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tmRNA translocation and MLD-loading on the ribosome: a 70S-tmRNA-EF-G complex

by single particle reconstruction, at 8.3 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 2, Image by UCSF CHIMERA

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

#3: Surface view with fitted model, atomic models: PDB-3j18, PDB-3j19, Surface level: 2, Image by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-3j18, Image by Jmol

#5: Simplified surface model with fitted atomic model: PDB-3j19, Image by Jmol

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 5386
TitletmRNA translocation and MLD-loading on the ribosome: a 70S-tmRNA-EF-G complex
MapOverall view of the 70S-tmRNA-SmpB-EF-G complex
SampleComplex of 70S-tmRNA-SmpB-EF-G
Keywordstrans-translation, MLD-loading, translocation, tmRNA, EF-G, SmpB
AuthorsRamrath DJF, Yamamoto H, Rother K, Wittek D, Pech M, Mielke T, Loerke J, Scheerer P, Ivanov P, Teraoka Y, Shpanchenko O, Nierhaus KH, Spahn CMT
DateDeposition: 2012-01-20, Header release: 2012-02-21, Map release: 2012-04-30, Last update: 2014-07-23
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 2, Image by UCSF CHIMERA

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

#3: Surface view with fitted model, atomic models: PDB-3j18, PDB-3j19, Surface level: 2, Image by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-3j18, Image by Jmol

#5: Simplified surface model with fitted atomic model: PDB-3j19, Image by Jmol

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

PDB-3j18

CiteFit

PDB-3j19

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PDB-4v6t

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Cite: data citing same article

Fit: output model of fitting

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List of similar structure data Omokage searchabout Omokage system
Article
Citation - Primary
ArticleNature, Vol. 485, Issue 7399, Page 526-9, Year 2012
TitleThe complex of tmRNA-SmpB and EF-G on translocating ribosomes.
AuthorsDavid J F Ramrath, Hiroshi Yamamoto, Kristian Rother, Daniela Wittek, Markus Pech, Thorsten Mielke, Justus Loerke, Patrick Scheerer, Pavel Ivanov, Yoshika Teraoka, Olga Shpanchenko, Knud H Nierhaus, Christian M T Spahn
Institut für Medizinische Physik und Biophysik, Charite - Universitätsmedizin Berlin, Ziegelstrasse 5-9, 10117 Berlin, Germany.
KeywordsBase Sequence, Cryoelectron Microscopy, Escherichia coli (chemistry), Fusidic Acid (metabolism), Ligands, Models, Molecular, Nucleic Acid Conformation, Peptide Elongation Factor G (chemistry), Protein Binding, Protein Biosynthesis, Protein Conformation, RNA, Bacterial (chemistry), RNA-Binding Proteins (chemistry), Ribosome Subunits (chemistry), Ribosomes (chemistry), small protein B, tmRNA
LinksDOI: 10.1038/nature11006, PubMed: 22622583
Map
Fileemd_5386.map.gz ( map file in CCP4 format, 105470 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
300 pix
1.26 A/pix
= 378. A
300 pix
1.26 A/pix
= 378. A
300 pix
1.26 A/pix
= 378. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:2 (by author), 2 (movie #1):
Minimum - Maximum: -3.38914657 - 9.00063801
Average (Standard dev.): 0.20524462 (0.75120121)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions300300300
Origin-150-150-150
Limit149149149
Spacing300300300
Unit CellA= B= C: 378 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.26 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.261.261.26
M x/y/z300300300
origin x/y/z0.0000.0000.000
length x/y/z378.000378.000378.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S123
start NC/NR/NS-150-150-150
NC/NR/NS300300300
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-3.3899.0010.205
Annotation DetailsOverall view of the 70S-tmRNA-SmpB-EF-G complex
Supplement
Images
Images
Sample
NameComplex of 70S-tmRNA-SmpB-EF-G
Number of Components5
Oligomeric StateMonomer
Theoretical Mass3MDa
Detailsthe sample was flash frozen in liquid ethane
Mass-estimation MethodSedimentation
Experimental Mass3MDa
Component #1: ribosome-prokaryote - 70S-tmRNA-EFG
Scientific nameRibosome
Common Name70S-tmRNA-EFG
Theoretical Mass3.05 MDa
Experimental Mass3 MDa
Detailsthe complex was stalled with fusidic acid
Scientific Name of SpeciesEscherichia coli

NCBI taxonomy562
StrainCAN20
ProkaryoteALL
Recombinant expressionNo
Experiment
Sample Preparation
Stainingflash frozen in liquid ethane
Specimen Conc0.15 mg/ml
Specimen Support DetailsQuantifoil R3-3 Cu 300 mesh with 2 nm carbon support film
Specimen Stateparticle
BufferDetails: 20 mM HEPES-KOH, pH 7.6, 4.5 mM Mg(Ac)2, 150 mM NH4Ac, 4 mM b-mercaptoethanol, 2 mM spermidine, and 0.05 mM spermine
pH: 7.6
Vitrification
Methodblot for 10 seconds before plunging
Cryogen NameETHANE
DetailsVitrification instrument: FEI VITROBOT
Humidity100
InstrumentFEI VITROBOT
Temperature96.15 Kelvin
Imaging
MicroscopeFEI POLARA 300
Date08-DEC-2009
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Electron Dose20 e/A**2
Illumination ModeSPOT SCAN
Lens
MagnificationNominal: 39000, Calibrated: 39000
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus2000 nm - 5000 nm
Specimen Holder
HolderCartridge
ModelGATAN HELIUM
Temperature77.15 K ( 77.15 - 81.15 K)
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
ScannerPRIMESCAN
Number of Digital Images302
Sampling Size4.7
Quant Bit Number16
Processing
Methodsingle particle reconstruction
3D reconstruction
Algorithmangular refinement
SoftwareSpider
CTF CorrectionDefocus groups
Resolution By Author8.3 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections68842
Applied SymmetryC1 (asymmetric)
Atomic Model Fitting
Model #0
Target Criteriacross-correlation
DetailsProtocol: Rigid Body
SoftwareChimera
Refinement Protocolrigid body
Refinement SpaceREAL
PDB Entry ID3R8S
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-5386.xml (8.3 KB)
Map dataemd_5386.map.gz (80.2 MB)
Imagesemd_5386_1.png (634.6 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-5386
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.3 MB
Session file for UCSF-Chimera, 27.9 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.9 MB
Session file for UCSF-Chimera, 28 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.8 MB
.webm (WebM/VP8 format), 5.6 MB
Session file for UCSF-Chimera, 43.9 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 4.9 MB
movie #5
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 4.6 MB