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- EMDB-11287: Human mitochondrial ribosome in complex with mRNA, A/A tRNA and P... -

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Basic information

Entry
Database: EMDB / ID: EMD-11287
TitleHuman mitochondrial ribosome in complex with mRNA, A/A tRNA and P/P tRNA, local-masked aligned on SSU head.
Map dataSharpened, local-resolution filtered and masked.
Sample
  • Complex: Ribosome with mRNA and tRNAs
    • Complex: SSU body
Biological speciesHomo sapiens (human)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsAndrell A / Itoh Y / Amunts A
Funding support Sweden, 1 items
OrganizationGrant numberCountry
European Research Council (ERC) Sweden
CitationJournal: Science / Year: 2021
Title: Mechanism of membrane-tethered mitochondrial protein synthesis.
Authors: Yuzuru Itoh / Juni Andréll / Austin Choi / Uwe Richter / Priyanka Maiti / Robert B Best / Antoni Barrientos / Brendan J Battersby / Alexey Amunts /
Abstract: Mitochondrial ribosomes (mitoribosomes) are tethered to the mitochondrial inner membrane to facilitate the cotranslational membrane insertion of the synthesized proteins. We report cryo-electron ...Mitochondrial ribosomes (mitoribosomes) are tethered to the mitochondrial inner membrane to facilitate the cotranslational membrane insertion of the synthesized proteins. We report cryo-electron microscopy structures of human mitoribosomes with nascent polypeptide, bound to the insertase oxidase assembly 1-like (OXA1L) through three distinct contact sites. OXA1L binding is correlated with a series of conformational changes in the mitoribosomal large subunit that catalyze the delivery of newly synthesized polypeptides. The mechanism relies on the folding of mL45 inside the exit tunnel, forming two specific constriction sites that would limit helix formation of the nascent chain. A gap is formed between the exit and the membrane, making the newly synthesized proteins accessible. Our data elucidate the basis by which mitoribosomes interact with the OXA1L insertase to couple protein synthesis and membrane delivery.
History
DepositionJul 1, 2020-
Header (metadata) releaseMar 3, 2021-
Map releaseMar 3, 2021-
UpdateMar 3, 2021-
Current statusMar 3, 2021Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_11287.png

Downloads & links

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Map

FileDownload / File: emd_11287.map.gz / Format: CCP4 / Size: 39.1 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened, local-resolution filtered and masked.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
0.83 Å/pix.
x 199 pix.
= 165.17 Å		0.83 Å/pix.
x 249 pix.
= 206.67 Å		0.83 Å/pix.
x 207 pix.
= 171.81 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

generated in cubic-lattice coordinate

Voxel sizeX=Y=Z: 0.83 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.16063106 - 0.3423674
Average (Standard dev.)0.0010136693 (±0.013199508)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin33136118
Dimensions249207199
Spacing207249199
CellA: 171.81 Å / B: 206.67 Å / C: 165.17 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z0.830.830.83
M x/y/z207249199
origin x/y/z0.0000.0000.000
length x/y/z171.810206.670165.170
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS13633118
NC/NR/NS207249199
D min/max/mean-0.1610.3420.001

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Supplemental data

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Mask #1

Fileemd_11287_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_11287_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_11287_half_map_2.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : Ribosome with mRNA and tRNAs

EntireName: Ribosome with mRNA and tRNAs
Components
  • Complex: Ribosome with mRNA and tRNAs
    • Complex: SSU body

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Supramolecule #1: Ribosome with mRNA and tRNAs

SupramoleculeName: Ribosome with mRNA and tRNAs / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#89
Details: Mitochondrial ribosome in complex with mRNA, A/A tRNA and P/P tRNA
Molecular weightTheoretical: 3 MDa

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Supramolecule #2: SSU body

SupramoleculeName: SSU body / type: complex / ID: 2 / Parent: 1 / Macromolecule list: #1-#53 / Details: The body part of the small subunit of ribosome
Source (natural)Organism: Homo sapiens (human)

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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
40.0 mMKClPotassium chloride
25.0 mMHEPES-KOH4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid-potassium hydroxide buffer
5.0 mMMg(CH3COO)2Magnesium acetate
0.05 %C24H46O11n-Dodecyl-beta-D-maltopyranoside
2.0 mMC4H10O2S21,4-Dithio-D-threitol
GridModel: Quantifoil R2/2 / Material: COPPER / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 3.0 nm / Pretreatment - Type: GLOW DISCHARGE
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: GIF Quantum LS / Energy filter - Slit width: 20 eV
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Dimensions - Width: 3838 pixel / Digitization - Dimensions - Height: 3710 pixel / Digitization - Frames/image: 1-20 / Number grids imaged: 2 / Number real images: 19655 / Average exposure time: 4.0 sec. / Average electron dose: 30.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated defocus max: 3.6 µm / Calibrated defocus min: 0.2 µm / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal magnification: 165000
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: 1308158
CTF correctionSoftware - Name: Gctf (ver. 1.06)
Startup modelType of model: EMDB MAP
EMDB ID:

2876

Final reconstructionNumber classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) / Number images used: 93615
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION (ver. 2.1)
Final angle assignmentType: ANGULAR RECONSTITUTION / Software - Name: RELION (ver. 3.0)
Final 3D classificationNumber classes: 3 / Software - Name: RELION (ver. 3.0)
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial model(PDB ID:

3j9m

,

5ool

,

6rw4

)
RefinementSpace: REAL / Protocol: AB INITIO MODEL / Overall B value: 44 / Target criteria: Correlation coefficient

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