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Structure of the E. coli trigger factor bound to a translating ribosome

by single particle reconstruction, at 19 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 200, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 200, Made by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-2vrh, Surface level: 200, Made by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-2vrh, Made by Jmol

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1499
TitleStructure of the E. coli trigger factor bound to a translating ribosome
MapStructure of the E. coli trigger factor bound to a translating ribosome
SampleEscherichia coli Trigger Factor associated with an Escherichia coli ribosome-nascent chain complex
Keywordstrigger factor, ribosome-nascent chain complex, translating ribosome, co-translational protein folding, chaperone
AuthorsMerz F, Boehringer D, Schaffitzel C, Preissler S, Hoffmann A, Maier T, Rutkowska A, Lozza J, Ban N, Bukau B, Deuerling E
DateDeposition: 2008-04-04, Header release: 2008-04-04, Map release: 2009-05-29, Last update: 2013-03-13
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 200, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 200, Made by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-2vrh, Surface level: 200, Made by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-2vrh, Made by Jmol

Supplemental images
Structure viewersYorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries

PDB-2vrh

CiteFit

Cite: data citing same article

Fit: output model of fitting

Similar strucutres (beta)
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleEMBO J., Vol. 27, Issue 11, Page 1622-32, Year 2008
TitleMolecular mechanism and structure of Trigger Factor bound to the translating ribosome.
AuthorsFrieder Merz, Daniel Boehringer, Christiane Schaffitzel, Steffen Preissler, Anja Hoffmann, Timm Maier, Anna Rutkowska, Jasmin Lozza, Nenad Ban, Bernd Bukau, Elke Deuerling
Zentrum für Molekulare Biologie Heidelberg, DKFZ-ZMBH Alliance, Universität Heidelberg, Heidelberg, Germany.
KeywordsAmino Acid Sequence, Cross-Linking Reagents (chemistry), Cryoelectron Microscopy, Escherichia coli Proteins (chemistry), Molecular Chaperones (chemistry), Peptides (chemistry), Peptidylprolyl Isomerase (chemistry, 5.2.1.8), Protein Biosynthesis, Protein Conformation, Protein Folding, Protein Structure, Tertiary, Ribosomes (chemistry), trigger factor, E coli (5.2.1.-)
LinksDOI: 10.1038/emboj.2008.89, PubMed: 18497744, PMC: PMC2426727
Map
Fileemd_1499.map.gz ( map file in CCP4 format, 3457 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)X (Row.)Y (Col.)
96 pix
4.2333333333333 A/pix
= 406.4 A
96 pix
4.2333333333333 A/pix
= 406.4 A
96 pix
4.2333333333333 A/pix
= 406.4 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:30 (by author), 200 (movie #1):
Minimum - Maximum: -3064.79 - 4637.19
Average (Standard dev.): -67.8371 (417.042)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderYXZ
Dimensions969696
Origin494949
Limit144144144
Spacing969696
Unit CellA= B= C: 406.4 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 4.23333 A
CCP4 map header info
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
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-3064.7944637.192-67.837
Annotation DetailsStructure of the E. coli trigger factor bound to a translating ribosome
Supplement
Images
Images
Sample
NameEscherichia coli Trigger Factor associated with an Escherichia coli ribosome-nascent chain complex
Number of Components2
Detailsmonodisperse sample
Experimental Mass2.6MDa
Component #1: ribosome-prokaryote - translating ribosome
Scientific nameribosome-nascent chain complex
Common Nametranslating ribosome
DetailsSecM-stalled E. coli ribosome complex
Scientific Name of SpeciesEscherichia coli

NCBI taxonomy562
ProkaryoteALL
Recombinant expressionNo
Component #2: protein - trigger factor
Scientific nametrigger factor
Detailstrigger factor crosslinked to the nascent chain. Mutant TFS61C E. coli
Oligomeric Detailsmonomer
Scientific Name of SpeciesEscherichia coli
NCBI taxonomy562
Strainmutant TFS61c
Recombinant expressionNo
Experiment
Sample Preparation
Specimen Stateparticle
BufferDetails: 50 mM Hepes-KOH pH 7.5, 100 mM KCl, 25 mM MgCl2, 0.5 mg/ml chloramphenicol
pH: 7.5
Vitrification
Cryogen NameETHANE
InstrumentNONE
Imaging
MicroscopeFEI TECNAI F20
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000, Calibrated: 50000
Imaging ModeBRIGHT FIELD
Defocus1500 nm - 3500 nm
Specimen Holder
HolderSide entry liquid nitrogen-cooled cryo specimen holder
ModelGATAN LIQUID NITROGEN
Temperature88 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
ScannerOTHER
Sampling Size6.35
Detailsrotating-drum scanner
Processing
Methodsingle particle reconstruction
3D reconstruction
Algorithmangular reconstitution
SoftwareIMAGIC-5, SPIDER
CTF Correctioneach image
DetailsFinal rounds of refinement were done using the Spider software
Resolution By Author19 A
Resolution MethodFSC 0.5
Atomic Model Fitting
Model #0
DetailsProtocol: Rigid Body. exhaustive search
Refinement Protocolrigid body
Refinement SpaceREAL
Target CriteriaCross Correlation
PDB Entry ID1W26
PDB Chain IDA
Model #1
Refinement SpaceREAL
Refinement Protocolrigid body
DetailsProtocol: Rigid Body
SoftwareMOLREP
PDB Entry ID2AW4
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-1499.xml (8.2 KB)
Map dataemd_1499.map.gz (3 MB)
Images1499.gif (59.4 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1499
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.3 MB
Session file for UCSF-Chimera, 26.3 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.1 MB
.webm (WebM/VP8 format), 4.5 MB
Session file for UCSF-Chimera, 26.4 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 4.8 MB
Session file for UCSF-Chimera, 157 KB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 4.3 MB