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- EMDB-2914: Cryo-EM reconstruction of the mammalian 55S mitoribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-2914
TitleCryo-EM reconstruction of the mammalian 55S mitoribosome
Map dataReconstruction of the 55S mammalian mitoribosome
Sample
  • Sample: 55S mammalian mitochondrial ribosome
  • Complex: 28S small subunit of the mitochondrial ribosome
  • Complex: 39S large subunit of the mitochondrial ribosome
Keywordsmammalian mitochondrial ribosome / 55S mitoribosome / translation / ribosomal proteins / rRNA / tRNA / mRNA / decoding / exit tunnel
Function / homology
Function and homology information


Mitochondrial translation elongation / Mitochondrial translation termination / translation release factor activity / rRNA import into mitochondrion / mitochondrial translational elongation / mitochondrial ribosome assembly / ribonuclease III activity / microprocessor complex / Mitochondrial protein degradation / mitochondrial large ribosomal subunit ...Mitochondrial translation elongation / Mitochondrial translation termination / translation release factor activity / rRNA import into mitochondrion / mitochondrial translational elongation / mitochondrial ribosome assembly / ribonuclease III activity / microprocessor complex / Mitochondrial protein degradation / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / mitochondrial ribosome / mitochondrial small ribosomal subunit / mitochondrial translation / organelle membrane / ribosomal small subunit binding / RNA processing / double-stranded RNA binding / large ribosomal subunit / cell junction / regulation of translation / small ribosomal subunit / 5S rRNA binding / nuclear body / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / protein domain specific binding / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Coiled-coil domain-containing protein 142 / Coiled-coil protein 142 / Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / 28S ribosomal protein S26 / Mitochondrial ribosome subunit S26 / Cysteine alpha-hairpin motif superfamily / Mitochondrial 28S ribosomal protein S31 / Mitochondrial 28S ribosomal protein S31 / 28S ribosomal protein S24, mitochondrial / Pentatricopeptide repeat domain-containing protein 3 ...Coiled-coil domain-containing protein 142 / Coiled-coil protein 142 / Coiled-coil-helix-coiled-coil-helix domain-containing protein 1 / 28S ribosomal protein S26 / Mitochondrial ribosome subunit S26 / Cysteine alpha-hairpin motif superfamily / Mitochondrial 28S ribosomal protein S31 / Mitochondrial 28S ribosomal protein S31 / 28S ribosomal protein S24, mitochondrial / Pentatricopeptide repeat domain-containing protein 3 / 28S ribosomal protein S17, mitochondrial / 28S ribosomal protein S18b, mitochondrial / : / Mitochondrial ribosome subunit S24 / Small ribosomal subunit protein uS5m, N-terminal / Small ribosomal subunit protein mS39, PPR / Pentatricopeptide repeat domain / Ribosomal protein S27/S33, mitochondrial / Ribosomal protein S24/S35, mitochondrial / Mitochondrial ribosomal subunit S27 / Mitochondrial ribosomal protein L46 NUDIX / Ribosomal protein S24/S35, mitochondrial, conserved domain / Mitochondrial ribosomal subunit protein / 39S ribosomal protein L52, mitochondrial / Mitoribosomal protein mL52 / : / Ribosomal protein L35, mitochondrial / MRPL44, double-stranded RNA binding domain / MRPL44 dsRNA-binding domain / Large ribosomal subunit protein mL44, endonuclease domain / : / Large ribosomal subunit protein bL9m C-terminal domain / Pentatricopeptide repeat / Ribosomal protein L46, N-terminal / 39S mitochondrial ribosomal protein L46 / Ribosomal protein L50, mitochondria / Ribosomal subunit 39S / 39S ribosomal protein L46, mitochondrial / : / 39S ribosomal protein L43/54S ribosomal protein L51 / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein, eukaryotic / PEBP-like superfamily / Peptide chain release factor class I / RF-1 domain / Ribonuclease III, endonuclease domain superfamily / Double stranded RNA-binding domain (dsRBD) profile. / Double-stranded RNA-binding domain / : / CHCH / CHCH domain / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / NUDIX hydrolase-like domain superfamily / Ribosomal protein L10-like domain superfamily / Ribosomal protein L10P / Ribosomal protein L10 / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11/L12 / Ribosomal protein L9, N-terminal domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal / Ribosomal protein L9, N-terminal domain / Ribosomal protein L9/RNase H1, N-terminal / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal proteins 50S L24/mitochondrial 39S L24 / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal L32p protein family / Ribosomal protein L32p / Ribosomal protein L24 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein L15, bacterial-type / Ribosomal protein S18 superfamily / 50S ribosomal protein uL4 / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein S2 signature 1. / Ribosomal protein S5, N-terminal, conserved site
Similarity search - Domain/homology
39S ribosomal protein L18, mitochondrial isoform 1 / 39S ribosomal protein L18, mitochondrial isoform 1 / Large ribosomal subunit protein uL24m / Large ribosomal subunit protein uL16m / Mitochondrial ribosomal protein S17 / : / : / Small ribosomal subunit protein mS31 / Large ribosomal subunit protein bL17m / Large ribosomal subunit protein uL14m ...39S ribosomal protein L18, mitochondrial isoform 1 / 39S ribosomal protein L18, mitochondrial isoform 1 / Large ribosomal subunit protein uL24m / Large ribosomal subunit protein uL16m / Mitochondrial ribosomal protein S17 / : / : / Small ribosomal subunit protein mS31 / Large ribosomal subunit protein bL17m / Large ribosomal subunit protein uL14m / Mitochondrial ribosomal protein S18A / Mitochondrial ribosomal protein L2 / 39S ribosomal protein L15, mitochondrial / 39S ribosomal protein L27, mitochondrial / Large ribosomal subunit protein uL11m / : / Large ribosomal subunit protein mL38 / Large ribosomal subunit protein uL10m / Large ribosomal subunit protein bL21m / 28S ribosomal protein S2, mitochondrial / : / Mitochondrial ribosomal protein L4 / Small ribosomal subunit protein mS26 / Small ribosomal subunit protein mS33 / Large ribosomal subunit protein mL43 / Large ribosomal subunit protein mL52 / 39S ribosomal protein L18, mitochondrial isoform 1 / 28S ribosomal protein S35, mitochondrial isoform 1 / Coiled-coil domain containing 142 / Large ribosomal subunit protein mL44 / Large ribosomal subunit protein mL46 / : / Mitochondrial ribosomal protein S24 / Large ribosomal subunit protein uL30m / Coiled-coil-helix-coiled-coil-helix domain containing 1 / Small ribosomal subunit protein uS5m / : / Large ribosomal subunit protein bL35m / : / Large ribosomal subunit protein mL50 / : / Large ribosomal subunit protein bL19m / : / Large ribosomal subunit protein bL9m / Large ribosomal subunit protein bL32m / Small ribosomal subunit protein mS39 / Small ribosomal subunit protein mS40 / Large ribosomal subunit protein mL62 / Large ribosomal subunit protein bL34m
Similarity search - Component
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsGreber BJ / Bieri P / Leibundgut M / Leitner A / Aebersold R / Boehringer D / Ban N
CitationJournal: Science / Year: 2015
Title: Ribosome. The complete structure of the 55S mammalian mitochondrial ribosome.
Authors: Basil J Greber / Philipp Bieri / Marc Leibundgut / Alexander Leitner / Ruedi Aebersold / Daniel Boehringer / Nenad Ban /
Abstract: Mammalian mitochondrial ribosomes (mitoribosomes) synthesize mitochondrially encoded membrane proteins that are critical for mitochondrial function. Here we present the complete atomic structure of ...Mammalian mitochondrial ribosomes (mitoribosomes) synthesize mitochondrially encoded membrane proteins that are critical for mitochondrial function. Here we present the complete atomic structure of the porcine 55S mitoribosome at 3.8 angstrom resolution by cryo-electron microscopy and chemical cross-linking/mass spectrometry. The structure of the 28S subunit in the complex was resolved at 3.6 angstrom resolution by focused alignment, which allowed building of a detailed atomic structure including all of its 15 mitoribosomal-specific proteins. The structure reveals the intersubunit contacts in the 55S mitoribosome, the molecular architecture of the mitoribosomal messenger RNA (mRNA) binding channel and its interaction with transfer RNAs, and provides insight into the highly specialized mechanism of mRNA recruitment to the 28S subunit. Furthermore, the structure contributes to a mechanistic understanding of aminoglycoside ototoxicity.
History
DepositionFeb 20, 2015-
Header (metadata) releaseMar 11, 2015-
Map releaseApr 15, 2015-
UpdateJun 24, 2015-
Current statusJun 24, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-5aj4
  • Surface level: 0.05
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMDB_2914_55...

Downloads & links

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Map

FileDownload / File: emd_2914.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the 55S mammalian mitoribosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 256 pix.
= 355.84 Å		1.39 Å/pix.
x 256 pix.
= 355.84 Å		1.39 Å/pix.
x 256 pix.
= 355.84 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.39 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.05 / Movie #1: 0.05
Minimum - Maximum-0.18619975 - 0.39100313
Average (Standard dev.)0.00375944 (±0.0204599)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin323232
Dimensions256256256
Spacing256256256
CellA=B=C: 355.84 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z355.840355.840355.840
α/β/γ90.00090.00090.000
start NX/NY/NZ-24-24-24
NX/NY/NZ494949
MAP C/R/S123
start NC/NR/NS323232
NC/NR/NS256256256
D min/max/mean-0.1860.3910.004

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Supplemental data

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Sample components

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Entire : 55S mammalian mitochondrial ribosome

EntireName: 55S mammalian mitochondrial ribosome
Components
  • Sample: 55S mammalian mitochondrial ribosome
  • Complex: 28S small subunit of the mitochondrial ribosome
  • Complex: 39S large subunit of the mitochondrial ribosome

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Supramolecule #1000: 55S mammalian mitochondrial ribosome

SupramoleculeName: 55S mammalian mitochondrial ribosome / type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 2
Molecular weightTheoretical: 2.7 MDa

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Supramolecule #1: 28S small subunit of the mitochondrial ribosome

SupramoleculeName: 28S small subunit of the mitochondrial ribosome / type: complex / ID: 1 / Recombinant expression: No
Ribosome-details: ribosome-eukaryote: SSU mitochondrial 28S, SSU mitochondrial RNA 12S
Ref GO0: GO:0005761
Source (natural)Organism: Sus scrofa (pig) / synonym: Domestic pig / Tissue: Liver / Organelle: Mitochondrion
Molecular weightTheoretical: 1.1 MDa

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Supramolecule #2: 39S large subunit of the mitochondrial ribosome

SupramoleculeName: 39S large subunit of the mitochondrial ribosome / type: complex / ID: 2 / Recombinant expression: No
Ribosome-details: ribosome-eukaryote: LSU mitochondrial 39S, LSU mitochondrial RNA 16S
Ref GO0: GO:0005761
Source (natural)Organism: Sus scrofa (pig) / synonym: Domestic pig / Tissue: Liver / Organelle: mitochondrion
Molecular weightTheoretical: 1.6 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

BufferpH: 7.4 / Details: 20 mM HEPES-KOH, 50 mM KCl, 1 mM DTT, 40 mM MgCl2
GridDetails: 200 mesh Quantifoil R 2/2 holey carbon grids with a thin continuous carbon support film applied
VitrificationCryogen name: ETHANE-PROPANE MIXTURE / Instrument: HOMEMADE PLUNGER

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Electron microscopy #1

Microscopy ID1
MicroscopeFEI TITAN KRIOS
Detailsmovie mode readout in FEI EPU: 7 frames per exposure
DateMay 3, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Sampling interval: 14 µm / Average electron dose: 20 e/Å2
Details: movie mode readout in FEI EPU: 7 frames per exposure
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 100720 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Electron microscopy #2

Microscopy ID2
MicroscopeFEI TITAN KRIOS
Detailsmovie mode readout in FEI EPU: 7 frames per exposure
DateMay 30, 2014
Image recordingCategory: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Digitization - Sampling interval: 14 µm / Average electron dose: 20 e/Å2
Details: movie mode readout in FEI EPU: 7 frames per exposure
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 100720 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.8 µm / Nominal magnification: 59000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

DetailsParticles were selected in batchboxer (EMAN 1.9) and extracted using RELION 1.2.
CTF correctionDetails: per detector frame
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: OTHER / Software - Name: CTFFIND3, RELION, 1.2, 1.3 / Number images used: 60872

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Atomic model buiding 1

Initial modelPDB ID:

4v1a

SoftwareName: Chimera
DetailsThe coordinate model of the 39S subunit was fitted into the cryo-EM density using Chimera. The model was then adjusted using COOT (RNA) and O (proteins).
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-5aj4:
Structure of the 55S mammalian mitoribosome.

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Atomic model buiding 2

Initial modelPDB ID:

4v19

SoftwareName: Chimera
DetailsThe coordinate model of the 39S subunit was fitted into the cryo-EM density using Chimera. The model was then adjusted using COOT (RNA) and O (proteins).
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-5aj4:
Structure of the 55S mammalian mitoribosome.

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