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- EMDB-53068: Cryo-EM map of P. furiosus 70S grown at 95 degrees -

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Basic information

Entry
Database: EMDB / ID: EMD-53068
TitleCryo-EM map of P. furiosus 70S grown at 95 degrees
Map datasharpened consensus map of P furiosus 70S grown at 95deg
Sample
  • Complex: P. furiosus 70S
KeywordsRNA modification / cryo-EM / ribosome
Biological speciesPyrococcus furiosus (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.59 Å
AuthorsMatzov D / Georgeson J / Westhof E / Schwartz S / Shalev-Benami M
Funding supportEuropean Union, 1 items
OrganizationGrant numberCountry
iNEXT-Discovery24433European Union
CitationJournal: Cell / Year: 2025
Title: Pan-modification profiling facilitates a cross-evolutionary dissection of the thermoregulated ribosomal epitranscriptome.
Authors: Miguel A Garcia-Campos / Joe Georgeson / Ronit Nir / Robert Reichelt / Kristin A Fluke / Donna Matzov / Vinithra Iyer / Brett W Burkhart / Lauren Lui / Anatoly Kustanovich / Felix ...Authors: Miguel A Garcia-Campos / Joe Georgeson / Ronit Nir / Robert Reichelt / Kristin A Fluke / Donna Matzov / Vinithra Iyer / Brett W Burkhart / Lauren Lui / Anatoly Kustanovich / Felix Grünberger / Supuni Thalalla-Gamage / Shereen A Howpay-Manage / Milan Gerovac / Nicolas Alexandre / Yuko Nobe / Jakub S Nowak / Manoj Perera / Alexander Apostle / Shiyue Fang / Sebastian Glatt / Ghil Jona / Sébastien Ferreira-Cerca / Jörg Vogel / Masato Taoka / Jordan L Meier / Eric Westhof / Thomas J Santangelo / Dina Grohmann / Moran Shalev-Benami / Schraga Schwartz /
Abstract: Ribosomal RNA (rRNA) constitutes the core of ribosomes and is extensively chemically modified. Technical challenges have precluded systematically dissecting rRNA modifications and their dynamics. We ...Ribosomal RNA (rRNA) constitutes the core of ribosomes and is extensively chemically modified. Technical challenges have precluded systematically dissecting rRNA modifications and their dynamics. We develop Pan-Mod-seq, permitting inference of 16 distinct modifications across dozens of samples in parallel. We applied Pan-Mod-seq to RNA from 14 species spanning all domains of life, cultured under highly diverse conditions. While dynamic modifications are rare in mesophiles, in extreme hyperthermophiles, ∼50% of modifications are dynamic. We dissect the biogenesis and function of a conserved module of tandem mC-acC modifications, co-induced at high temperatures, via enzymes intrinsically regulated by temperature and required for growth at higher temperatures. Cryo-electron microscopy (cryo-EM) structures of ribosomes from wild-type (WT) and enzyme-deficient archaea reveal recurrent molecular interactions through which they confer structural stability, and biophysical studies demonstrate their synergistic thermostabilizing role. Our findings systematically dissect rRNA modification plasticity and pave the way for surveying the rRNA epitranscriptome in health and disease.
History
DepositionMar 10, 2025-
Header (metadata) releaseNov 26, 2025-
Map releaseNov 26, 2025-
UpdateDec 10, 2025-
Current statusDec 10, 2025Processing site: PDBe / Status: Released

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Structure visualization

Supplemental images

emd_53068.png

Downloads & links

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Map

FileDownload / File: emd_53068.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationsharpened consensus map of P furiosus 70S grown at 95deg
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.99 Å/pix.
x 448 pix.
= 443.52 Å		0.99 Å/pix.
x 448 pix.
= 443.52 Å		0.99 Å/pix.
x 448 pix.
= 443.52 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.99 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-1.7563571 - 2.7156396
Average (Standard dev.)0.0007705374 (±0.082193695)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions448448448
Spacing448448448
CellA=B=C: 443.52002 Å
α=β=γ: 90.0 °

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Supplemental data

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Additional map: sharpened consensus map of P furiosus 70S grown at 95deg

Fileemd_53068_additional_1.map
Annotationsharpened consensus map of P furiosus 70S grown at 95deg
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: consensus map of P furiosus 70S grown at 95deg - halfmap B

Fileemd_53068_half_map_1.map
Annotationconsensus map of P furiosus 70S grown at 95deg - halfmap B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: consensus map of P furiosus 70S grown at 95deg - halfmap A

Fileemd_53068_half_map_2.map
Annotationconsensus map of P furiosus 70S grown at 95deg - halfmap A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : P. furiosus 70S

EntireName: P. furiosus 70S
Components
  • Complex: P. furiosus 70S

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Supramolecule #1: P. furiosus 70S

SupramoleculeName: P. furiosus 70S / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Pyrococcus furiosus (archaea)

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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 (6k x 4k) / Average electron dose: 1.01 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.5 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: PDB ENTRY
PDB model - PDB ID:

4v6u

Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.59 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 169992
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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