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- EMDB-2913: Cryo-EM reconstruction of the mammalian 28S mitoribosomal subunit -

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Basic information

Entry
Database: EMDB / ID: EMD-2913
TitleCryo-EM reconstruction of the mammalian 28S mitoribosomal subunit
Map dataReconstruction of the porcine 28S mitoribosomal subunit
Sample
  • Sample: 28S mammalian mitochondrial ribosome
  • Complex: 28S mammalian mitochondrial ribosome subunit
Keywordsmammalian mitochondrial ribosome / 28S small ribosomal subunit / translation / ribosomal proteins / rRNA / tRNA / mRNA / decoding
Function / homology
Function and homology information


Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial ribosome assembly / Mitochondrial protein degradation / mitochondrial ribosome / mitochondrial small ribosomal subunit / mitochondrial translation / ribosomal small subunit binding / small ribosomal subunit rRNA binding / regulation of translation ...Mitochondrial translation elongation / Mitochondrial translation termination / mitochondrial ribosome assembly / Mitochondrial protein degradation / mitochondrial ribosome / mitochondrial small ribosomal subunit / mitochondrial translation / ribosomal small subunit binding / small ribosomal subunit rRNA binding / regulation of translation / small ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / apoptotic process / mitochondrion / RNA binding / nucleoplasm / cytoplasm
Similarity search - Function
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 / Ribosomal protein S29, mitochondrial / Ribosomal protein S28, mitochondrial / 28S ribosomal protein S10, mitochondrial / Mitochondrial ribosomal protein MRP-S35 ...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 / Ribosomal protein S29, mitochondrial / Ribosomal protein S28, mitochondrial / 28S ribosomal protein S10, mitochondrial / Mitochondrial ribosomal protein MRP-S35 / 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 / 28S ribosomal protein S25, mitochondrial / Pentatricopeptide repeat domain / Ribosomal protein S27/S33, mitochondrial / Ribosomal protein S24/S35, mitochondrial / Mitochondrial ribosomal subunit S27 / Ribosomal protein S24/S35, mitochondrial, conserved domain / Mitochondrial ribosomal subunit protein / Ribosomal protein S23/S29, mitochondrial / Mitochondrial ribosomal death-associated protein 3 / Pentatricopeptide repeat / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial mRNA-processing protein COX24, C-terminal / Mitochondrial domain of unknown function (DUF1713) / CHCH / CHCH domain / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein S2, bacteria/mitochondria/plastid / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein S12, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein S18 superfamily / Ribosomal protein S2 signature 1. / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S2, conserved site / Ribosomal protein S2 / Ribosomal protein S2, flavodoxin-like domain superfamily / Ribosomal protein S2 / Ribosomal protein S5 / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / Ribosomal protein S5, C-terminal / Ribosomal protein S5, C-terminal domain / Ribosomal protein S14 / Ribosomal protein S14p/S29e / Ribosomal protein S10p/S20e / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / Ribosomal protein S9, conserved site / Ribosomal protein S9 signature. / Ribosomal protein S12 signature. / Tetratricopeptide-like helical domain superfamily / Ribosomal protein S9 / Ribosomal protein S9/S16 / Ribosomal protein S12/S23 / Ribosomal protein S12/S23 / Ribosomal protein S17/S11 / Ribosomal protein S17 / Thioredoxin-like superfamily / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Small ribosomal subunit protein uS12m / 28S ribosomal protein S14, mitochondrial / 28S ribosomal protein S18c, mitochondrial isoform 1 / Small ribosomal subunit protein mS25 / 28S ribosomal protein S28, mitochondrial / Small ribosomal subunit protein mS38 / Mitoribosomal protein us9m, mrps9 / Mitochondrial ribosomal protein S17 / Small ribosomal subunit protein mS29 / Small ribosomal subunit protein mS31 ...Small ribosomal subunit protein uS12m / 28S ribosomal protein S14, mitochondrial / 28S ribosomal protein S18c, mitochondrial isoform 1 / Small ribosomal subunit protein mS25 / 28S ribosomal protein S28, mitochondrial / Small ribosomal subunit protein mS38 / Mitoribosomal protein us9m, mrps9 / Mitochondrial ribosomal protein S17 / Small ribosomal subunit protein mS29 / Small ribosomal subunit protein mS31 / Small ribosomal subunit protein uS10m / : / 28S ribosomal protein S2, mitochondrial / Small ribosomal subunit protein mS26 / Small ribosomal subunit protein mS33 / 28S ribosomal protein S35, mitochondrial isoform 1 / : / Mitochondrial ribosomal protein S24 / Coiled-coil-helix-coiled-coil-helix domain containing 1 / Small ribosomal subunit protein uS5m / : / : / Mitochondrial ribosomal protein S6 / Small ribosomal subunit protein mS39 / Small ribosomal subunit protein mS40
Similarity search - Component
Biological speciesSus scrofa (pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.6 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: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-5aj3
  • Surface level: 0.06
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMDB_2913_28...

Downloads & links

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Map

FileDownload / File: emd_2913.map.gz / Format: CCP4 / Size: 37.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the porcine 28S mitoribosomal subunit
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.39 Å/pix.
x 216 pix.
= 300.24 Å		1.39 Å/pix.
x 216 pix.
= 300.24 Å		1.39 Å/pix.
x 216 pix.
= 300.24 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: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.25009429 - 0.52919853
Average (Standard dev.)0.00261802 (±0.02017874)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin232323
Dimensions216216216
Spacing216216216
CellA=B=C: 300.24 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.391.391.39
M x/y/z216216216
origin x/y/z0.0000.0000.000
length x/y/z300.240300.240300.240
α/β/γ90.00090.00090.000
start NX/NY/NZ-24-24-24
NX/NY/NZ494949
MAP C/R/S123
start NC/NR/NS232323
NC/NR/NS216216216
D min/max/mean-0.2500.5290.003

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Supplemental data

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Sample components

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Entire : 28S mammalian mitochondrial ribosome

EntireName: 28S mammalian mitochondrial ribosome
Components
  • Sample: 28S mammalian mitochondrial ribosome
  • Complex: 28S mammalian mitochondrial ribosome subunit

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Supramolecule #1000: 28S mammalian mitochondrial ribosome

SupramoleculeName: 28S mammalian mitochondrial ribosome / type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 1
Molecular weightTheoretical: 2.7 MDa

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Supramolecule #1: 28S mammalian mitochondrial ribosome subunit

SupramoleculeName: 28S mammalian mitochondrial ribosome subunit / 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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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: 3.6 Å / Resolution method: OTHER / Software - Name: CTFFIND3, RELION, 1.2, 1.3 / Number images used: 78783

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Atomic model buiding 1

Initial modelPDB ID:

3v2c
PDB Unreleased entry

SoftwareName: Chimera
DetailsThe initial coordinate model was fitted into the cryo-EM density using Chimera. The model was then extended and completely rebuilt using COOT (RNA) and O (proteins) aided by PHYRE models for ribosomal proteins.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-5aj3:
Structure of the small subunit of the mammalian mitoribosome

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