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- EMDB-2490: Structure of the 39S Large Subunit of the Mammalian Mitochondrial... -

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Basic information

Entry
Database: EMDB / ID: EMD-2490
TitleStructure of the 39S Large Subunit of the Mammalian Mitochondrial Ribosome
Map dataStructure of the 39S Large Subunit of the Mammalian Mitochondrial Ribosome
Sample
  • Sample: 39S large subunit of the porcine mitochondrial ribosome
  • Organelle or cellular component: 39S large subunit of the mitochondrial ribosome
Keywordsmammalian mitochondrial ribosome / 39S large ribosomal subunit / translation / ribosomal proteins / rRNA / polypeptide exit site / membrane association
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 / peptidyl-tRNA hydrolase activity / mitochondrial translation / organelle membrane / RNA processing / double-stranded RNA binding / large ribosomal subunit / 5S rRNA binding / mitochondrial inner membrane / rRNA binding / nuclear body / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / protein domain specific binding / nucleotide binding / mitochondrion / RNA binding / nucleus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Ribosomal protein L35, mitochondrial / : / : / MRPL44, double-stranded RNA binding domain / : / : / MRPL44 dsRNA-binding domain / Large ribosomal subunit protein mL44, endonuclease domain / : / : ...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 / Large ribosomal subunit protein bL9m N-terminal domain / Tim44-like domain / Tim44-like domain / Tim44 / : / : / : / Ribosomal protein L47, mitochondrial / MRP-L47 superfamily, mitochondrial / 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 / Beta-grasp domain superfamily / NTF2-like domain superfamily / Ribosomal protein L9 / Ribosomal protein L9, N-terminal domain superfamily / 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 L21 / Ribosomal protein L19 superfamily / 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 L24 / Ribosomal protein L15, bacterial-type / 50S ribosomal protein uL4 / : / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L16p/L10e / Ribosomal Proteins L2, RNA binding N-terminal domain / Ribosomal protein L24 signature. / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L24/L26, conserved site / Ribosomal Proteins L2, RNA binding domain / Ribosomal protein L2 / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal protein L23 / Ribosomal protein L30, ferredoxin-like fold domain / Ribosomal protein L30p/L7e / Ribosomal protein L25/L23 / Ribosomal protein L30, ferredoxin-like fold domain superfamily / Ribosomal protein L15 / Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A / Ribosomal protein S11 superfamily / Ribosomal protein L14p/L23e / Ribosomal protein L14P / Ribosomal protein L14 superfamily / Ribosomal protein L14p/L23e / Ribosomal protein L22/L17 / Ribosomal protein L22p/L17e / Ribosomal protein L22/L17 superfamily / Ribosomal protein L26/L24, KOW domain / Ribosomal protein L18e/L15P / Ribosomal L18e/L15P superfamily / Ribosomal protein L4/L1e / Ribosomal protein L4 domain superfamily / Ribosomal protein L4/L1 family / Translation protein SH3-like domain superfamily / Ribosomal protein L23/L15e core domain superfamily
Similarity search - Domain/homology
Large ribosomal subunit protein uL18m / 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 / Mitochondrial ribosomal protein L2 / 39S ribosomal protein L15, mitochondrial / Large ribosomal subunit protein bL27m ...Large ribosomal subunit protein uL18m / 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 / Mitochondrial ribosomal protein L2 / 39S ribosomal protein L15, mitochondrial / Large ribosomal subunit protein bL27m / Large ribosomal subunit protein mL38 / Large ribosomal subunit protein uL18m / Large ribosomal subunit protein bL21m / : / Mitochondrial ribosomal protein L4 / Large ribosomal subunit protein uL18m / Large ribosomal subunit protein uL29m / Large ribosomal subunit protein mL39 / Large ribosomal subunit protein mL44 / Large ribosomal subunit protein uL30m / Large ribosomal subunit protein bL35m / : / Large ribosomal subunit protein mL45 / Large ribosomal subunit protein bL19m / Large ribosomal subunit protein bL9m / Large ribosomal subunit protein bL32m / Large ribosomal subunit protein uL22m / Large ribosomal subunit protein uL23m / 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: 4.9 Å
AuthorsGreber BJ / Boehringer D / Leitner A / Bieri P / Voigts-Hoffmann F / Erzberger JP / Leibundgut M / Aebersold R / Ban N
CitationJournal: Nature / Year: 2014
Title: Architecture of the large subunit of the mammalian mitochondrial ribosome.
Authors: Basil J Greber / Daniel Boehringer / Alexander Leitner / Philipp Bieri / Felix Voigts-Hoffmann / Jan P Erzberger / Marc Leibundgut / Ruedi Aebersold / Nenad Ban /
Abstract: Mitochondrial ribosomes synthesize a number of highly hydrophobic proteins encoded on the genome of mitochondria, the organelles in eukaryotic cells that are responsible for energy conversion by ...Mitochondrial ribosomes synthesize a number of highly hydrophobic proteins encoded on the genome of mitochondria, the organelles in eukaryotic cells that are responsible for energy conversion by oxidative phosphorylation. The ribosomes in mammalian mitochondria have undergone massive structural changes throughout their evolution, including ribosomal RNA shortening and acquisition of mitochondria-specific ribosomal proteins. Here we present the three-dimensional structure of the 39S large subunit of the porcine mitochondrial ribosome determined by cryo-electron microscopy at 4.9 Å resolution. The structure, combined with data from chemical crosslinking and mass spectrometry experiments, reveals the unique features of the 39S subunit at near-atomic resolution and provides detailed insight into the architecture of the polypeptide exit site. This region of the mitochondrial ribosome has been considerably remodelled compared to its bacterial counterpart, providing a specialized platform for the synthesis and membrane insertion of the highly hydrophobic protein components of the respiratory chain.
History
DepositionOct 20, 2013-
Header (metadata) releaseNov 27, 2013-
Map releaseDec 25, 2013-
UpdateJan 22, 2014-
Current statusJan 22, 2014Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 11
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 11
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-4ce4
  • Surface level: 11
  • Imaged by UCSF Chimera
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2490-ima...

Downloads & links

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Map

FileDownload / File: emd_2490.map.gz / Format: CCP4 / Size: 62.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the 39S Large Subunit of the Mammalian Mitochondrial Ribosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.41 Å/pix.
x 256 pix.
= 360.96 Å		1.41 Å/pix.
x 256 pix.
= 360.96 Å		1.41 Å/pix.
x 256 pix.
= 360.96 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.41 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 11.0 / Movie #1: 11
Minimum - Maximum-45.891220089999997 - 48.92898941
Average (Standard dev.)-0.04675274 (±3.829741)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin444
Dimensions256256256
Spacing256256256
CellA=B=C: 360.96 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.411.411.41
M x/y/z256256256
origin x/y/z0.0000.0000.000
length x/y/z360.960360.960360.960
α/β/γ90.00090.00090.000
start NX/NY/NZ00-40
NX/NY/NZ555581
MAP C/R/S123
start NC/NR/NS444
NC/NR/NS256256256
D min/max/mean-45.89148.929-0.047

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Supplemental data

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Sample components

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Entire : 39S large subunit of the porcine mitochondrial ribosome

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

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Supramolecule #1000: 39S large subunit of the porcine mitochondrial ribosome

SupramoleculeName: 39S large subunit of the porcine mitochondrial ribosome
type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 1
Molecular weightTheoretical: 1.6 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: 7.9 / Details: 20 mM HEPES-KOH, 100 mM KCl, 1 mM DTT, 20 mM MgCl2
GridDetails: 200 mesh Quantifoil R2/1 and R 2/2 holey carbon grids
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER

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Electron microscopy #1

Microscopy ID1
MicroscopeFEI TITAN KRIOS
DateJun 21, 2013
Image recordingCategory: CCD / Film or detector model: FEI FALCON I (4k x 4k) / Digitization - Sampling interval: 14 µm / Average electron dose: 20 e/Å2
Details: For data processing Falcon 2 data were resampled to 1.41 Angstrom per pixel
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 141510 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.3 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 75000
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
DateMay 2, 2013
Image recordingCategory: CCD / Film or detector model: FEI FALCON I (4k x 4k) / Digitization - Sampling interval: 14 µm / Average electron dose: 20 e/Å2
Details: For data processing Falcon 2 data were resampled to 1.41 Angstrom per pixel
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 99290 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.6 µm / Nominal defocus min: 1.2 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 #3

Microscopy ID3
MicroscopeFEI TITAN KRIOS
DateApr 15, 2013
Image recordingCategory: CCD / Film or detector model: FEI FALCON I (4k x 4k) / Digitization - Sampling interval: 14 µm / Average electron dose: 20 e/Å2
Details: For data processing Falcon 2 data were resampled to 1.41 Angstrom per pixel
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 99290 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.6 µm / Nominal defocus min: 1.2 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 #4

Microscopy ID4
MicroscopeFEI TITAN KRIOS
DateMar 17, 2013
Image recordingCategory: CCD / Film or detector model: FEI FALCON I (4k x 4k) / Digitization - Sampling interval: 14 µm / Average electron dose: 20 e/Å2
Details: For data processing Falcon 2 data were resampled to 1.41 Angstrom per pixel
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 99290 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.6 µm / Nominal defocus min: 1.2 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 #5

Microscopy ID5
MicroscopeFEI TITAN KRIOS
DateFeb 19, 2013
Image recordingCategory: CCD / Film or detector model: FEI FALCON I (4k x 4k) / Digitization - Sampling interval: 14 µm / Average electron dose: 20 e/Å2
Details: For data processing Falcon 2 data were resampled to 1.41 Angstrom per pixel
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 99290 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.6 µm / Nominal defocus min: 1.2 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 #6

Microscopy ID6
MicroscopeFEI TITAN KRIOS
DateJan 21, 2013
Image recordingCategory: CCD / Film or detector model: FEI FALCON I (4k x 4k) / Digitization - Sampling interval: 14 µm / Average electron dose: 20 e/Å2
Details: For data processing Falcon 2 data were resampled to 1.41 Angstrom per pixel
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 99290 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.6 µm / Nominal defocus min: 1.2 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 #7

Microscopy ID7
MicroscopeFEI TITAN KRIOS
DateDec 19, 2012
Image recordingCategory: CCD / Film or detector model: FEI FALCON I (4k x 4k) / Digitization - Sampling interval: 14 µm / Average electron dose: 20 e/Å2
Details: For data processing Falcon 2 data were resampled to 1.41 Angstrom per pixel
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 99290 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.6 µm / Nominal defocus min: 1.2 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 #8

Microscopy ID8
MicroscopeFEI TITAN KRIOS
DateNov 30, 2012
Image recordingCategory: CCD / Film or detector model: FEI FALCON I (4k x 4k) / Digitization - Sampling interval: 14 µm / Average electron dose: 20 e/Å2
Details: For data processing Falcon 2 data were resampled to 1.41 Angstrom per pixel
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 99290 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 3.6 µm / Nominal defocus min: 1.2 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 and extracted in batchboxer (EMAN 1.9).
CTF correctionDetails: per detector frame
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 4.9 Å / Resolution method: OTHER / Software - Name: Spider, IMAGIC-5, CTFFIND3, RELION
Details: An initial reconstruction was obtained using the angular reconstitution approach in Imagic-5. For visualization purposes the final map was amplitude and MTF-corrected in RELION.
Number images used: 232181

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Atomic model buiding 1

Initial modelPDB ID:

3v2d
PDB Unreleased entry

SoftwareName: Chimera, O, COOT
DetailsRibosomal proteins and rRNA were docked into the density using Chimera. Individual domains were manually fitted an rebuild using COOT and O.
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-4ce4:
39S large subunit of the porcine mitochondrial ribosome

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