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- EMDB-2787: The structure of the large subunit of the mammalian mitoribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-2787
TitleThe structure of the large subunit of the mammalian mitoribosome
Map dataReconstruction of the mammalian mitoribosomal 39S subunit at 3.4 Angstrom resolution
Sample
  • Sample: mammalian mitochondrial ribosome
  • Organelle or cellular component: 39S large subunit of the mitochondrial ribosome
Keywordsmammalian mitochondrial ribosome / 39S large ribosomal subunit / translation / ribosomal proteins / rRNA / tRNA / polypeptide exit site / peptidyl transferase center
Function / homology
Function and homology information


Mitochondrial translation elongation / Mitochondrial translation termination / rRNA import into mitochondrion / mitochondrial translational termination / mitochondrial translational elongation / ribonuclease III activity / translation release factor activity, codon nonspecific / Mitochondrial protein degradation / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase ...Mitochondrial translation elongation / Mitochondrial translation termination / rRNA import into mitochondrion / mitochondrial translational termination / mitochondrial translational elongation / ribonuclease III activity / translation release factor activity, codon nonspecific / Mitochondrial protein degradation / mitochondrial large ribosomal subunit / peptidyl-tRNA hydrolase / mitochondrial ribosome / peptidyl-tRNA hydrolase activity / mitochondrial translation / organelle membrane / RNA processing / cell junction / large ribosomal subunit / double-stranded RNA binding / 5S rRNA binding / rRNA binding / nuclear body / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / protein domain specific binding / nucleotide binding / intracellular membrane-bounded organelle / mitochondrion / RNA binding / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Coiled-coil domain-containing protein 142 / : / : / Coiled-coil protein 142 / CC142 N-terminal / Mitochondrial ribosomal protein L48 / Ribosomal protein L35, mitochondrial / 39S ribosomal protein L52, mitochondrial / Mitoribosomal protein mL52 / : ...Coiled-coil domain-containing protein 142 / : / : / Coiled-coil protein 142 / CC142 N-terminal / Mitochondrial ribosomal protein L48 / Ribosomal protein L35, mitochondrial / 39S ribosomal protein L52, mitochondrial / Mitoribosomal protein mL52 / : / 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 / Large ribosomal subunit protein bL9m N-terminal domain / : / Mitochondrial ribosomal protein L46 NUDIX / Ribosomal protein L46, N-terminal / 39S mitochondrial ribosomal protein L46 / Ribosomal protein L50, mitochondria / Ribosomal subunit 39S / : / 39S ribosomal protein L46, mitochondrial / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / 39S ribosomal protein L43/54S ribosomal protein L51 / Mitochondrial 39-S ribosomal protein L47 (MRP-L47) / Phosphatidylethanolamine-binding protein, eukaryotic / Phosphatidylethanolamine-binding protein / Phosphatidylethanolamine-binding protein / PEBP-like superfamily / Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily / TGS-like / TGS domain profile. / TGS / 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 / : / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Ribosomal protein/NADH dehydrogenase domain / Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain / Beta-grasp domain superfamily / 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/L12 / Ribosomal protein L11, RNA binding domain / 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 L18 / Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast / Ribosomal protein L16 / Ribosomal protein L30, bacterial-type / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal L32p protein family / Ribosomal protein L19 / Ribosomal protein L19 / Ribosomal protein L19 superfamily / Ribosomal protein L21 / Ribosomal protein L32p / Large ribosomal subunit protein uL24, C-terminal domain / Ribosomal protein L17 / Ribosomal protein L17 superfamily / Ribosomal protein L17 / Ribosomal protein L21-like / L21-like superfamily / Ribosomal prokaryotic L21 protein / Ribosomal protein L34 / Ribosomal protein L34 / Ribosomal protein S18 / Ribosomal protein S18 / Ribosomal protein L24 / Ribosomal protein S18 superfamily / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / : / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e / Ribosomal protein S10p/S20e / Ribosomal protein S10 domain / Ribosomal protein S10 domain superfamily / Ribosomal protein S10p/S20e / Ribosomal Proteins L2, RNA binding N-terminal domain / Ribosomal protein L24 signature.
Similarity search - Domain/homology
Large ribosomal subunit protein uL18m / Large ribosomal subunit protein mL48 / Large ribosomal subunit protein uL18m / Large ribosomal subunit protein uL24m / Large ribosomal subunit protein uL16m / : / : / Large ribosomal subunit protein bL17m / Large ribosomal subunit protein uL14m / Large ribosomal subunit protein mL66 ...Large ribosomal subunit protein uL18m / Large ribosomal subunit protein mL48 / Large ribosomal subunit protein uL18m / Large ribosomal subunit protein uL24m / Large ribosomal subunit protein uL16m / : / : / Large ribosomal subunit protein bL17m / Large ribosomal subunit protein uL14m / Large ribosomal subunit protein mL66 / Mitochondrial ribosomal protein L2 / 39S ribosomal protein L15, mitochondrial / Large ribosomal subunit protein bL27m / Large ribosomal subunit protein uL11m / Large ribosomal subunit protein mL38 / Large ribosomal subunit protein uL10m / Large ribosomal subunit protein bL21m / : / Mitochondrial ribosomal protein L4 / Large ribosomal subunit protein mL43 / Large ribosomal subunit protein mL52 / Large ribosomal subunit protein uL18m / : / Large ribosomal subunit protein uL29m / Large ribosomal subunit protein mL39 / Coiled-coil domain containing 142 / Large ribosomal subunit protein mL44 / Large ribosomal subunit protein mL46 / Large ribosomal subunit protein uL30m / 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 / Large ribosomal subunit protein mL62 / Large ribosomal subunit protein bL34m
Similarity search - Component
Biological speciesSus scrofa domesticus (domestic pig)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.4 Å
AuthorsGreber BJ / Boehringer D / Leibundgut M / Bieri P / Leitner A / Schmitz N / Aebersold R / Ban N
CitationJournal: Nature / Year: 2014
Title: The complete structure of the large subunit of the mammalian mitochondrial ribosome.
Authors: Basil J Greber / Daniel Boehringer / Marc Leibundgut / Philipp Bieri / Alexander Leitner / Nikolaus Schmitz / Ruedi Aebersold / Nenad Ban /
Abstract: Mitochondrial ribosomes (mitoribosomes) are extensively modified ribosomes of bacterial descent specialized for the synthesis and insertion of membrane proteins that are critical for energy ...Mitochondrial ribosomes (mitoribosomes) are extensively modified ribosomes of bacterial descent specialized for the synthesis and insertion of membrane proteins that are critical for energy conversion and ATP production inside mitochondria. Mammalian mitoribosomes, which comprise 39S and 28S subunits, have diverged markedly from the bacterial ribosomes from which they are derived, rendering them unique compared to bacterial, eukaryotic cytosolic and fungal mitochondrial ribosomes. We have previously determined at 4.9 Å resolution the architecture of the porcine (Sus scrofa) 39S subunit, which is highly homologous to the human mitoribosomal large subunit. Here we present the complete atomic structure of the porcine 39S large mitoribosomal subunit determined in the context of a stalled translating mitoribosome at 3.4 Å resolution by cryo-electron microscopy and chemical crosslinking/mass spectrometry. The structure reveals the locations and the detailed folds of 50 mitoribosomal proteins, shows the highly conserved mitoribosomal peptidyl transferase active site in complex with its substrate transfer RNAs, and defines the path of the nascent chain in mammalian mitoribosomes along their idiosyncratic exit tunnel. Furthermore, we present evidence that a mitochondrial tRNA has become an integral component of the central protuberance of the 39S subunit where it architecturally substitutes for the absence of the 5S ribosomal RNA, a ubiquitous component of all cytoplasmic ribosomes.
History
DepositionSep 25, 2014-
Header (metadata) releaseOct 8, 2014-
Map releaseOct 8, 2014-
UpdateNov 26, 2014-
Current statusNov 26, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4v19, PDB-4v1a
  • Surface level: 0.07
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4v19
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4v1a
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2787-ima...

Downloads & links

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Map

FileDownload / File: emd_2787.map.gz / Format: CCP4 / Size: 37.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the mammalian mitoribosomal 39S subunit at 3.4 Angstrom resolution
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.4 Å/pix.
x 216 pix.
= 302.4 Å		1.4 Å/pix.
x 216 pix.
= 302.4 Å		1.4 Å/pix.
x 216 pix.
= 302.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.4 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.07 / Movie #1: 0.07
Minimum - Maximum-0.25651765 - 0.55974966
Average (Standard dev.)0.00404575 (±0.02541414)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin727272
Dimensions216216216
Spacing216216216
CellA=B=C: 302.4 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.41.41.4
M x/y/z216216216
origin x/y/z0.0000.0000.000
length x/y/z302.400302.400302.400
α/β/γ90.00090.00090.000
start NX/NY/NZ-40-32-96
NX/NY/NZ8165193
MAP C/R/S123
start NC/NR/NS727272
NC/NR/NS216216216
D min/max/mean-0.2570.5600.004

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Supplemental data

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Sample components

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Entire : mammalian mitochondrial ribosome

EntireName: mammalian mitochondrial ribosome
Components
  • Sample: mammalian mitochondrial ribosome
  • Organelle or cellular component: 39S large subunit of the mitochondrial ribosome

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Supramolecule #1000: mammalian mitochondrial ribosome

SupramoleculeName: 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: 39S large subunit of the mitochondrial ribosome

SupramoleculeName: 39S large subunit of the mitochondrial ribosome / type: organelle_or_cellular_component / ID: 1 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: No
Ref GO0: GO:0005761
Source (natural)Organism: Sus scrofa domesticus (domestic 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
Detailssingle movie frame readout: 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: individual movie frame readout: 7 frames per exposure
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 100000 / 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
Detailssingle movie frame readout: 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: individual movie frame readout: 7 frames per exposure
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 100000 / 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: 3.4 Å / Resolution method: OTHER / Software - Name: CTFFIND3, RELION, 1.2 / Number images used: 141675

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Atomic model buiding 1

Initial modelPDB ID:

4ce4

SoftwareName: Chimera, O, COOT
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).
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-4v19:
Structure of the large subunit of the mammalian mitoribosome, part 1 of 2

PDB-4v1a:
Structure of the large subunit of the mammalian mitoribosome, part 2 of 2

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