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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: 1499
TitleStructure of the E. coli trigger factor bound to a translating ribosome
Keywordstrigger factor / ribosome-nascent chain complex / translating ribosome / co-translational protein folding / chaperone
SampleEscherichia coli Trigger Factor associated with an Escherichia coli ribosome-nascent chain complex
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataStructure of the E. coli trigger factor bound to a translating ribosome
Methodsingle particle reconstruction, at 19 A resolution
AuthorsMerz F / Boehringer D / Schaffitzel C / Preissler S / Hoffmann A / Maier T / Rutkowska A / Lozza J / Ban N / Bukau B / Deuerling E
CitationEMBO J., 2008, 27, 1622-1632

EMBO J., 2008, 27, 1622-1632 StrPapers
Molecular mechanism and structure of Trigger Factor bound to the translating ribosome.
Frieder Merz / Daniel Boehringer / Christiane Schaffitzel / Steffen Preissler / Anja Hoffmann / Timm Maier / Anna Rutkowska / Jasmin Lozza / Nenad Ban / Bernd Bukau / Elke Deuerling

DateDeposition: Apr 4, 2008 / Header (metadata) release: Apr 4, 2008 / Map release: May 29, 2009 / Last update: Apr 4, 2008

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 200
  • Imaged by UCSF CHIMERA
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  • 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
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Map

Fileemd_1499.map.gz (map file in CCP4 format, 3457 KB)
Projections & slices
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Others
AxesZ (Sec.)X (Row.)Y (Col.)
96 pix
4.23 A/pix
= 406.4 A
96 pix
4.23 A/pix
= 406.4 A
96 pix
4.23 A/pix
= 406.4 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 4.23333 A
Density
Contour Level:30 (by author), 200 (movie #1):
Minimum - Maximum-3064.79 - 4637.19
Average (Standard dev.)-67.8371 (417.042)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderYXZ
Dimensions969696
Origin494949
Limit144144144
Spacing969696
CellA=B=C: 406.4 A
Alpha=beta=gamma: 90 deg.

CCP4 map header:

modeImage stored as Reals
A/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
alpha/beta/gamma90.00090.00090.000
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
Details: monodisperse sample / Number of components: 2
MassExperimental: 2.6 MDa

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Component #1: ribosome-prokaryote, ribosome-nascent chain complex

Ribosome-prokaryoteName: ribosome-nascent chain complex / a.k.a: translating ribosome / Details: SecM-stalled E. coli ribosome complex / Prokaryote: ALL / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #2: protein, trigger factor

ProteinName: trigger factor / a.k.a: trigger factor / Oligomeric Details: monomer
Details: trigger factor crosslinked to the nascent chain. Mutant TFS61C E. coli
Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Strain: mutant TFS61c

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionBuffer solution: 50 mM Hepes-KOH pH 7.5, 100 mM KCl, 25 mM MgCl2, 0.5 mg/ml chloramphenicol
pH: 7.5
VitrificationInstrument: NONE / Cryogen name: ETHANE

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Electron microscopy imaging

ImagingMicroscope: FEI TECNAI F20
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal), 50000 X (calibrated) / Imaging mode: BRIGHT FIELD / Defocus: 1500 - 3500 nm
Specimen HolderHolder: Side entry liquid nitrogen-cooled cryo specimen holder
Model: GATAN LIQUID NITROGEN / Temperature: 88 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionScanner: OTHER / Sampling size: 6.35 microns / Details: rotating-drum scanner

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Image processing

ProcessingMethod: single particle reconstruction / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: angular reconstitution / Software: IMAGIC-5, SPIDER / CTF correction: each image
Details: Final rounds of refinement were done using the Spider software
Resolution: 19 A / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Refinement protocol: rigid body / Target criteria: Cross Correlation / Refinement space: REAL / Details: Protocol: Rigid Body. exhaustive search
Input PDB model: 1W26
Chain ID: A
Modeling #2Software: MOLREP / Refinement protocol: rigid body / Refinement space: REAL / Details: Protocol: Rigid Body
Input PDB model: 2AW4
Output model

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