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- EMDB-6329: Electron cryo-microscopy of the 73S Neurospora crassa mitochondri... -

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Entry
Database: EMDB / ID: EMD-6329
TitleElectron cryo-microscopy of the 73S Neurospora crassa mitochondrial ribosome
Map data73S mitochondrial ribosome
Sample
  • Sample: 73S mitochondrial ribosome from Neurospora crassa
  • Complex: 73S mitochondrial ribosome
KeywordsMitochondrial ribosome
Biological speciesNeurospora crassa (fungus)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.5 Å
AuthorsVan der Sluis EO / Bauerschmitt H / Becker T / Mielke T / Frauenfeld J / Berninghausen O / Neupert W / Herrmann JM / Beckmann R
CitationJournal: Genome Biol Evol / Year: 2015
Title: Parallel Structural Evolution of Mitochondrial Ribosomes and OXPHOS Complexes.
Authors: Eli O van der Sluis / Heike Bauerschmitt / Thomas Becker / Thorsten Mielke / Jens Frauenfeld / Otto Berninghausen / Walter Neupert / Johannes M Herrmann / Roland Beckmann /
Abstract: The five macromolecular complexes that jointly mediate oxidative phosphorylation (OXPHOS) in mitochondria consist of many more subunits than those of bacteria, yet, it remains unclear by which ...The five macromolecular complexes that jointly mediate oxidative phosphorylation (OXPHOS) in mitochondria consist of many more subunits than those of bacteria, yet, it remains unclear by which evolutionary mechanism(s) these novel subunits were recruited. Even less well understood is the structural evolution of mitochondrial ribosomes (mitoribosomes): while it was long thought that their exceptionally high protein content would physically compensate for their uniquely low amount of ribosomal RNA (rRNA), this hypothesis has been refuted by structural studies. Here, we present a cryo-electron microscopy structure of the 73S mitoribosome from Neurospora crassa, together with genomic and proteomic analyses of mitoribosome composition across the eukaryotic domain. Surprisingly, our findings reveal that both structurally and compositionally, mitoribosomes have evolved very similarly to mitochondrial OXPHOS complexes via two distinct phases: A constructive phase that mainly acted early in eukaryote evolution, resulting in the recruitment of altogether approximately 75 novel subunits, and a reductive phase that acted during metazoan evolution, resulting in gradual length-reduction of mitochondrially encoded rRNAs and OXPHOS proteins. Both phases can be well explained by the accumulation of (slightly) deleterious mutations and deletions, respectively, in mitochondrially encoded rRNAs and OXPHOS proteins. We argue that the main role of the newly recruited (nuclear encoded) ribosomal- and OXPHOS proteins is to provide structural compensation to the mutationally destabilized mitochondrially encoded components. While the newly recruited proteins probably provide a selective advantage owing to their compensatory nature, and while their presence may have opened evolutionary pathways toward novel mitochondrion-specific functions, we emphasize that the initial events that resulted in their recruitment was nonadaptive in nature. Our framework is supported by population genetic studies, and it can explain the complete structural evolution of mitochondrial ribosomes and OXPHOS complexes, as well as many observed functions of individual proteins.
History
DepositionApr 27, 2015-
Header (metadata) releaseMay 13, 2015-
Map releaseMay 13, 2015-
UpdateJun 3, 2015-
Current statusJun 3, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0005
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0005
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

400_6329.gif

Downloads & links

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Map

FileDownload / File: emd_6329.map.gz / Format: CCP4 / Size: 185.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation73S mitochondrial ribosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.23 Å/pix.
x 368 pix.
= 452.64 Å		1.23 Å/pix.
x 368 pix.
= 452.64 Å		1.23 Å/pix.
x 368 pix.
= 452.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.23 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0005 / Movie #1: 0.0005
Minimum - Maximum-0.00102285 - 0.00170785
Average (Standard dev.)0.0000068 (±0.00011548)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions368368368
Spacing368368368
CellA=B=C: 452.64 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.231.231.23
M x/y/z368368368
origin x/y/z0.0000.0000.000
length x/y/z452.640452.640452.640
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS368368368
D min/max/mean-0.0010.0020.000

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Supplemental data

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Sample components

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Entire : 73S mitochondrial ribosome from Neurospora crassa

EntireName: 73S mitochondrial ribosome from Neurospora crassa
Components
  • Sample: 73S mitochondrial ribosome from Neurospora crassa
  • Complex: 73S mitochondrial ribosome

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Supramolecule #1000: 73S mitochondrial ribosome from Neurospora crassa

SupramoleculeName: 73S mitochondrial ribosome from Neurospora crassa / type: sample / ID: 1000 / Number unique components: 1
Molecular weightTheoretical: 3.7 MDa

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Supramolecule #1: 73S mitochondrial ribosome

SupramoleculeName: 73S mitochondrial ribosome / type: complex / ID: 1 / Name.synonym: 73S mitoribosome / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-eukaryote: mitochondrial ALL
Source (natural)Organism: Neurospora crassa (fungus) / Strain: K5-15-23-1 / Organelle: mitochondrion
Molecular weightTheoretical: 3.7 MDa

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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

Concentration0.3 mg/mL
BufferpH: 7.5
Details: 30 mM Tris-HCl, pH 7.5, 100 mM NH4Cl, 10 mM MgCl2, 4 mM 2-mercaptoethanol, 0.05% beta-D dodecyl maltoside, 0.0075% cardiolipin
GridDetails: Quantifoil grids pre-coated with 2 nm carbon on top
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 95 K / Instrument: FEI VITROBOT MARK IV / Method: Blot for 3 seconds before plunging

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Electron microscopy

MicroscopeFEI POLARA 300
DateApr 10, 2008
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Number real images: 132 / Average electron dose: 20 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 38900 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 3.7 µm / Nominal defocus min: 1.4 µm / Nominal magnification: 39000
Sample stageSpecimen holder: nitrogen-cooled / Specimen holder model: SIDE ENTRY, EUCENTRIC
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

DetailsParticles were selected using SIGNATURE and processed with SPIDER.
CTF correctionDetails: Micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.5 Å / Resolution method: OTHER / Software - Name: Spider / Number images used: 208737
Final angle assignmentDetails: Spider

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