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- EMDB-10039: Cryo-EM structures of Lsg1-TAP pre-60S ribosomal particles (State... -

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Entry
Database: EMDB / ID: EMD-10039
TitleCryo-EM structures of Lsg1-TAP pre-60S ribosomal particles (State V - subclass 1)
Map data
SampleLsg1-TAP 60s ribosomal subunit
Biological speciesSaccharomyces cerevisiae (baker's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.3 Å
AuthorsKargas V / Warren AJ
CitationJournal: Elife / Year: 2019
Title: Mechanism of completion of peptidyltransferase centre assembly in eukaryotes.
Authors: Vasileios Kargas / Pablo Castro-Hartmann / Norberto Escudero-Urquijo / Kyle Dent / Christine Hilcenko / Carolin Sailer / Gertrude Zisser / Maria J Marques-Carvalho / Simone Pellegrino / Leszek Wawiórka / Stefan Mv Freund / Jane L Wagstaff / Antonina Andreeva / Alexandre Faille / Edwin Chen / Florian Stengel / Helmut Bergler / Alan John Warren /
Abstract: During their final maturation in the cytoplasm, pre-60S ribosomal particles are converted to translation-competent large ribosomal subunits. Here, we present the mechanism of peptidyltransferase ...During their final maturation in the cytoplasm, pre-60S ribosomal particles are converted to translation-competent large ribosomal subunits. Here, we present the mechanism of peptidyltransferase centre (PTC) completion that explains how integration of the last ribosomal proteins is coupled to release of the nuclear export adaptor Nmd3. Single-particle cryo-EM reveals that eL40 recruitment stabilises helix 89 to form the uL16 binding site. The loading of uL16 unhooks helix 38 from Nmd3 to adopt its mature conformation. In turn, partial retraction of the L1 stalk is coupled to a conformational switch in Nmd3 that allows the uL16 P-site loop to fully accommodate into the PTC where it competes with Nmd3 for an overlapping binding site (base A2971). Our data reveal how the central functional site of the ribosome is sculpted and suggest how the formation of translation-competent 60S subunits is disrupted in leukaemia-associated ribosomopathies.
DateDeposition: Jun 5, 2019 / Header (metadata) release: Jul 10, 2019 / Map release: Jul 10, 2019 / Update: Jul 10, 2019

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.06
  • Imaged by UCSF Chimera
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Structure viewerEM map:
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Supplemental images

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Map

FileDownload / File: emd_10039.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.)
1.07 Å/pix.
x 360 pix.
= 383.4 Å
1.07 Å/pix.
x 360 pix.
= 383.4 Å
1.07 Å/pix.
x 360 pix.
= 383.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.065 Å
Density
Contour LevelBy AUTHOR: 0.06 / Movie #1: 0.06
Minimum - Maximum-0.20977771 - 0.4142455
Average (Standard dev.)0.0023380755 (±0.01746915)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions360360360
Spacing360360360
CellA=B=C: 383.40002 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.0651.0651.065
M x/y/z360360360
origin x/y/z0.0000.0000.000
length x/y/z383.400383.400383.400
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS360360360
D min/max/mean-0.2100.4140.002

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Supplemental data

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Sample components

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Entire Lsg1-TAP 60s ribosomal subunit

EntireName: Lsg1-TAP 60s ribosomal subunit / Number of components: 1

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Component #1: protein, Lsg1-TAP 60s ribosomal subunit

ProteinName: Lsg1-TAP 60s ribosomal subunit / Recombinant expression: No
SourceSpecies: Saccharomyces cerevisiae (baker's yeast)

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Experimental details

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Sample preparation

SpecimenSpecimen state: Particle / Method: cryo EM
Sample solutionpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
ImagingMicroscope: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Electron dose: 63 e/Å2 / Illumination mode: FLOOD BEAM
LensImaging mode: BRIGHT FIELD
Specimen HolderModel: OTHER
CameraDetector: FEI FALCON III (4k x 4k)

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric) / Number of projections: 52800
3D reconstructionSoftware: RELION / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF

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Atomic model buiding

Modeling #1Refinement protocol: flexible
Input PDB model: 4V88

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