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Ribosome Binding of a Single Copy of the SecY Complex: Implications for Protein Translocation

by single particle reconstruction, at 9.6 A resolution

Movie

Orientation:

#1: Surface view with section colored by density value, Surface level: 1.5, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 1.5, Made by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-3bo0, Surface level: 1.5, Made by UCSF CHIMERA

#4: Surface view with fitted model, atomic models: PDB-3kc4, PDB-3kcr, Surface level: 1.5, Made by UCSF CHIMERA

#5: Simplified surface model with fitted atomic model: PDB-3bo0, Made by Jmol

#6: Simplified surface model with fitted atomic model: PDB-3bo1, Made by Jmol

#7: Simplified surface model with fitted atomic model: PDB-3kc4, Made by Jmol

#8: Simplified surface model with fitted atomic model: PDB-3kcr, Made by Jmol

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1484
TitleRibosome Binding of a Single Copy of the SecY Complex: Implications for Protein Translocation
MapEscherichia coli ribosome secY complex
SampleRibosome SecY complex
Keywordsribosome, secY, translocation, electron microscopy
AuthorsMenetret JF, Schaletzky J, Clemons WM Jr, Osborne AR, Skanland SS, Denison C, Gygi SP, Kirkpatrick DS, Park E, Ludtke SJ, Rapoport TA, Akey CW
DateDeposition: 2008-02-26, Header release: 2008-02-26, Map release: 2009-05-29, 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: 1.5, Made by UCSF CHIMERA

#2: Surface view colored by height, Surface level: 1.5, Made by UCSF CHIMERA

#3: Surface view with fitted model, atomic models: PDB-3bo0, Surface level: 1.5, Made by UCSF CHIMERA

#4: Surface view with fitted model, atomic models: PDB-3kc4, PDB-3kcr, Surface level: 1.5, Made by UCSF CHIMERA

#5: Simplified surface model with fitted atomic model: PDB-3bo0, Made by Jmol

#6: Simplified surface model with fitted atomic model: PDB-3bo1, Made by Jmol

#7: Simplified surface model with fitted atomic model: PDB-3kc4, Made by Jmol

#8: Simplified surface model with fitted atomic model: PDB-3kcr, Made by Jmol

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

PDB-3bo0

CiteFit

PDB-3bo1

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
ArticleMol. Cell, Vol. 28, Issue 6, Page 1083-92, Year 2007
TitleRibosome binding of a single copy of the SecY complex: implications for protein translocation.
AuthorsJean-François Ménétret, Julia Schaletzky, William M Clemons, Andrew R Osborne, Sigrid S Skånland, Carilee Denison, Steven P Gygi, Don S Kirkpatrick, Eunyong Park, Steven J Ludtke, Tom A Rapoport, Christopher W Akey
Department of Physiology and Biophysics, Boston University School of Medicine, 700 Albany Street, Boston, MA 02118-2526, USA.
KeywordsArchaeal Proteins (chemistry), Cell Membrane (metabolism), Cryoelectron Microscopy, Crystallization, Electrophoresis, Polyacrylamide Gel, Escherichia coli (genetics), Escherichia coli Proteins (chemistry), Models, Molecular, Point Mutation, Protein Binding, Protein Structure, Tertiary, Protein Transport, RNA, Ribosomal (metabolism), Ribosomes (chemistry), SecY protein, E coli
LinksPII: S1097-2765(07)00825-8, DOI: 10.1016/j.molcel.2007.10.034, PubMed: 18158904
Map
Fileemd_1484.map.gz ( map file in CCP4 format, 11665 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
144 pix
2.73 A/pix
= 393.12 A
144 pix
2.73 A/pix
= 393.12 A
144 pix
2.73 A/pix
= 393.12 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:0.95 (by author), 1.5 (movie #1):
Minimum - Maximum: -4.99671 - 10.6495
Average (Standard dev.): 0.149684 (0.868322)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions144144144
Origin-72-72-72
Limit717171
Spacing144144144
Unit CellA= B= C: 393.12 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.73 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.732.732.73
M x/y/z144144144
origin x/y/z0.0000.0000.000
length x/y/z393.120393.120393.120
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ-55-55-55
NX/NY/NZ111111111
MAP C/R/S123
start NC/NR/NS-72-72-72
NC/NR/NS144144144
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-4.99710.6490.150
Annotation DetailsEscherichia coli ribosome secY complex
Supplement
Images
Images
Sample
NameRibosome SecY complex
Number of Components1
Oligomeric Statemonomer
Theoretical Mass3.2MDa
Component #1: ribosome-prokaryote - ribosome
Scientific name70S ribosome
Common Nameribosome
Theoretical Mass3.2 MDa
Scientific Name of SpeciesEscherichia coli

NCBI taxonomy562
ProkaryoteALL
Recombinant expressionNo
Experiment
Sample Preparation
Specimen Conc0.3 mg/ml
Specimen Support Details400 mesh Cu grids with continuous carbon film
Specimen Stateparticle
BufferDetails: 50mM Hepes-KOH, 100mM KOAc, 10mM Mg(OAc)2, 0.05% DDM
pH: 7.5
Vitrification
Method1 second blot
Cryogen NameETHANE
DetailsVitrification instrument: home-made
Humidity95
InstrumentHOMEMADE PLUNGER
Temperature90 Kelvin
Imaging
MicroscopeFEI TECNAI 20
DetailsAbout 30 percent of the data were collected at 30 degree tilt and micrographs were processed in small strips parallel to the tilt axis to correct for the defocus ramp.
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose20 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000, Calibrated: 51000
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus1000 nm - 2500 nm
Specimen Holder
Holdereucentric
ModelGATAN LIQUID NITROGEN
Tilt Angle0 degrees - 30 degrees
Temperature90 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
Od Range1
ScannerOTHER
Number of Digital Images351
Sampling Size4.5
Quant Bit Number16
DetailsCreoscitex Eversmart scanner was used
Processing
Methodsingle particle reconstruction
3D reconstruction
Algorithmprojection matching
SoftwareEMAN
CTF Correctionby micrograph
Resolution By Author9.6 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections39000
Details1900 classes were used in EMAN 3D refinement
Atomic Model Fitting
Model #0
DetailsProtocol: manual in O and Chimera. Loop geometry was regularized in Coot.
Softwarecoot
Refinement Protocolrigid body
Refinement SpaceREAL
PDB Entry ID1RHZ, 2I2T, 2I2P
Fitted Coordinate
PDB entry ID
Download
Data from EMDB
Header (meta data in XML format)emd-1484.xml (8.1 KB)
Map dataemd_1484.map.gz (10.7 MB)
Images1484.png (666 KB)
FTP directoryftp://ftp.pdbj.org/pub/emdb/structures/EMD-1484
Movie files
movie #1
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 5.4 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), 4.8 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), 4.6 MB
Session file for UCSF-Chimera, 819.8 KB
movie #4
.mp4 (H.264/MPEG-4 AVC format), 3.8 MB
.webm (WebM/VP8 format), 5.7 MB
Session file for UCSF-Chimera, 39.8 MB
movie #5
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 4.9 MB
movie #6
.mp4 (H.264/MPEG-4 AVC format), 3.5 MB
.webm (WebM/VP8 format), 4.8 MB
movie #7
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 4.8 MB
movie #8
.mp4 (H.264/MPEG-4 AVC format), 3.6 MB
.webm (WebM/VP8 format), 4.9 MB