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- EMDB-2695: Cryo-EM map of Trigger Factor bound to a translating ribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-2695
TitleCryo-EM map of Trigger Factor bound to a translating ribosome
Map dataHigh resolution map of ribosome-bound Trigger Factor
Sample
  • Sample: TnaC-stalled-RNC with Trigger factor
  • Complex: cytosolic 70S ribosome
  • Protein or peptide: Trigger factor
Keywordstranslation / co-translational protein folding
Function / homology
Function and homology information


'de novo' cotranslational protein folding / stress response to copper ion / protein unfolding / : / protein folding chaperone / peptidyl-prolyl cis-trans isomerase activity / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / protein transport ...'de novo' cotranslational protein folding / stress response to copper ion / protein unfolding / : / protein folding chaperone / peptidyl-prolyl cis-trans isomerase activity / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / protein transport / ribosome binding / response to heat / cell division / identical protein binding / membrane / cytosol
Similarity search - Function
Trigger factor / Trigger factor, C-terminal / Trigger factor, ribosome-binding, bacterial / Trigger factor ribosome-binding domain superfamily / Bacterial trigger factor protein (TF) / Bacterial trigger factor protein (TF) C-terminus / Trigger factor, C-terminal domain superfamily / Trigger factor/SurA domain superfamily / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase ...Trigger factor / Trigger factor, C-terminal / Trigger factor, ribosome-binding, bacterial / Trigger factor ribosome-binding domain superfamily / Bacterial trigger factor protein (TF) / Bacterial trigger factor protein (TF) C-terminus / Trigger factor, C-terminal domain superfamily / Trigger factor/SurA domain superfamily / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / Peptidyl-prolyl cis-trans isomerase domain superfamily
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 7.7 Å
AuthorsDeeng J / Chan KY / van der Sluis E / Bischoff L / Berninghausen O / Han W / Gumbart J / Schulten K / Beatrix B / Beckmann R
CitationJournal: J Mol Biol / Year: 2016
Title: Dynamic Behavior of Trigger Factor on the Ribosome.
Authors: J Deeng / K Y Chan / E O van der Sluis / O Berninghausen / W Han / J Gumbart / K Schulten / B Beatrix / R Beckmann /
Abstract: Trigger factor (TF) is the only ribosome-associated chaperone in bacteria. It interacts with hydrophobic segments in nascent chain (NCs) as they emerge from the ribosome. TF binds via its N-terminal ...Trigger factor (TF) is the only ribosome-associated chaperone in bacteria. It interacts with hydrophobic segments in nascent chain (NCs) as they emerge from the ribosome. TF binds via its N-terminal ribosome-binding domain (RBD) mainly to ribosomal protein uL23 at the tunnel exit on the large ribosomal subunit. Whereas earlier structural data suggested that TF binds as a rigid molecule to the ribosome, recent comparisons of structural data on substrate-bound, ribosome-bound, and TF in solution from different species suggest that this chaperone is a rather flexible molecule. Here, we present two cryo-electron microscopy structures of TF bound to ribosomes translating an mRNA coding for a known TF substrate from Escherichia coli of a different length. The structures reveal distinct degrees of flexibility for the different TF domains, a conformational rearrangement of the RBD upon ribosome binding, and an increase in rigidity within TF when the NC is extended. Molecular dynamics simulations agree with these data and offer a molecular basis for these observations.
History
DepositionJun 27, 2014-
Header (metadata) releaseAug 6, 2014-
Map releaseJul 15, 2015-
UpdateSep 28, 2016-
Current statusSep 28, 2016Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4urd
  • Surface level: 0.12
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4urd
  • Surface level: 0.07
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4urd
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

EMD-2695.png

Downloads & links

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Map

FileDownload / File: emd_2695.map.gz / Format: CCP4 / Size: 94.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationHigh resolution map of ribosome-bound Trigger Factor
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.24 Å/pix.
x 294 pix.
= 363.825 Å		1.24 Å/pix.
x 294 pix.
= 363.825 Å		1.24 Å/pix.
x 294 pix.
= 363.825 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.2375 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy EMDB: 0.09 / Movie #1: 0.12
Minimum - Maximum-0.30618721 - 0.65773547
Average (Standard dev.)0.00660606 (±0.04793993)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-147-147-146
Dimensions294294294
Spacing294294294
CellA=B=C: 363.82498 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.23751.23751.2375
M x/y/z294294294
origin x/y/z0.0000.0000.000
length x/y/z363.825363.825363.825
α/β/γ90.00090.00090.000
start NX/NY/NZ-147-147-146
NX/NY/NZ294294294
MAP C/R/S213
start NC/NR/NS-147-147-146
NC/NR/NS294294294
D min/max/mean-0.3060.6580.007

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Supplemental data

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Sample components

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Entire : TnaC-stalled-RNC with Trigger factor

EntireName: TnaC-stalled-RNC with Trigger factor
Components
  • Sample: TnaC-stalled-RNC with Trigger factor
  • Complex: cytosolic 70S ribosome
  • Protein or peptide: Trigger factor

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Supramolecule #1000: TnaC-stalled-RNC with Trigger factor

SupramoleculeName: TnaC-stalled-RNC with Trigger factor / type: sample / ID: 1000 / Oligomeric state: monomer / Number unique components: 2

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Supramolecule #1: cytosolic 70S ribosome

SupramoleculeName: cytosolic 70S ribosome / type: complex / ID: 1 / Name.synonym: 70S / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL
Source (natural)Organism: Escherichia coli (E. coli) / Strain: KC6

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Macromolecule #1: Trigger factor

MacromoleculeName: Trigger factor / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: 1 / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightExperimental: 48 KDa / Theoretical: 48 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)

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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

BufferpH: 7.4 / Details: 20 mM HEPES, 100 mM KOAc, 10 mM Mg(OAc)2, 2 mM DTT
StainingType: NEGATIVE / Details: Cryo-EM
GridDetails: Quantifoil R3/3 holey carbon supported grids
VitrificationCryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK III
Method: Blot for 10 seconds before plunging, use 2 layers of filter paper V

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Electron microscopy

MicroscopeFEI TECNAI F30
DateNov 21, 2010
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 4.35 µm / Number real images: 221 / Average electron dose: 20 e/Å2 / Od range: 1.2 / Bits/pixel: 16
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 38900 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: -3.5 µm / Nominal defocus min: -1.2 µm / Nominal magnification: 39000
Sample stageSpecimen holder model: OTHER
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

DetailsThe particles were selected using SIGNATURE and processed using SPIDER
CTF correctionDetails: on volumes (SPIDER)
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 7.7 Å / Resolution method: OTHER / Software - Name: SPIDER / Number images used: 100931

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