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- EMDB-5113: The Structure of Leishmania Mitochondrial Ribosome with Minimal RNA. -

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Basic information

Entry
Database: EMDB / ID: EMD-5113
TitleThe Structure of Leishmania Mitochondrial Ribosome with Minimal RNA.
Map dataLeishmania mitoribosome
Sample
  • Sample: Leishmania Mitochondrial 50S Ribosome
  • Complex: 50S RibosomeProkaryotic large ribosomal subunit
KeywordsLeishmania tarentolae / Mitochondrial ribosome / CryoEM / Minimal RNA.
Function / homology
Function and homology information


Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / mitochondrial large ribosomal subunit / mitochondrial ribosome / mitochondrial translation / misfolded RNA binding / Group I intron splicing ...Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation elongation / Mitochondrial translation termination / Mitochondrial translation initiation / mitochondrial large ribosomal subunit / mitochondrial ribosome / mitochondrial translation / misfolded RNA binding / Group I intron splicing / RNA folding / four-way junction DNA binding / regulation of mRNA stability / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / DNA endonuclease activity / maintenance of translational fidelity / mRNA 5'-UTR binding / small ribosomal subunit rRNA binding / ribosomal large subunit assembly / ribosomal small subunit assembly / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / regulation of translation / cytoplasmic translation / small ribosomal subunit / cytosolic large ribosomal subunit / mitochondrial inner membrane / tRNA binding / negative regulation of translation / rRNA binding / molecular adaptor activity / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / protein domain specific binding / response to antibiotic / mRNA binding / mitochondrion / RNA binding / zinc ion binding / nucleoplasm / cytosol / cytoplasm
Similarity search - Function
Ribosomal protein L11, bacterial-type / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain ...Ribosomal protein L11, bacterial-type / Ribosomal protein S16, conserved site / Ribosomal protein S16 signature. / Ribosomal protein L21, conserved site / Ribosomal protein L21 signature. / Ribosomal protein L11, N-terminal / Ribosomal protein L9 signature. / Ribosomal protein L9, bacteria/chloroplast / Ribosomal protein L9, C-terminal / Ribosomal protein L9, C-terminal domain / Ribosomal protein L9, C-terminal domain superfamily / 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, N-terminal domain / 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 L20 signature. / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S11, bacterial-type / Ribosomal protein S9, bacterial/plastid / Ribosomal protein L14P, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein L33 / Ribosomal protein L33 / Ribosomal protein L33 superfamily / : / Ribosomal protein L30, bacterial-type / Ribosomal protein L16 / Ribosomal protein S18, conserved site / Ribosomal protein S18 signature. / Ribosomal protein L20 / Ribosomal protein S16 / Ribosomal protein S16 / Ribosomal protein S16 domain superfamily / Ribosomal protein L20 / Ribosomal protein L20, C-terminal / Ribosomal protein L21 / Ribosomal protein L27 / Ribosomal L27 protein / Ribosomal protein S15, bacterial-type / 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 protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Ribosomal protein L24 / Ribosomal protein S12, bacterial-type / Ribosomal protein L13, bacterial-type / Translation elongation factor EF1B/ribosomal protein S6 / Ribosomal protein L23/L25, conserved site / Ribosomal protein L3, bacterial/organelle-type / Ribosomal protein L15, bacterial-type / Ribosomal protein S18 / Ribosomal protein S18 / 50S ribosomal protein uL4 / Ribosomal protein S18 superfamily / Ribosomal protein L23 signature. / Ribosomal protein L30, conserved site / : / Ribosomal protein L29, conserved site / Ribosomal protein L30 signature. / : / Ribosomal protein S17, conserved site / Ribosomal protein L15, conserved site / Ribosomal protein L10e/L16 / Ribosomal protein L10e/L16 superfamily / Ribosomal protein L29 signature. / Ribosomal protein L16p/L10e / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / Ribosomal S11, conserved site / Ribosomal protein L14P, conserved site / S5 double stranded RNA-binding domain profile. / Ribosomal protein S5, C-terminal / Ribosomal protein S9, conserved site / Ribosomal protein S5, N-terminal domain / Ribosomal protein S8 / Ribosomal protein L15 signature. / Ribosomal protein S17 signature. / Ribosomal protein S5, C-terminal domain / Ribosomal protein L29/L35
Similarity search - Domain/homology
Large ribosomal subunit protein bL33m / Small ribosomal subunit protein bS6 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS5 ...Large ribosomal subunit protein bL33m / Small ribosomal subunit protein bS6 / Large ribosomal subunit protein uL15 / Large ribosomal subunit protein bL20 / Large ribosomal subunit protein uL29 / Large ribosomal subunit protein bL9 / Small ribosomal subunit protein uS11 / Small ribosomal subunit protein uS12 / Small ribosomal subunit protein bS16 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS9 / Large ribosomal subunit protein uL13 / Large ribosomal subunit protein uL14 / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein bL21 / Large ribosomal subunit protein uL30 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL3 / 30S ribosomal protein S18 / Large ribosomal subunit protein uL2m / Large ribosomal subunit protein uL11m / Large ribosomal subunit protein uL24m / Large ribosomal subunit protein uL22m / Large ribosomal subunit protein bL17m / Large ribosomal subunit protein uL2m / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein uL24m / Large ribosomal subunit protein uL4m / Large ribosomal subunit protein bL17m / Large ribosomal subunit protein uL22m / Large ribosomal subunit protein uL16m / Large ribosomal subunit protein bL27m / Large ribosomal subunit protein uL11m
Similarity search - Component
Biological speciesLeishmania tarentolae (eukaryote)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 14.1 Å
AuthorsSharma MR / Booth TM / Simpson L / Maslov DA / Agrawal RK
CitationJournal: Proc Natl Acad Sci U S A / Year: 2009
Title: Structure of a mitochondrial ribosome with minimal RNA.
Authors: Manjuli R Sharma / Timothy M Booth / Larry Simpson / Dmitri A Maslov / Rajendra K Agrawal /
Abstract: The Leishmania tarentolae mitochondrial ribosome (Lmr) is a minimal ribosomal RNA (rRNA)-containing ribosome. We have obtained a cryo-EM map of the Lmr. The map reveals several features that have not ...The Leishmania tarentolae mitochondrial ribosome (Lmr) is a minimal ribosomal RNA (rRNA)-containing ribosome. We have obtained a cryo-EM map of the Lmr. The map reveals several features that have not been seen in previously-determined structures of eubacterial or eukaryotic (cytoplasmic or organellar) ribosomes to our knowledge. Comparisons of the Lmr map with X-ray crystallographic and cryo-EM maps of the eubacterial ribosomes and a cryo-EM map of the mammalian mitochondrial ribosome show that (i) the overall structure of the Lmr is considerably more porous, (ii) the topology of the intersubunit space is significantly different, with fewer intersubunit bridges, but more tunnels, and (iii) several of the functionally-important rRNA regions, including the alpha-sarcin-ricin loop, have different relative positions within the structure. Furthermore, the major portions of the mRNA channel, the tRNA passage, and the nascent polypeptide exit tunnel contain Lmr-specific proteins, suggesting that the mechanisms for mRNA recruitment, tRNA interaction, and exiting of the nascent polypeptide in Lmr must differ markedly from the mechanisms deduced for ribosomes in other organisms. Our study identifies certain structural features that are characteristic solely of mitochondrial ribosomes and other features that are characteristic of both mitochondrial and chloroplast ribosomes (i.e., organellar ribosomes).
History
DepositionMar 16, 2009-
Header (metadata) releaseMay 15, 2009-
Map releaseMay 15, 2009-
UpdateApr 16, 2014-
Current statusApr 16, 2014Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00055
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  • Surface view colored by height
  • Surface level: 0.00055
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  • Surface view with fitted model
  • Atomic models: PDB-3iy8, PDB-3iy9
  • Surface level: 0.00055
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3iy8
  • Imaged by Jmol
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3iy9
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_5113_1.jpg

Downloads & links

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Map

FileDownload / File: emd_5113.map.gz / Format: CCP4 / Size: 8.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationLeishmania mitoribosome
Voxel sizeX=Y=Z: 2.76 Å
Density
Contour LevelBy AUTHOR: 0.00055 / Movie #1: 0.00055
Minimum - Maximum-0.00191628 - 0.00403481
Average (Standard dev.)0.00008317 (±0.00023827)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-65-65-65
Dimensions130130130
Spacing130130130
CellA=B=C: 358.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.762.762.76
M x/y/z130130130
origin x/y/z0.0000.0000.000
length x/y/z358.800358.800358.800
α/β/γ90.00090.00090.000
start NX/NY/NZ-34-26-72
NX/NY/NZ6953145
MAP C/R/S123
start NC/NR/NS-65-65-65
NC/NR/NS130130130
D min/max/mean-0.0020.0040.000

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Supplemental data

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Sample components

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Entire : Leishmania Mitochondrial 50S Ribosome

EntireName: Leishmania Mitochondrial 50S Ribosome
Components
  • Sample: Leishmania Mitochondrial 50S Ribosome
  • Complex: 50S RibosomeProkaryotic large ribosomal subunit

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Supramolecule #1000: Leishmania Mitochondrial 50S Ribosome

SupramoleculeName: Leishmania Mitochondrial 50S Ribosome / type: sample / ID: 1000 / Oligomeric state: Monomer / Number unique components: 1
Molecular weightExperimental: 2.1 MDa / Method: Proteomics

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Supramolecule #1: 50S Ribosome

SupramoleculeName: 50S Ribosome / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-prokaryote: LSU 50S
Source (natural)Organism: Leishmania tarentolae (eukaryote) / Organelle: mitochondrion
Molecular weightExperimental: 2.1 MDa

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.067 mg/mL
BufferpH: 7.5
Details: 50 mM Tris-HCl, pH 7.5, 100 mM KCl, 10 mM MgCl2, 3 mM DTT, 0.1 mM EDTA and 0.05% dodecyl maltoside
StainingType: NEGATIVE / Details: Cryo EM
GridDetails: 300 copper Mesh grid
VitrificationCryogen name: ETHANE / Chamber humidity: 90 % / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50760 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.6 µm / Nominal magnification: 50000
Sample stageSpecimen holder: eucentric / Specimen holder model: OTHER
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 267 / Bits/pixel: 12
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each Micrograph
Final reconstructionAlgorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 53475

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