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- EMDB-47667: Cryo-EM structure of the Pyrobaculum calidifontis 70S ribosome in... -

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Basic information

Entry
Database: EMDB / ID: EMD-47667
TitleCryo-EM structure of the Pyrobaculum calidifontis 70S ribosome in complex with Dri (30S head focused refinement)
Map dataPyrobaculum calidifontis 70S ribosome in complex with Dri 30S head focused refinement
Sample
  • Complex: 70S ribosome
    • Complex: 30S subunit
KeywordsRibosome / Translation / Hibernation / RNA
Biological speciesPyrobaculum calidifontis JCM 11548 (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.79 Å
AuthorsNissley AJ / Cate JHD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-2002182 United States
CitationJournal: Nat Microbiol / Year: 2025
Title: Structure of an archaeal ribosome reveals a divergent active site and hibernation factor.
Authors: Amos J Nissley / Yekaterina Shulgina / Roan W Kivimae / Blake E Downing / Petar I Penev / Jillian F Banfield / Dipti D Nayak / Jamie H D Cate /
Abstract: Ribosomes translate mRNA into protein. Despite divergence in ribosome structure over the course of evolution, the catalytic site, known as the peptidyl transferase centre (PTC), is thought to be ...Ribosomes translate mRNA into protein. Despite divergence in ribosome structure over the course of evolution, the catalytic site, known as the peptidyl transferase centre (PTC), is thought to be nearly universally conserved. Here we identify clades of archaea that have highly divergent ribosomal RNA sequences in the PTC. To understand how these PTC sequences fold, we determined cryo-EM structures of the 70S and 50S ribosomes to 2.4 Å and 2 Å, respectively, from the hyperthermophilic archaeon Pyrobaculum calidifontis. PTC sequence variation leads to the rearrangement of key base triples, and differences between archaeal and bacterial ribosomal proteins enable sequence variation in archaeal PTCs. Finally, we identify an archaeal ribosome hibernation factor, Dri, that differs from known bacterial and eukaryotic hibernation factors and is found in multiple archaeal phyla. Overall, this work identifies factors that regulate ribosome function in archaea and reveals a larger diversity of the most ancient sequences in the ribosome.
History
DepositionNov 1, 2024-
Header (metadata) releaseNov 20, 2024-
Map releaseNov 20, 2024-
UpdateJul 30, 2025-
Current statusJul 30, 2025Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47667.png

Downloads & links

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Map

FileDownload / File: emd_47667.map.gz / Format: CCP4 / Size: 857.4 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationPyrobaculum calidifontis 70S ribosome in complex with Dri 30S head focused refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 608 pix.
= 504.214 Å		0.83 Å/pix.
x 608 pix.
= 504.214 Å		0.83 Å/pix.
x 608 pix.
= 504.214 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8293 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.13
Minimum - Maximum-0.32002047 - 0.6495962
Average (Standard dev.)-0.00046660326 (±0.019341407)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions608608608
Spacing608608608
CellA=B=C: 504.2144 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_47667_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Pyrobaculum calidifontis 70S ribosome in complex with Dri...

Fileemd_47667_half_map_1.map
AnnotationPyrobaculum calidifontis 70S ribosome in complex with Dri 30S head focused refinement (half map)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Pyrobaculum calidifontis 70S ribosome in complex with Dri...

Fileemd_47667_half_map_2.map
AnnotationPyrobaculum calidifontis 70S ribosome in complex with Dri 30S head focused refinement (half 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 : 70S ribosome

EntireName: 70S ribosome
Components
  • Complex: 70S ribosome
    • Complex: 30S subunit

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Supramolecule #1: 70S ribosome

SupramoleculeName: 70S ribosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#70
Source (natural)Organism: Pyrobaculum calidifontis JCM 11548 (archaea)

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Supramolecule #2: 30S subunit

SupramoleculeName: 30S subunit / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #4, #42-#70
Source (natural)Organism: Pyrobaculum calidifontis JCM 11548 (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

Concentration0.12 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
20.0 mMC8H18N2O4SHEPES
10.0 mMKClPotassium Chloride
20.0 mMMg(CH3COO)2Magnesium Acetate
3.0 mMC10H26N4Spermine
2.0 mMC4H10O2S2DTT
GridModel: UltrAuFoil R1.2/1.3 / Material: GOLD / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277.15 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 grids imaged: 1 / Number real images: 7318 / Average electron dose: 40.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 1.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 105000
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 2360632
CTF correctionSoftware - Name: cryoSPARC (ver. 4.4) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.79 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.4) / Number images used: 72157
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.4)
FSC plot (resolution estimation)

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Atomic model buiding 1

RefinementProtocol: AB INITIO MODEL

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