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- EMDB-11038: The mitochondrial ribosome from Tetrahymena thermophila, small su... -

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Basic information

Entry
Database: EMDB / ID: EMD-11038
TitleThe mitochondrial ribosome from Tetrahymena thermophila, small subunit back protuberance mask
Map data
Sample
  • Complex: Mitochondrial ribosome from Tetrahymena thermophila
    • Complex: Mitochondrial ribosomal large subunit from Tetrahymena thermophila
    • Complex: Mitochondrial ribosomal small subunit from Tetrahymena thermophila
Biological speciesTetrahymena thermophila SB210 (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 Å
AuthorsTobiasson V / Amunts A
Funding support Sweden, 2 items
OrganizationGrant numberCountry
Swedish Research CouncilNT_2015-04107 Sweden
Knut and Alice Wallenberg Foundation2018.0080
CitationJournal: Elife / Year: 2020
Title: Ciliate mitoribosome illuminates evolutionary steps of mitochondrial translation.
Authors: Victor Tobiasson / Alexey Amunts /
Abstract: To understand the steps involved in the evolution of translation, we used , a ciliate with high coding capacity of the mitochondrial genome, as the model organism and characterized its mitochondrial ...To understand the steps involved in the evolution of translation, we used , a ciliate with high coding capacity of the mitochondrial genome, as the model organism and characterized its mitochondrial ribosome (mitoribosome) using cryo-EM. The structure of the mitoribosome reveals an assembly of 94-ribosomal proteins and four-rRNAs with an additional protein mass of ~700 kDa on the small subunit, while the large subunit lacks 5S rRNA. The structure also shows that the small subunit head is constrained, tRNA binding sites are formed by mitochondria-specific protein elements, conserved protein bS1 is excluded, and bacterial RNA polymerase binding site is blocked. We provide evidence for anintrinsic protein targeting system through visualization of mitochondria-specific mL105 by the exit tunnel that would facilitate the recruitment of a nascent polypeptide. Functional protein uS3m is encoded by three complementary genes from the nucleus and mitochondrion, establishing a link between genetic drift and mitochondrial translation. Finally, we reannotated nine open reading frames in the mitochondrial genome that code for mitoribosomal proteins.
History
DepositionMay 14, 2020-
Header (metadata) releaseJul 22, 2020-
Map releaseJul 22, 2020-
UpdateJul 22, 2020-
Current statusJul 22, 2020Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.025
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.025
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11038.png

Downloads & links

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Map

FileDownload / File: emd_11038.map.gz / Format: CCP4 / Size: 634.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 550 pix.
= 588.5 Å		1.07 Å/pix.
x 550 pix.
= 588.5 Å		1.07 Å/pix.
x 550 pix.
= 588.5 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.07 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.025 / Movie #1: 0.025
Minimum - Maximum-0.0380448 - 0.087524526
Average (Standard dev.)0.0000364918 (±0.0039079776)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions550550550
Spacing550550550
CellA=B=C: 588.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.071.071.07
M x/y/z550550550
origin x/y/z0.0000.0000.000
length x/y/z588.500588.500588.500
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ250250250
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS550550550
D min/max/mean-0.0380.0880.000

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Supplemental data

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Mask #1

Fileemd_11038_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_11038_half_map_1.map
Projections & Slices
AxesZYX

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Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_11038_half_map_2.map
Projections & Slices
AxesZYX

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Histogram (log scale)

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Sample components

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Entire : Mitochondrial ribosome from Tetrahymena thermophila

EntireName: Mitochondrial ribosome from Tetrahymena thermophila
Components
  • Complex: Mitochondrial ribosome from Tetrahymena thermophila
    • Complex: Mitochondrial ribosomal large subunit from Tetrahymena thermophila
    • Complex: Mitochondrial ribosomal small subunit from Tetrahymena thermophila

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Supramolecule #1: Mitochondrial ribosome from Tetrahymena thermophila

SupramoleculeName: Mitochondrial ribosome from Tetrahymena thermophila / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#94
Source (natural)Organism: Tetrahymena thermophila SB210 (eukaryote)

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Supramolecule #2: Mitochondrial ribosomal large subunit from Tetrahymena thermophila

SupramoleculeName: Mitochondrial ribosomal large subunit from Tetrahymena thermophila
type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#48
Source (natural)Organism: Tetrahymena thermophila SB210 (eukaryote)

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Supramolecule #3: Mitochondrial ribosomal small subunit from Tetrahymena thermophila

SupramoleculeName: Mitochondrial ribosomal small subunit from Tetrahymena thermophila
type: complex / ID: 3 / Parent: 1 / Macromolecule list: #49-#94
Source (natural)Organism: Tetrahymena thermophila SB210 (eukaryote)

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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: 7.45
GridModel: Quantifoil R2/2 / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 3.0 nm
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 99300
Initial angle assignmentType: RANDOM ASSIGNMENT
Final angle assignmentType: MAXIMUM LIKELIHOOD

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