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- EMDB-1499: Structure of the E. coli trigger factor bound to a translating ri... -

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Basic information

Entry
Database: EMDB / ID: EMD-1499
TitleStructure of the E. coli trigger factor bound to a translating ribosome
Map dataStructure of the E. coli trigger factor bound to a translating ribosome
Sample
  • Sample: Escherichia coli Trigger Factor associated with an Escherichia coli ribosome-nascent chain complex
  • Complex: ribosome-nascent chain complex
  • Protein or peptide: trigger factor
Keywordstrigger factor / ribosome-nascent chain complex / translating ribosome / co-translational protein folding / chaperone
Function / homology
Function and homology information


'de novo' cotranslational protein folding / stress response to copper ion / protein unfolding / : / protein folding chaperone / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein transport / ribosome binding / response to heat ...'de novo' cotranslational protein folding / stress response to copper ion / protein unfolding / : / protein folding chaperone / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein transport / ribosome binding / response to heat / ribosomal large subunit assembly / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / rRNA binding / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / cell division / identical protein binding / membrane / cytoplasm / 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 / FKBP-type peptidyl-prolyl cis-trans isomerase domain ...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 / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / : / Large ribosomal subunit protein uL24, C-terminal domain / Ribosomal protein L24 / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal protein L29, conserved site / Ribosomal protein L29 signature. / Ribosomal L29 protein / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal protein L24 signature. / Ribosomal protein L24/L26, conserved site / KOW (Kyprides, Ouzounis, Woese) motif. / Ribosomal protein L23 / Ribosomal protein L25/L23 / Ribosomal protein L26/L24, KOW domain / Translation protein SH3-like domain superfamily / Ribosomal protein L23/L15e core domain superfamily / KOW motif / KOW / Ribosomal protein L2, domain 2 / Nucleotide-binding alpha-beta plait domain superfamily
Similarity search - Domain/homology
Large ribosomal subunit protein uL29 / Trigger factor / Large ribosomal subunit protein uL23 / Large ribosomal subunit protein uL24 / Large ribosomal subunit protein uL23
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 19.0 Å
AuthorsMerz F / Boehringer D / Schaffitzel C / Preissler S / Hoffmann A / Maier T / Rutkowska A / Lozza J / Ban N / Bukau B / Deuerling E
CitationJournal: EMBO J / Year: 2008
Title: Molecular mechanism and structure of Trigger Factor bound to the translating ribosome.
Authors: Frieder Merz / Daniel Boehringer / Christiane Schaffitzel / Steffen Preissler / Anja Hoffmann / Timm Maier / Anna Rutkowska / Jasmin Lozza / Nenad Ban / Bernd Bukau / Elke Deuerling /
Abstract: Ribosome-associated chaperone Trigger Factor (TF) initiates folding of newly synthesized proteins in bacteria. Here, we pinpoint by site-specific crosslinking the sequence of molecular interactions ...Ribosome-associated chaperone Trigger Factor (TF) initiates folding of newly synthesized proteins in bacteria. Here, we pinpoint by site-specific crosslinking the sequence of molecular interactions of Escherichia coli TF and nascent chains during translation. Furthermore, we provide the first full-length structure of TF associated with ribosome-nascent chain complexes by using cryo-electron microscopy. In its active state, TF arches over the ribosomal exit tunnel accepting nascent chains in a protective void. The growing nascent chain initially follows a predefined path through the entire interior of TF in an unfolded conformation, and even after folding into a domain it remains accommodated inside the protective cavity of ribosome-bound TF. The adaptability to accept nascent chains of different length and folding states may explain how TF is able to assist co-translational folding of all kinds of nascent polypeptides during ongoing synthesis. Moreover, we suggest a model of how TF's chaperoning function can be coordinated with the co-translational processing and membrane targeting of nascent polypeptides by other ribosome-associated factors.
History
DepositionApr 4, 2008-
Header (metadata) releaseApr 4, 2008-
Map releaseMay 29, 2009-
UpdateMar 13, 2013-
Current statusMar 13, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 200
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 200
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2vrh
  • Surface level: 200
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2vrh
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1499.gif

Downloads & links

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Map

FileDownload / File: emd_1499.map.gz / Format: CCP4 / Size: 3.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationStructure of the E. coli trigger factor bound to a translating ribosome
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
4.23 Å/pix.
x 96 pix.
= 406.4 Å		4.23 Å/pix.
x 96 pix.
= 406.4 Å		4.23 Å/pix.
x 96 pix.
= 406.4 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 4.23333 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 30.0 / Movie #1: 200
Minimum - Maximum-3064.789999999999964 - 4637.1899999999996
Average (Standard dev.)-67.837100000000007 (±417.041999999999973)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin494949
Dimensions969696
Spacing969696
CellA=B=C: 406.4 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z4.23333333333334.23333333333334.2333333333333
M x/y/z969696
origin x/y/z0.0000.0000.000
length x/y/z406.400406.400406.400
α/β/γ90.00090.00090.000
start NX/NY/NZ494949
NX/NY/NZ969696
MAP C/R/S213
start NC/NR/NS494949
NC/NR/NS969696
D min/max/mean-3064.7944637.192-67.837

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Supplemental data

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Sample components

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Entire : Escherichia coli Trigger Factor associated with an Escherichia co...

EntireName: Escherichia coli Trigger Factor associated with an Escherichia coli ribosome-nascent chain complex
Components
  • Sample: Escherichia coli Trigger Factor associated with an Escherichia coli ribosome-nascent chain complex
  • Complex: ribosome-nascent chain complex
  • Protein or peptide: trigger factor

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Supramolecule #1000: Escherichia coli Trigger Factor associated with an Escherichia co...

SupramoleculeName: Escherichia coli Trigger Factor associated with an Escherichia coli ribosome-nascent chain complex
type: sample / ID: 1000 / Details: monodisperse sample / Number unique components: 2
Molecular weightExperimental: 2.6 MDa

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Supramolecule #1: ribosome-nascent chain complex

SupramoleculeName: ribosome-nascent chain complex / type: complex / ID: 1 / Name.synonym: translating ribosome / Details: SecM-stalled E. coli ribosome complex / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: trigger factor

MacromoleculeName: trigger factor / type: protein_or_peptide / ID: 1 / Name.synonym: trigger factor
Details: trigger factor crosslinked to the nascent chain. Mutant TFS61C E. coli
Oligomeric state: monomer / Recombinant expression: No
Source (natural)Organism: Escherichia coli (E. coli) / Strain: mutant TFS61c

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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
Details: 50 mM Hepes-KOH pH 7.5, 100 mM KCl, 25 mM MgCl2, 0.5 mg/ml chloramphenicol
VitrificationCryogen name: ETHANE / Instrument: OTHER

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureAverage: 88 K
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: OTHER / Digitization - Sampling interval: 6.35 µm / Details: rotating-drum scanner
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Side entry liquid nitrogen-cooled cryo specimen holder
Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: each image
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 19.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: IMAGIC-5, SPIDER
Details: Final rounds of refinement were done using the Spider software

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Atomic model buiding 1

Initial modelPDB ID:

1w26


Chain - Chain ID: A
DetailsProtocol: Rigid Body. exhaustive search
RefinementSpace: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross Correlation
Output model

PDB-2vrh:
Structure of the E. coli trigger factor bound to a translating ribosome

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Atomic model buiding 2

Initial modelPDB ID:

2aw4
PDB Unreleased entry

SoftwareName: MOLREP
DetailsProtocol: Rigid Body
RefinementSpace: REAL / Protocol: RIGID BODY FIT
Output model

PDB-2vrh:
Structure of the E. coli trigger factor bound to a translating ribosome

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