACCGU CAAAUUGCG GGAAAGGGGU CAACAGCCGU UCAGUACCAA GUCUCAGGGG AAACUUUGAG AUGGCCUUGC AAAGGGUAUG G UAAUAAGC ...String:
GGAGGGAAAA GUUAUCAGGC AUGCACCUGG UAGCUAGUCU UUAAACCAAU AGAUUGCAUC GGUUUAAAAG GCAAGACCGU CAAAUUGCG GGAAAGGGGU CAACAGCCGU UCAGUACCAA GUCUCAGGGG AAACUUUGAG AUGGCCUUGC AAAGGGUAUG G UAAUAAGC UGACGGACAU GGUCCUAACC ACGCAGCCAA GUCCUAAGUC AACAGAUCUU CUGUUGAUAU GGAUGCAGUU CA CAGACUA AAUGUCGGUC GGGGAAGAUG UAUUCUUCUC AUAAGAUAUA GUCGGACCUC UCCUUAAUGG GAGCUAGCGG AUG AAGUGA UGCAACACUG GAGCCGCUGG GAACUAAUUU GUAUGCGAAA GUAUAUUGAU UAGUUUUGGA G

GENBANK: GENBANK: X54512.1

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Macromolecule #2: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 2 / Number of copies: 22 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #3: water

MacromoleculeName: water / type: ligand / ID: 3 / Number of copies: 140 / Formula: HOH
Molecular weightTheoretical: 18.015 Da
Chemical component information

ChemComp-HOH:
WATER

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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

Concentration3.125 mg/mL
BufferpH: 8
Component:
ConcentrationFormulaName
50.0 mMNa-C8H18N2O4SSodium HEPES
10.0 mMMgCl2Magnesium Chloride
GridModel: Quantifoil R2/1 / Material: COPPER / Mesh: 200 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Atmosphere: AIR
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 278 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number real images: 18365 / Average exposure time: 2.5 sec. / Average electron dose: 57.25 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: 2.0 µm / Nominal defocus min: 0.5 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: 3804753
Startup modelType of model: INSILICO MODEL
Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: FOURIER SPACE / Resolution.type: BY AUTHOR / Resolution: 2.31 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Software - details: Non-uniform Refinement / Number images used: 473325
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Software - details: Ab initio reconstruction multi-class
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC / Software - details: Non-uniform Refinement
Final 3D classificationNumber classes: 4 / Avg.num./class: 295333 / Software - Name: cryoSPARC / Software - details: 3D variability

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Atomic model buiding 1

Initial modelPDB ID:

7ez0


Chain - Source name: PDB / Chain - Initial model type: experimental model
RefinementSpace: REAL / Protocol: FLEXIBLE FIT / Overall B value: 66
Output model

PDB-9cbw:
Tetrahymena ribozyme with consensus water and magnesium ions

PDB-9cby:
Tetrahymena ribozyme with automatically identified water and magnesium ions

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