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- EMDB-3845: 40S from Trypanosoma cruzi -

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Basic information

Entry
Database: EMDB / ID: EMD-3845
Title40S from Trypanosoma cruzi
Map data
Sample
  • Complex: 40S ribosome from Trypanosoma cruzi
Biological speciesTrypanosoma cruzi (eukaryote)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.4 Å
AuthorsBrito Querido J / Mancera Martinez E / Vicens Q / Bochler A / Chicher J / Simonetti A / Hashem Y
CitationJournal: Structure / Year: 2017
Title: The cryo-EM Structure of a Novel 40S Kinetoplastid-Specific Ribosomal Protein.
Authors: Jailson Brito Querido / Eder Mancera-Martínez / Quentin Vicens / Anthony Bochler / Johana Chicher / Angelita Simonetti / Yaser Hashem /
Abstract: Kinetoplastids are potentially lethal protozoan pathogens affecting more than 20 million people worldwide. There is a critical need for more specific targets for the development of safer anti- ...Kinetoplastids are potentially lethal protozoan pathogens affecting more than 20 million people worldwide. There is a critical need for more specific targets for the development of safer anti-kinetoplastid therapeutic molecules that can replace the scarce and highly cytotoxic current drugs. The kinetoplastid ribosome represents a potential therapeutic target due to its relative structural divergence when compared with its human counterpart. However, several kinetoplastid-specific ribosomal features remain uncharacterized. Here, we present the near-atomic cryoelectron microscopy structure of a novel bona fide kinetoplastid-specific ribosomal (r-) protein (KSRP) bound to the ribosome. KSRP is an essential protein located at the solvent face of the 40S subunit, where it binds and stabilizes kinetoplastid-specific domains of rRNA, suggesting its role in ribosome integrity. KSRP also interacts with the r-protein eS6 at a region that is only conserved in kinetoplastids. The kinetoplastid-specific ribosomal environment of KSRP provides a promising target for the design of safer anti-kinetoplastidian drugs.
History
DepositionAug 11, 2017-
Header (metadata) releaseNov 15, 2017-
Map releaseNov 15, 2017-
UpdateDec 13, 2017-
Current statusDec 13, 2017Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0484
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0484
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_3845.png

Downloads & links

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Map

FileDownload / File: emd_3845.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.56 Å/pix.
x 360 pix.
= 561.6 Å		1.56 Å/pix.
x 360 pix.
= 561.6 Å		1.56 Å/pix.
x 360 pix.
= 561.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.56 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0484 / Movie #1: 0.0484
Minimum - Maximum-0.1229998 - 0.3691025
Average (Standard dev.)-0.00004011167 (±0.01171487)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 561.6 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.561.561.56
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z561.600561.600561.600
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.1230.369-0.000

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Supplemental data

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Sample components

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Entire : 40S ribosome from Trypanosoma cruzi

EntireName: 40S ribosome from Trypanosoma cruzi
Components
  • Complex: 40S ribosome from Trypanosoma cruzi

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Supramolecule #1: 40S ribosome from Trypanosoma cruzi

SupramoleculeName: 40S ribosome from Trypanosoma cruzi / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#35
Source (natural)Organism: Trypanosoma cruzi (eukaryote)

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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: 7.2
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 2.2 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Final reconstructionResolution.type: BY AUTHOR / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 178000
Initial angle assignmentType: PROJECTION MATCHING
Final angle assignmentType: PROJECTION MATCHING

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