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- EMDB-74854: Methanosarcina acetivorans 70S ribosome in complex with SriA and ... -

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Basic information

Entry
Database: EMDB / ID: EMD-74854
TitleMethanosarcina acetivorans 70S ribosome in complex with SriA and SriB 30S head focused refinement
Map dataMethanosarcina acetivorans 70S ribosome in complex with SriA and SriB 30S head focused refinement
Sample
  • Complex: 70S ribosome
    • Complex: 50S subunit
    • Complex: 30S subunit
KeywordsRibosome / Hibernation / Archaea
Biological speciesMethanosarcina acetivorans (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.48 Å
AuthorsNissley AJ / Cate JHD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States) United States
CitationJournal: Biorxiv / Year: 2026
Title: A family of archaeal hibernation factors that bind in tandem and protect ribosomes in dormant cells
Authors: Nissley AJ / Williams MC / Shulgina Y / Kivimae RW / Nayak DD / Cate JHD
History
DepositionDec 29, 2025-
Header (metadata) releaseJan 28, 2026-
Map releaseJan 28, 2026-
UpdateJan 28, 2026-
Current statusJan 28, 2026Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_74854.png

Downloads & links

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Map

FileDownload / File: emd_74854.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMethanosarcina acetivorans 70S ribosome in complex with SriA and SriB 30S head focused refinement
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 512 pix.
= 423.117 Å		0.83 Å/pix.
x 512 pix.
= 423.117 Å		0.83 Å/pix.
x 512 pix.
= 423.117 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.8264 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0877
Minimum - Maximum-0.18610214 - 0.41648102
Average (Standard dev.)0.0017366625 (±0.012457758)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions512512512
Spacing512512512
CellA=B=C: 423.1168 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_74854_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Methanosarcina acetivorans 70S ribosome in complex with SriA...

Fileemd_74854_additional_1.map
AnnotationMethanosarcina acetivorans 70S ribosome in complex with SriA and SriB 30S head focused refinement sharpened map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: Methanosarcina acetivorans 70S ribosome in complex with SriA...

Fileemd_74854_half_map_1.map
AnnotationMethanosarcina acetivorans 70S ribosome in complex with SriA and SriB 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: Methanosarcina acetivorans 70S ribosome in complex with SriA...

Fileemd_74854_half_map_2.map
AnnotationMethanosarcina acetivorans 70S ribosome in complex with SriA and SriB 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: 50S subunit
    • Complex: 30S subunit

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Supramolecule #1: 70S ribosome

SupramoleculeName: 70S ribosome / type: complex / ID: 1 / Parent: 0
Source (natural)Organism: Methanosarcina acetivorans (archaea)

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Supramolecule #2: 50S subunit

SupramoleculeName: 50S subunit / type: complex / ID: 2 / Parent: 1
Source (natural)Organism: Methanosarcina acetivorans (archaea)

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Supramolecule #3: 30S subunit

SupramoleculeName: 30S subunit / type: complex / ID: 3 / Parent: 1
Source (natural)Organism: Methanosarcina acetivorans (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

Concentration0.42 mg/mL
BufferpH: 7.5
Component:
ConcentrationFormulaName
25.0 mMC8H18N2O4SHEPES
50.0 mMKClpotassium chloride
10.0 mMMgCl2Magnesium chloride
2.0 mMC4H10O2S2DTT
GridModel: UltrAuFoil R1.2/1.3 / Support film - Material: CARBON / Support film - topology: CONTINUOUS
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeTFS KRIOS
SoftwareName: SerialEM
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 9090 / 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: 2488798
CTF correctionSoftware - Name: cryoSPARC / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: INSILICO MODEL
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.48 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC / Number images used: 95430
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC
Final 3D classificationSoftware - Name: cryoSPARC
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelChain - Source name: Other / Chain - Initial model type: other / Details: ModelAngelo

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