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- EMDB-66541: Structure of the old Killifish Ribosome (head focus-refined with ... -

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Basic information

Entry
Database: EMDB / ID: EMD-66541
TitleStructure of the old Killifish Ribosome (head focus-refined with partial mask)
Map dataStructure of the old Killifish Ribosome (head focus-refined with partial mask and sharpen)
Sample
  • Complex: Old killifish ribosome
KeywordsRibosome / ribosome dynamics / ribosome associated quality control / Nothobranchius furzeri / aging / skeletal muscle
Biological speciesNothobranchius furzeri (turquoise killifish)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.0 Å
AuthorsKim J / Song JJ / Kim Y
Funding support Korea, Republic Of, 2 items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)RS-2024-00333346 Korea, Republic Of
National Research Foundation (NRF, Korea)RS-2023-00266300 Korea, Republic Of
CitationJournal: To Be Published
Title: Ribosome remodels in age-dependent manner
Authors: Kim J / Hyeon DY / Lee S / Ryu BH / Gwak N / Choi Y / Vu HM / Huh S / Kim S / Myung K / Dieterich C / Valenzano DR / Kim MS / Hwang D / Song JJ / Kim Y
History
DepositionOct 10, 2025-
Header (metadata) releaseOct 7, 2026-
Map releaseOct 7, 2026-
UpdateOct 7, 2026-
Current statusOct 7, 2026Processing site: PDBj / Status: Released

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Structure visualization

Supplemental images

emd_66541.png

Downloads & links

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Map

FileDownload / File: emd_66541.map.gz / Format: CCP4 / Size: 1000 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the old Killifish Ribosome (head focus-refined with partial mask and sharpen)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 640 pix.
= 529.92 Å		0.83 Å/pix.
x 640 pix.
= 529.92 Å		0.83 Å/pix.
x 640 pix.
= 529.92 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 0.828 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025
Minimum - Maximum-0.102286495 - 0.2547753
Average (Standard dev.)0.00029675852 (±0.0066298447)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions640640640
Spacing640640640
CellA=B=C: 529.92 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_66541_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: Structure of the old Killifish Ribosome (head focus-refined...

Fileemd_66541_additional_1.map
AnnotationStructure of the old Killifish Ribosome (head focus-refined with partial mask and unfiltered)
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_66541_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_66541_half_map_2.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 : Old killifish ribosome

EntireName: Old killifish ribosome
Components
  • Complex: Old killifish ribosome

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Supramolecule #1: Old killifish ribosome

SupramoleculeName: Old killifish ribosome / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#77
Source (natural)Organism: Nothobranchius furzeri (turquoise killifish) / Tissue: skeletal muscle

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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
Component:
ConcentrationFormulaName
100.0 mMKClPotassium Chloride
15.0 mMMgCl2Magnesium Chloride
20.0 mMTris-HClTris-hydrochloride
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: GRAPHENE OXIDE
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV
Details: Blot time 3 seconds Blot force 10 Wait time 30 seconds.

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Electron microscopy

MicroscopeTFS KRIOS
Specialist opticsEnergy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV / Details: BioQuantum K3 Imaging Filter
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number real images: 9136 / Average exposure time: 5.87 sec. / Average electron dose: 60.23 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 1.0 µm / Nominal defocus min: 0.3 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Particle selectionNumber selected: 283531
CTF correctionSoftware - Name: cryoSPARC (ver. 4.2.1) / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.0 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cryoSPARC (ver. 4.2.1) / Number images used: 115566
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cryoSPARC (ver. 4.2.1)
FSC plot (resolution estimation)

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