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- EMDB-1664: Alpha-helical nascent polypeptide chains visualized within distin... -

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Basic information

Entry
Database: EMDB / ID: EMD-1664
TitleAlpha-helical nascent polypeptide chains visualized within distinct regions of the ribosomal exit tunnel
Map data80S.Helix1_RNC
Sample
  • Sample: This map represents a wheat germ 80S ribosomal nascent chain complex with different nascent chains
  • Complex: Ribosome
KeywordsRibosome / Protein exit tunnel / co-translational protein folding
Biological speciesTriticum sp. (plant)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 7.1 Å
AuthorsBhushan S / Gartmann M / Halic M / Armache JP / Jarasch A / Mielke T / Berninghausen O / Wilson DN / Beckmann R
CitationJournal: Nat Struct Mol Biol / Year: 2010
Title: alpha-Helical nascent polypeptide chains visualized within distinct regions of the ribosomal exit tunnel.
Authors: Shashi Bhushan / Marco Gartmann / Mario Halic / Jean-Paul Armache / Alexander Jarasch / Thorsten Mielke / Otto Berninghausen / Daniel N Wilson / Roland Beckmann /
Abstract: As translation proceeds, the nascent polypeptide chain passes through a tunnel in the large ribosomal subunit. Although this ribosomal exit tunnel was once thought only to be a passive conduit for ...As translation proceeds, the nascent polypeptide chain passes through a tunnel in the large ribosomal subunit. Although this ribosomal exit tunnel was once thought only to be a passive conduit for the growing nascent chain, accumulating evidence suggests that it may in fact play a more active role in regulating translation and initial protein folding events. Here we have determined single-particle cryo-electron microscopy reconstructions of eukaryotic 80S ribosomes containing nascent chains with high alpha-helical propensity located within the exit tunnel. The maps enable direct visualization of density for helices as well as allowing the sites of interaction with the tunnel wall components to be elucidated. In particular regions of the tunnel, the nascent chain adopts distinct conformations and establishes specific contacts with tunnel components, both ribosomal RNA and proteins, that have been previously implicated in nascent chain-ribosome interaction.
History
DepositionNov 24, 2009-
Header (metadata) releaseJan 6, 2010-
Map releaseFeb 5, 2010-
UpdateMay 6, 2015-
Current statusMay 6, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 100
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 100
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_1664.map.gz / Format: CCP4 / Size: 185.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotation80S.Helix1_RNC
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.24 Å/pix.
x 368 pix.
= 456.32 Å
1.24 Å/pix.
x 368 pix.
= 456.32 Å
1.24 Å/pix.
x 368 pix.
= 456.32 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.24 Å
Density
Contour LevelBy AUTHOR: 0.167 / Movie #1: 100
Minimum - Maximum-245.240000000000009 - 623.317999999999984
Average (Standard dev.)3.53117 (±34.907699999999998)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-184-184-183
Dimensions368368368
Spacing368368368
CellA=B=C: 456.32 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.241.241.24
M x/y/z368368368
origin x/y/z0.0000.0000.000
length x/y/z456.320456.320456.320
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S213
start NC/NR/NS-184-184-183
NC/NR/NS368368368
D min/max/mean-245.240623.3183.531

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Supplemental data

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Sample components

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Entire : This map represents a wheat germ 80S ribosomal nascent chain comp...

EntireName: This map represents a wheat germ 80S ribosomal nascent chain complex with different nascent chains
Components
  • Sample: This map represents a wheat germ 80S ribosomal nascent chain complex with different nascent chains
  • Complex: Ribosome

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Supramolecule #1000: This map represents a wheat germ 80S ribosomal nascent chain comp...

SupramoleculeName: This map represents a wheat germ 80S ribosomal nascent chain complex with different nascent chains
type: sample / ID: 1000 / Number unique components: 1
Molecular weightExperimental: 4.1 MDa / Theoretical: 4.1 MDa / Method: Known for 80S ribosomes

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Supramolecule #1: Ribosome

SupramoleculeName: Ribosome / type: complex / ID: 1 / Name.synonym: Ribosome / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL
Source (natural)Organism: Triticum sp. (plant) / synonym: Bread wheat
Molecular weightExperimental: 4.1 MDa / Theoretical: 4.1 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

Concentration0.02 mg/mL
BufferpH: 7.5
Details: 20 mM Hepes/KOH ph 7.5, 100 mM KOAc, 10 mM Mg(oAc)2, 1.5 mM DTT, 0.1% (w/v) Nikol
StainingType: NEGATIVE / Details: Cryo-EM
GridDetails: Quantifoil grids (3/3) with 2nm carbon
VitrificationCryogen name: ETHANE / Chamber humidity: 95 % / Instrument: OTHER / Details: Vitrification instrument: Vitrobot / Method: Blot for 10 seconds before plunging

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Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 38000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.26 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 39000
Sample stageSpecimen holder: FEI Polara cartridge system / Specimen holder model: OTHER
TemperatureAverage: 84 K
Alignment procedureLegacy - Astigmatism: Objective lens astigmatism was corrected at 100,000 times magnification
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Digitization - Sampling interval: 4.76 µm / Number real images: 150 / Average electron dose: 25 e/Å2 / Details: Scanned at 5334 dpi / Od range: 1.2 / Bits/pixel: 16
Tilt angle min0
Tilt angle max0
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Defocus group volumes
Final angle assignmentDetails: SPIDER
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.1 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER / Number images used: 120000
DetailsSignature for particle selection and web for visual inspection

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