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- EMDB-74841: Methanosarcina acetivorans 70S ribosome in complex with SriA and ... -

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Basic information

Entry
Database: EMDB / ID: EMD-74841
TitleMethanosarcina acetivorans 70S ribosome in complex with SriA and SriB consensus map
Map dataMethanosarcina acetivorans 70S ribosome in complex with SriA and SriB consensus map
Sample
  • Complex: 70S ribosome
    • Complex: 50S subunit
    • Complex: 30S subunit
KeywordsRibosome / Hibernation / Archaea
Biological speciesMethanosarcina acetivorans (archaea)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.03 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 28, 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_74841.png

Downloads & links

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Map

FileDownload / File: emd_74841.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 consensus map
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: 0.0899
Minimum - Maximum-0.19977629 - 0.6675943
Average (Standard dev.)0.0014454264 (±0.01928763)
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_74841_msk_1.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_74841_half_map_1.map
AnnotationMethanosarcina acetivorans 70S ribosome in complex with SriA and SriB consensus 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_74841_half_map_2.map
AnnotationMethanosarcina acetivorans 70S ribosome in complex with SriA and SriB consensus 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: 2.03 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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