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- EMDB-0203: Cryo-EM structure of a RNaseI treated 80S ribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-0203
TitleCryo-EM structure of a RNaseI treated 80S ribosome
Map dataRNaseI treated uL4-RNCs.
Sample
  • Complex: RNaseI treated uL4-RNCs
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 6.7 Å
AuthorsKnorr AG / Berninghausen O / Becker T / Beckmann R
CitationJournal: Nat Struct Mol Biol / Year: 2019
Title: Ribosome-NatA architecture reveals that rRNA expansion segments coordinate N-terminal acetylation.
Authors: Alexandra G Knorr / Christian Schmidt / Petr Tesina / Otto Berninghausen / Thomas Becker / Birgitta Beatrix / Roland Beckmann /
Abstract: The majority of eukaryotic proteins are N-terminally α-acetylated by N-terminal acetyltransferases (NATs). Acetylation usually occurs co-translationally and defects have severe consequences. ...The majority of eukaryotic proteins are N-terminally α-acetylated by N-terminal acetyltransferases (NATs). Acetylation usually occurs co-translationally and defects have severe consequences. Nevertheless, it is unclear how these enzymes act in concert with the translating ribosome. Here, we report the structure of a native ribosome-NatA complex from Saccharomyces cerevisiae. NatA (comprising Naa10, Naa15 and Naa50) displays a unique mode of ribosome interaction by contacting eukaryotic-specific ribosomal RNA expansion segments in three out of four binding patches. Thereby, NatA is dynamically positioned directly underneath the ribosomal exit tunnel to facilitate modification of the emerging nascent peptide chain. Methionine amino peptidases, but not chaperones or signal recognition particle, would be able to bind concomitantly. This work assigns a function to the hitherto enigmatic ribosomal RNA expansion segments and provides mechanistic insights into co-translational protein maturation by N-terminal acetylation.
History
DepositionAug 17, 2018-
Header (metadata) releaseAug 29, 2018-
Map releaseDec 19, 2018-
UpdateJan 16, 2019-
Current statusJan 16, 2019Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0141
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.0141
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_0203.png

Downloads & links

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Map

FileDownload / File: emd_0203.map.gz / Format: CCP4 / Size: 10.5 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRNaseI treated uL4-RNCs.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
3.25 Å/pix.
x 140 pix.
= 455.28 Å		3.25 Å/pix.
x 140 pix.
= 455.28 Å		3.25 Å/pix.
x 140 pix.
= 455.28 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 3.252 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.0141 / Movie #1: 0.0141
Minimum - Maximum-0.02608649 - 0.07086801
Average (Standard dev.)0.00057176186 (±0.005988945)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions140140140
Spacing140140140
CellA=B=C: 455.28 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.2523.2523.252
M x/y/z140140140
origin x/y/z0.0000.0000.000
length x/y/z455.280455.280455.280
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS140140140
D min/max/mean-0.0260.0710.001

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Supplemental data

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Sample components

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Entire : RNaseI treated uL4-RNCs

EntireName: RNaseI treated uL4-RNCs
Components
  • Complex: RNaseI treated uL4-RNCs

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Supramolecule #1: RNaseI treated uL4-RNCs

SupramoleculeName: RNaseI treated uL4-RNCs / type: complex / ID: 1 / Parent: 0
Details: Amongst others, features like expansion segment are missing.
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)

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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: 7.5
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: 2.5 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

CTF correctionSoftware - Name: Gctf
Final reconstructionResolution.type: BY AUTHOR / Resolution: 6.7 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0beta) / Number images used: 5909
Initial angle assignmentType: PROJECTION MATCHING / Software - Name: RELION
Final angle assignmentType: PROJECTION MATCHING / Software - Name: RELION

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Atomic model buiding 1

RefinementProtocol: RIGID BODY FIT

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