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Structure of the ribosome-SecYE complex in the membrane environment

by single particle reconstruction, at 7.1 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 0.7, Image by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 0.7, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-3j00, PDB-3j01, Surface level: 0.8, Image by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-3j00, Image by Jmol

#5: Simplified surface model with fitted atomic model: PDB-3j01, Image by Jmol

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1858
TitleStructure of the ribosome-SecYE complex in the membrane environment
MapThis map represents an E.coli 70S ribosome carrying an elongation arrested nascent chain of 118 amino acid residues, with the first 102 residues representing the N-terminus of the membrane protein FtsQ with the signal anchor, a tRNA in the P-site and the E.coli SecYEG complex embedded in a E.coli lipid bilayer (Nanodisc).
SampleAn active E.coli SecYEG complex embedded in a lipid bilayer (Nanodisc), bound to a translating E.coli ribosome
AuthorsFrauenfeld J, Gumbart J, Sluis EO, Funes S, Gartmann M, Beatrix B, Mielke T, Berninghausen O, Becker T, Schulten K, Beckmann R
DateDeposition: 2011-01-17, Header release: 2011-04-21, Map release: 2011-04-21, Last update: 2013-12-11
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 0.7, Image by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 0.7, Image by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-3j00, PDB-3j01, Surface level: 0.8, Image by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-3j00, Image by Jmol

#5: Simplified surface model with fitted atomic model: PDB-3j01, Image by Jmol

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

PDB-3j00

CiteFit

PDB-3j01

CiteFit

Cite: data citing same article

Fit: output model of fitting

Similar strucutres
List of similar structure data Omokage searchabout Omokage system
Article
Citation - Primary
ArticleNat. Struct. Mol. Biol., Vol. 18, Issue 5, Page 614-21, Year 2011
TitleCryo-EM structure of the ribosome-SecYE complex in the membrane environment.
AuthorsJens Frauenfeld, James Gumbart, Eli O van der Sluis, Soledad Funes, Marco Gartmann, Birgitta Beatrix, Thorsten Mielke, Otto Berninghausen, Thomas Becker, Klaus Schulten, Roland Beckmann
Gene Center, Department for Biochemistry, University of Munich, Munich, Germany.
KeywordsCell Membrane (metabolism), Cryoelectron Microscopy, Escherichia coli, Escherichia coli Proteins (chemistry), Lipoproteins, HDL (chemistry), Membrane Proteins (chemistry), Models, Molecular, Protein Transport, Ribosomes (chemistry), SecE protein, E coli, SecY protein, E coli, SecYEG protein, E coli, Signal Recognition Particle (physiology)
LinksDOI: 10.1038/nsmb.2026, PubMed: 21499241, PMC: PMC3412285
Map
Fileemd_1858.map.gz ( map file in CCP4 format, 128001 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)X (Row.)Y (Col.)
320 pix
1.2375 A/pix
= 396. A
320 pix
1.2375 A/pix
= 396. A
320 pix
1.2375 A/pix
= 396. A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.5 (by author), 0.7 (movie #1):
Minimum - Maximum: -3.53351 - 6.82334
Average (Standard dev.): 0.0507365 (0.456442)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderYXZ
Dimensions320320320
Origin-160-160-159
Limit159159160
Spacing320320320
Unit CellA= B= C: 396 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 1.2375 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z1.23751.23751.2375
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z396.000396.000396.000
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-160-160-159
NX/NY/NZ320320320
MAP C/R/S213
start NC/NR/NS-160-160-159
NC/NR/NS320320320
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-3.5346.8230.051
Annotation DetailsThis map represents an E.coli 70S ribosome carrying an elongation arrested nascent chain of 118 amino acid residues, with the first 102 residues representing the N-terminus of the membrane protein FtsQ with the signal anchor, a tRNA in the P-site and the E.coli SecYEG complex embedded in a E.coli lipid bilayer (Nanodisc).
Supplement
Images
Images
Sample
NameAn active E.coli SecYEG complex embedded in a lipid bilayer (Nanodisc), bound to a translating E.coli ribosome
Number of Components2
Oligomeric State70S ribosome bound to one copy of the E.coli SecYEG complex in a lipid bilayer
Theoretical Mass2.7MDa
DetailsThe heterotrimeric SecYEG complex was embedded in a lipid bilayer (nascent HDL, Nanodisc)
Component #1: ribosome-prokaryote - 70S RNC
Scientific name70S ribosome nascent chain complex
Common Name70S RNC
Theoretical Mass2.7 MDa
Scientific Name of SpeciesEscherichia coli

NCBI taxonomy562
ProkaryoteALL
Recombinant expressionNo
Component #2: ligand - SecYEG embedded in a Nanodisc
Scientific nameNd-SecYEG
Common NameSecYEG embedded in a Nanodisc
Oligomeric DetailsHeterotrimeric
Number of Copies1
Scientific Name of SpeciesEscherichia coli
NCBI taxonomy562
Recombinant expressionYes
Natural SourceCell Location: Plasma membrane
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Experiment
Sample Preparation
Specimen Stateparticle
BufferDetails: 20 mM Hepes (pH 7.2), 100 mM KOAc, 10 mM Mg(OAc)2, 1 mM DTT, 250 microg/ml chloramphenicol
pH: 7.2
Vitrification
Cryogen NameETHANE
InstrumentNONE
Imaging
MicroscopeFEI POLARA 300
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Electron Dose22 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 39000, Calibrated: 38000
Nominal Cs2.26 mm
Imaging ModeBRIGHT FIELD
Defocus1000 nm - 4500 nm
Specimen Holder
HolderFEI Polara cartridge system
ModelOTHER
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
ScannerPRIMESCAN
Sampling Size4.76
DetailsScanned at 5334 dpi
Processing
Methodsingle particle reconstruction
3D reconstruction
SoftwareSPIDER
CTF CorrectionDefocus group volumes
Resolution By Author7.1 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections85664
Applied SymmetryC1 (asymmetric)
Atomic Model Fitting
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-1858.xml (8 KB)
Map dataemd_1858.map.gz (8.5 MB)
ImagesEMD-1858_image.jpg (322.7 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1858
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 5.1 MB
Session file for UCSF-Chimera, 26.3 KB
movie #2
.mp4 (H.264/MPEG-4 AVC format), 3.2 MB
.webm (WebM/VP8 format), 4.7 MB
Session file for UCSF-Chimera, 26.4 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, 41.8 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 2.9 MB
movie #5
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 3.4 MB