EMDB-1484: Ribosome Binding of a Single Copy of the SecY Complex:...

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 1484
Title	Ribosome Binding of a Single Copy of the SecY Complex: Implications for Protein Translocation
Map	Escherichia coli ribosome secY complex
Sample	Ribosome SecY complex
Keywords	ribosome, secY, translocation, electron microscopy
Authors	Menetret JF, Schaletzky J, Clemons WM Jr, Osborne AR, Skanland SS, Denison C, Gygi SP, Kirkpatrick DS, Park E, Ludtke SJ, Rapoport TA, Akey CW
Date	Deposition: 2008-02-26, Header release: 2008-02-26, Map release: 2009-05-29, Last update: 2012-10-24
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie 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	1484.png
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	PDB-3bo0 CiteFit PDB-3bo1 CiteFit PDB-3kc4 Fit PDB-3kcr Fit Cite: data citing same article Fit: output model of fitting
Similar strucutres (beta)	Diagram EMDB-1122 EMDB-1143 EMDB-1250 EMDB-1312 EMDB-5141 EMDB-1762 List of similar structure data about Omokage system

Article
Citation - Primary
Article	Mol. Cell, Vol. 28, Issue 6, Page 1083-92, Year 2007
Title	Ribosome binding of a single copy of the SecY complex: implications for protein translocation.
Authors	Jean-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.
Keywords	Archaeal 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
Links	PII: S1097-2765(07)00825-8, DOI: 10.1016/j.molcel.2007.10.034, PubMed: 18158904

Map

File

EMD-1484.map ( map file in CCP4 format, 11945 KB )

Projections & Slices

Size of images:

Axes	Z (Sec.)	Y (Row.)	X (Col.)
Surface
Projections
Slices (1/3)
Slices (1/2)
Slices (2/3)

Images are generated by Spider package.

Density

Histogram

Histogram (log scale)

Contour Level:	0.95 (by author), 1.5 (movie #1):
Minimum - Maximum:	-4.99671 - 10.6495
Average (Standard dev.):	0.149684 (0.868322)

Data Type

Image stored as Reals

Space Group Number

Map Geometry

Axis order	X	Y	Z
Dimensions	144	144	144
Origin	-72	-72	-72
Limit	71	71	71
Spacing	144	144	144

Unit Cell

A= B= C: 393.12 A
Alpha=beta=gamma: 90 degrees

Pixel Spacing

X= Y= Z: 2.73 A

CCP4 map header info

mode	Image stored as Reals
A/pix X/Y/Z	2.73	2.73	2.73
M x/y/z	144	144	144
origin x/y/z	0.000	0.000	0.000
length x/y/z	393.120	393.120	393.120
alpha/beta/gamma	90.000	90.000	90.000
start NX/NY/NZ	-55	-55	-55
NX/NY/NZ	111	111	111
MAP C/R/S	1	2	3
start NC/NR/NS	-72	-72	-72
NC/NR/NS	144	144	144
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean	-4.997	10.649	0.150

Annotation Details

Escherichia coli ribosome secY complex

Supplement
Images
Images	1484.png

Sample
Name	Ribosome SecY complex
Number of Components	1
Oligomeric State	monomer
Theoretical Mass	3.2MDa
Component #1: ribosome-prokaryote - ribosome
Scientific name	70S ribosome
Common Name	ribosome
Theoretical Mass	3.2 MDa
Scientific Name of Species	Escherichia coli
NCBI taxonomy	562
Prokaryote	ALL
Recombinant expression	No

Experiment
Sample Preparation
Specimen Conc	0.3 mg/ml
Specimen Support Details	400 mesh Cu grids with continuous carbon film
Specimen State	particle
Buffer	Details: 50mM Hepes-KOH, 100mM KOAc, 10mM Mg(OAc)2, 0.05% DDM pH: 7.5
Vitrification
Method	1 second blot
Cryogen Name	ETHANE
Details	Vitrification instrument: home-made
Humidity	95
Instrument	HOMEMADE PLUNGER
Temperature	90 Kelvin
Imaging
Microscope	FEI TECNAI 20
Details	About 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 Source	FIELD EMISSION GUN
Accelerating Voltage	200 kV
Electron Dose	20 e/A**2
Illumination Mode	FLOOD BEAM
Lens
Magnification	Nominal: 50000, Calibrated: 51000
Nominal Cs	2 mm
Imaging Mode	BRIGHT FIELD
Defocus	1000 nm - 2500 nm
Specimen Holder
Holder	eucentric
Model	GATAN LIQUID NITROGEN
Tilt Angle	0 degrees - 30 degrees
Temperature	90 K
Camera
Detector	Kodak SO163
Image Acquisition
Od Range	1
Scanner	OTHER
Number of Digital Images	351
Sampling Size	4.5
Quant Bit Number	16
Details	Creoscitex Eversmart scanner was used

Processing
Method	single particle reconstruction
3D reconstruction
Algorithm	projection matching
Software	EMAN
CTF Correction	by micrograph
Resolution By Author	9.6 A
Resolution Method	FSC 0.5
Single Particle
Number of Projections	39000
Details	1900 classes were used in EMAN 3D refinement
Atomic Model Fitting
Model #0
Details	Protocol: manual in O and Chimera. Loop geometry was regularized in Coot.
Software	coot
Refinement Protocol	rigid body
Refinement Space	REAL
PDB Entry ID	1RHZ, 2I2T, 2I2P PDB-1rhz PDB-2i2t PDB-2i2p
Fitted Coordinate
PDB entry ID	PDB-3bo0 PDB-3bo1 PDB-3kc4 PDB-3kcr

Download

Data from EMDB

Header (meta data in XML format)

emd-1484.xml (8.1 KB)

Map data

emd_1484.map.gz (10.7 MB)

Images

1484.png (666 KB)

FTP directory

ftp://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