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- EMDB-6583: Cryo-EM structure of the large ribosomal subunit from the eukaryo... -

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Basic information

Entry
Database: EMDB / ID: EMD-6583
TitleCryo-EM structure of the large ribosomal subunit from the eukaryotic parasite Leishmania
Map dataReconstruction of the large ribosomal subunit from the eukaryotic parasite Leishmania donovani
Sample
  • Sample: Leishimania donovani 91S ribosome
  • Complex: 91S ribosome
KeywordsThe large ribosomal subunit from Leishmania donovani
Function / homology
Function and homology information


protein-RNA complex assembly / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / structural constituent of ribosome ...protein-RNA complex assembly / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / 5S rRNA binding / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / mRNA binding / RNA binding / zinc ion binding / membrane
Similarity search - Function
Ribosomal protein L14, KOW motif / Ribosomal protein L28e / Ribosomal protein L23 / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L22e / Ribosomal protein L22e superfamily ...Ribosomal protein L14, KOW motif / Ribosomal protein L28e / Ribosomal protein L23 / : / Ribosomal L28e/Mak16 / Ribosomal L28e protein family / Ribosomal protein L29e / Ribosomal L29e protein family / Ribosomal protein L22e / Ribosomal protein L22e superfamily / Ribosomal L22e protein family / Ribosomal protein L38e / Ribosomal protein L38e superfamily / Ribosomal L38e protein family / Ribosomal protein L10e, conserved site / Ribosomal protein L10e signature. / Ribosomal protein L19, eukaryotic / Ribosomal protein L10e / Ribosomal protein L44e signature. / 60S ribosomal protein L18a/ L20, eukaryotes / : / Ribosomal protein L5 eukaryotic, C-terminal / Ribosomal L18 C-terminal region / Ribosomal protein L44e / Ribosomal protein L44 / 50S ribosomal protein L18Ae/60S ribosomal protein L20 and L18a / Ribosomal protein L30e signature 1. / Ribosomal protein 50S-L18Ae/60S-L20/60S-L18A / Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A / Ribosomal protein 60S L18 and 50S L18e / Eukaryotic Ribosomal Protein L27, KOW domain / Ribosomal protein L27e / Ribosomal protein L27e superfamily / Ribosomal L27e protein family / Ribosomal protein L30e signature 2. / Ribosomal protein L39e, conserved site / Ribosomal protein L30e, conserved site / Ribosomal protein L39e signature. / 60S ribosomal protein L35 / : / 60S ribosomal protein L19 / Ribosomal protein L34Ae / Ribosomal protein L34e / Ribosomal protein L7A/L8 / Ribosomal protein L30/YlxQ / Ribosomal protein L7, eukaryotic / Ribosomal protein L30, N-terminal / Ribosomal L30 N-terminal domain / 60S ribosomal protein L4, C-terminal domain / 60S ribosomal protein L4 C-terminal domain / Ribosomal protein L18e / Ribosomal protein L36e / Ribosomal protein L36e domain superfamily / Ribosomal protein L36e / Ribosomal protein L19e, C-terminal domain / Ribosomal_L19e / Ribosomal protein L19/L19e / Ribosomal protein L14e domain / Ribosomal protein L19/L19e, domain 1 / Ribosomal protein L19/L19e superfamily / Ribosomal protein L19e, N-terminal domain / Ribosomal protein L14 / Ribosomal protein L37ae / Ribosomal L37ae protein family / Ribosomal protein L35A / Ribosomal protein L35Ae / Ribosomal protein L35A superfamily / Ribosomal protein L6, conserved site-2 / Ribosomal protein L6 signature 2. / Ribosomal protein L39e / Ribosomal protein L39e domain superfamily / Ribosomal L39 protein / Ribosomal protein L5 eukaryotic/L18 archaeal / Ribosomal large subunit proteins 60S L5, and 50S L18 / Ribosomal protein L14 / Ribosomal protein L4/L1e, eukaryotic/archaeal, conserved site / Ribosomal protein L1e signature. / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal protein L31e / Ribosomal_L31e / Ribosomal protein L21e / Ribosomal protein L21e, conserved site / Ribosomal protein L21 superfamily / Ribosomal protein L21e / Ribosomal protein L21e signature. / Ribosomal protein L37e, conserved site / Ribosomal protein L37e signature. / Ribosomal protein L22/L17, eukaryotic/archaeal / Ribosomal protein L37e / Ribosomal protein L37e / Ribosomal_L15e / Ribosomal protein L4, eukaryotic and archaeal type / Ribosomal protein L15e / Ribosomal protein L15e core domain superfamily / Ribosomal L15 / Ribosomal protein L32e / Ribosomal protein L37ae/L37e / Ribosomal protein L32e superfamily / Ribosomal protein L32
Similarity search - Domain/homology
Large ribosomal subunit protein eL38 / 60S ribosomal protein L10, putative / 60S ribosomal protein L19, putative / 60S ribosomal protein L23a, putative / 60S ribosomal protein L7a / 60S ribosomal protein L28, putative / 60S ribosomal protein L44, putative / 60S ribosomal protein L39, putative / 60S ribosomal protein L36, Putative / 60S ribosomal protein L9, putative ...Large ribosomal subunit protein eL38 / 60S ribosomal protein L10, putative / 60S ribosomal protein L19, putative / 60S ribosomal protein L23a, putative / 60S ribosomal protein L7a / 60S ribosomal protein L28, putative / 60S ribosomal protein L44, putative / 60S ribosomal protein L39, putative / 60S ribosomal protein L36, Putative / 60S ribosomal protein L9, putative / 60S ribosomal protein L32 / 60S ribosomal protein L37a / Large ribosomal subunit protein uL5 / 40S ribosomal protein L14, putative / 60S ribosomal protein L17, putative / 60S ribosomal protein L7, putative / 60S ribosomal protein L35, putative / Ribosomal protein L1a, putative / Ribosomal protein L15 / Ribosomal L27e family protein / Ribosomal protein L37 / Ribosomal protein L35Ae family protein / 60S ribosomal protein L21, putative / 60S ribosomal protein L30 / 60S ribosomal protein L18a / 60S ribosomal protein L5, putative / 60S ribosomal subunit protein L31, putative / 60S ribosomal protein L27A/L29, putative / 60S ribosomal protein L23, putative / Large ribosomal subunit protein eL22 / 60S ribosomal protein L29 / 60S ribosomal protein L34, putative / 60S ribosomal protein L18, putative / Large ribosomal subunit protein eL37
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 2.8 Å
AuthorsShalev-Benami M / Zhang Y / Matzov D / Halfon Y / Zackay A / Rozenberg H / Zimmerman E / Bashan A / Jaffe CL / Yonath A / Skiniotis G
CitationJournal: Cell Rep / Year: 2016
Title: 2.8-Å Cryo-EM Structure of the Large Ribosomal Subunit from the Eukaryotic Parasite Leishmania.
Authors: Moran Shalev-Benami / Yan Zhang / Donna Matzov / Yehuda Halfon / Arie Zackay / Haim Rozenberg / Ella Zimmerman / Anat Bashan / Charles L Jaffe / Ada Yonath / Georgios Skiniotis /
Abstract: Leishmania is a single-cell eukaryotic parasite of the Trypanosomatidae family, whose members cause an array of tropical diseases. The often fatal outcome of infections, lack of effective vaccines, ...Leishmania is a single-cell eukaryotic parasite of the Trypanosomatidae family, whose members cause an array of tropical diseases. The often fatal outcome of infections, lack of effective vaccines, limited selection of therapeutic drugs, and emerging resistant strains, underline the need to develop strategies to combat these pathogens. The Trypanosomatid ribosome has recently been highlighted as a promising therapeutic target due to structural features that are distinct from other eukaryotes. Here, we present the 2.8-Å resolution structure of the Leishmania donovani large ribosomal subunit (LSU) derived from a cryo-EM map, further enabling the structural observation of eukaryotic rRNA modifications that play a significant role in ribosome assembly and function. The structure illustrates the unique fragmented nature of leishmanial LSU rRNA and highlights the irregular distribution of rRNA modifications in Leishmania, a characteristic with implications for anti-parasitic drug development.
History
DepositionJan 20, 2016-
Header (metadata) releaseMar 9, 2016-
Map releaseJul 20, 2016-
UpdateAug 24, 2016-
Current statusAug 24, 2016Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.02
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.02
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  • Surface view with fitted model
  • Atomic models: PDB-3jcs
  • Surface level: 0.02
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6583.tif

Downloads & links

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Map

FileDownload / File: emd_6583.map.gz / Format: CCP4 / Size: 210.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of the large ribosomal subunit from the eukaryotic parasite Leishmania donovani
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1 Å/pix.
x 384 pix.
= 384. Å		1 Å/pix.
x 384 pix.
= 384. Å		1 Å/pix.
x 384 pix.
= 384. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.02 / Movie #1: 0.02
Minimum - Maximum-0.11835618 - 0.2307336
Average (Standard dev.)0.00044537 (±0.00627039)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions384384384
Spacing384384384
CellA=B=C: 384.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z111
M x/y/z384384384
origin x/y/z0.0000.0000.000
length x/y/z384.000384.000384.000
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS384384384
D min/max/mean-0.1180.2310.000

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Supplemental data

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Sample components

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Entire : Leishimania donovani 91S ribosome

EntireName: Leishimania donovani 91S ribosome
Components
  • Sample: Leishimania donovani 91S ribosome
  • Complex: 91S ribosome

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Supramolecule #1000: Leishimania donovani 91S ribosome

SupramoleculeName: Leishimania donovani 91S ribosome / type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: 91S ribosome

SupramoleculeName: 91S ribosome / type: complex / ID: 1 / Recombinant expression: No / Database: NCBI
Ribosome-details: ribosome-eukaryote: LSU 60S, LSU RNA 28S, LSU RNA 5.8S, LSU RNA 5S
Source (natural)Organism: Leishmania donovani (eukaryote) / Location in cell: cytoplasm

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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

Concentration0.3 mg/mL
BufferpH: 7.6
Details: 20 mM HEPES-KOH, pH 7.6, 100 mM KOAc, 10 mM Mg(OAc)2, 10 mM NH4OAc, 1 mM DTT
GridDetails: 25 seconds on glow-discharged holey carbon grids (Quantifoil R2/2) coated with continuous thin carbon film
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Specialist opticsEnergy filter - Name: FEI
DateJul 7, 2015
Image recordingCategory: CCD / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 30 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 25000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.6 µm / Nominal magnification: 29000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Each particle
Final reconstructionResolution.type: BY AUTHOR / Resolution: 2.8 Å / Resolution method: OTHER / Software - Name: RELION / Number images used: 107134

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