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- EMDB-47666: Cryo-EM structure of the Pyrobaculum calidifontis 70S ribosome in... -

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Basic information

Entry
Database: EMDB / ID: EMD-47666
TitleCryo-EM structure of the Pyrobaculum calidifontis 70S ribosome in complex with Dri (30S focused refinement)
Map dataPyrobaculum calidifontis 70S ribosome in complex with Dri 30S 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: 2.67 Å
AuthorsNissley AJ / Cate JHD
Funding support United States, 1 items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)CHE-2002182 United States
CitationJournal: To Be Published
Title: Structure of an Archaeal Ribosome with a Divergent Active Site
Authors: Nissley AJ / Shulgina Y / Kivimae RW / Downing BE / Penev PI / Banfield JF / Nayak DD / Cate JHD
History
DepositionNov 1, 2024-
Header (metadata) releaseNov 20, 2024-
Map releaseNov 20, 2024-
UpdateNov 20, 2024-
Current statusNov 20, 2024Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_47666.png

Downloads & links

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Map

FileDownload / File: emd_47666.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 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: 0.1
Minimum - Maximum-0.31668174 - 0.6269347
Average (Standard dev.)-0.00046988865 (±0.017997669)
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_47666_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_47666_half_map_1.map
AnnotationPyrobaculum calidifontis 70S ribosome in complex with Dri 30S 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_47666_half_map_2.map
AnnotationPyrobaculum calidifontis 70S ribosome in complex with Dri 30S 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
Startup modelType of model: OTHER
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.67 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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