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Structure of the E. coli protein-conducting channel bound to a translating ribosome.

by single particle reconstruction, at 14.9 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 50, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 50, Made by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-2akh, PDB-2aki, PDB-2gyb, PDB-2gyc, Surface level: 50, Made by UCSF CHIMERA

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

#5: Simplified surface model with fitted atomic model: PDB-2aki, Made by Jmol

#6: Simplified surface model with fitted atomic model: PDB-2gyb, Made by Jmol

#7: Simplified surface model with fitted atomic model: PDB-2gyc, Made by Jmol

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1143
TitleStructure of the E. coli protein-conducting channel bound to a translating ribosome.
MapEM map of the E.coli proten-conducting channel bound to a translating ribosome
Sampleco-translational E. coli 70S ribosome-nascent chain complexed with SecYEG
AuthorsMitra K, Schaffitzel C, Shaikh T, Tama F, Jenni S, Brooks III CL, Ban N, Frank J
DateDeposition: 2005-08-03, Header release: 2005-08-03, Map release: 2006-06-13, Last update: 2012-10-24
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

#1: Surface view with section colored by density value, Surface level: 50, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 50, Made by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-2akh, PDB-2aki, PDB-2gyb, PDB-2gyc, Surface level: 50, Made by UCSF CHIMERA

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

#5: Simplified surface model with fitted atomic model: PDB-2aki, Made by Jmol

#6: Simplified surface model with fitted atomic model: PDB-2gyb, Made by Jmol

#7: Simplified surface model with fitted atomic model: PDB-2gyc, Made by Jmol

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

PDB-2akh

CiteFit

PDB-2aki

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
ArticleNature, Vol. 438, Issue 7066, Page 318-24, Year 2005
TitleStructure of the E. coli protein-conducting channel bound to a translating ribosome.
AuthorsKakoli Mitra, Christiane Schaffitzel, Tanvir Shaikh, Florence Tama, Simon Jenni, Charles L Brooks, Nenad Ban, Joachim Frank
Howard Hughes Medical Institute, Health Research Inc. at the Wadsworth Center, Empire State Plaza, Albany, New York 12201-0509, USA.
KeywordsCell Membrane (chemistry), Cryoelectron Microscopy, Escherichia coli Proteins (biosynthesis), Membrane Proteins (chemistry), Models, Molecular, Multiprotein Complexes (chemistry), Pliability, Protein Binding, Protein Biosynthesis, Protein Structure, Quaternary, Protein Transport, Ribosomes (metabolism), SecE protein, E coli, SecG protein, E coli, SecY protein, E coli
LinksDOI: 10.1038/nature04133, PubMed: 16292303, PMC: PMC1351281
Map
Fileemd_1143.map.gz ( map file in CCP4 format, 6922 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
121 pix
2.82 A/pix
= 341.22 A
121 pix
2.82 A/pix
= 341.22 A
121 pix
2.82 A/pix
= 341.22 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:46.1, 50 (movie #1):
Minimum - Maximum: -299.714 - 454.815
Average (Standard dev.): 5.83623 (33.8063)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions121121121
Origin-60-60-60
Limit606060
Spacing121121121
Unit CellA= B= C: 341.22 A
Alpha=beta=gamma: 90 degrees
Pixel Spacing
XYZ
EMDB info.2.822.822.82
CCP4 map header2.822.822.82
EM Navigator Movie #13.593.593.59
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.822.822.82
M x/y/z121121121
origin x/y/z0.0000.0000.000
length x/y/z341.220341.220341.220
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-90-90-190
NX/NY/NZ180180380
MAP C/R/S123
start NC/NR/NS-60-60-60
NC/NR/NS121121121
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-299.714454.8155.836
Annotation DetailsEM map of the E.coli proten-conducting channel bound to a translating ribosome
Supplement
Images
Images
Sample
Nameco-translational E. coli 70S ribosome-nascent chain complexed with SecYEG
Number of Components8
Component #1: ribosome-prokaryote - small subunit
Scientific name30S
Common Namesmall subunit
Scientific Name of SpeciesEscherichia coli

NCBI taxonomy562
ProkaryoteSSU 30S
Recombinant expressionNo
Component #2: ribosome-prokaryote - large subunit
Scientific name50S
Common Namelarge subunit
Scientific Name of SpeciesEscherichia coli
NCBI taxonomy562
ProkaryoteLSU 50S
Recombinant expressionNo
Component #3: nucleic-acid - A-site tRNA
Scientific nameA-site tRNA
Scientific Name of SpeciesEscherichia coli
NCBI taxonomy562
SyntheticNo
StructureDOUBLE HELIX
ClassRNA
Component #4: nucleic-acid - P-site tRNA
Scientific nameP-site tRNA
Scientific Name of SpeciesEscherichia coli
NCBI taxonomy562
SyntheticNo
StructureDOUBLE HELIX
ClassRNA
Component #5: nucleic-acid - E-site tRNA
Scientific nameE-site tRNA
Scientific Name of SpeciesEscherichia coli
NCBI taxonomy562
StructureDOUBLE HELIX
ClassRNA
SyntheticNo
Component #6: nucleic-acid - mRNA
Scientific namemRNA
Scientific Name of SpeciesEscherichia coli
NCBI taxonomy562
StructureSINGLE STRANDED
ClassRNA
SyntheticYes
Component #7: protein - translocon, SecYEG
Scientific nameprotein-conducting channel
Common Nametranslocon, SecYEG
Oligomeric Detailsdimer of heterotrimer
Number of Copies2
Scientific Name of SpeciesEscherichia coli
Common Name of Speciestranslocon
NCBI taxonomy562
Recombinant expressionYes
Natural SourceCell Location: inner membrane
Engineered SourceNCBI taxonomy: 562
Expression system: Escherichia coli
Component #8: protein - nascent chain
Scientific namenascent chain
DetailsStrep-II-FtsQ-SecM construct
Scientific Name of Speciesunidentified
Common Name of Speciestranslocon
NCBI taxonomy32644
Recombinant expressionYes
Experiment
Sample Preparation
Specimen Stateparticle
Vitrification
Cryogen NameETHANE
Humidity90
Temperature93 Kelvin
InstrumentHOMEMADE PLUNGER
MethodBlot for 2 seconds before plunging
DetailsVitrification instrument: two sided blotting plunger
Imaging
MicroscopeFEI TECNAI F30
Date2004-03-09
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage300 kV
Electron Dose11 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 39000, Calibrated: 39000
Nominal Cs2.26 mm
Imaging ModeBRIGHT FIELD
Defocus1500 nm - 4300 nm
Specimen Holder
HolderCryo stage
ModelOTHER
Temperature93 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
Number of Digital Images385
Sampling Size14
Od Range1.2
Quant Bit Number12
ScannerZEISS SCAI
Processing
Methodsingle particle reconstruction
3D reconstruction
Algorithmreference projection
SoftwareSPIDER package
CTF Correctiondefocus groups
Resolution By Author14.9 A
Resolution MethodFSC 0.5
Euler Angles DetailsSPIDER: theta 15 degrees, phi 15 degrees
DetailsThe falloff of Fourier amplitudes toward higher spatial frequencies was corrected using the x-ray solution scattering intensity distribution of 70S ribosomes from E. coli during each round of refinement
Single Particle
Number of Projections53325
Applied SymmetryC1 (asymmetric)
Atomic Model Fitting
Model #0
Refinement Protocolflexible
Target Criteriacorrelation coefficient
Refinement SpaceREAL
DetailsProtocol: normal mode-based flexible fitting. Fitting of SecYEG atomic model into isolated EM density of protein-conducting channels
Model #1
Refinement Protocolflexible
Target Criteriacorrelation coefficient
Refinement SpaceREAL
DetailsProtocol: normal mode-based flexible fitting. Fitting of SecYEG atomic model into isolated EM density of protein-conducting channels
Model #2
Refinement Protocolrigid body
Target CriteriaR-factor
SoftwareRSR2000
Refinement SpaceREAL
DetailsProtocol: real space refinement
Model #3
Refinement Protocolrigid body
Target CriteriaR-factor
SoftwareRSR2000
Refinement SpaceREAL
DetailsProtocol: real space refinement
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-1143.xml (12.4 KB)
Map dataemd_1143.map.gz (6.2 MB)
Images1143.gif (67.6 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1143
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.3 MB
.webm (WebM/VP8 format), 5.2 MB
Session file for UCSF-Chimera, 26.6 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, 26.2 KB
movie #3
.mp4 (H.264/MPEG-4 AVC format), 3.7 MB
.webm (WebM/VP8 format), 5.5 MB
Session file for UCSF-Chimera, 39.7 MB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 4.4 MB
movie #5
.mp4 (H.264/MPEG-4 AVC format), 3.4 MB
.webm (WebM/VP8 format), 4.8 MB
movie #6
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 4.6 MB
movie #7
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 4.5 MB