EMDB-1003: Solution structure of the E. coli 70S ribosome at 11.5...

Entry
Summary
Database / ID	EM DATA BANK (EMDB) / 1003
Authors	Gabashvili IS
EMDB Sites	EMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
Movies	Movie 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-1eg0, Surface level: 50, Made by UCSF CHIMERA #4: Simplified surface model with fitted atomic model: PDB-1eg0, Made by Jmol
Supplemental images	1003.gif
Structure viewers	Yorodumi, Launch PeppeR (About PeppeR), Volume viewer (RCSB, PDBe)
Related Structure Data
Related Entries	PDB-1eg0 CiteFit Cite: data citing same article Fit: output model of fitting
Similar strucutres (beta)	Diagram EMDB-5036 EMDB-1854 EMDB-1829 EMDB-1849 EMDB-5363 EMDB-1657 List of similar structure data about Omokage system

Article
Citation - Primary
Article	Cell, Vol. 100, Issue 5, Page 537-49, Year 2000
Title	Solution structure of the E. coli 70S ribosome at 11.5 A resolution.
Authors	I S Gabashvili, R K Agrawal, C M Spahn, R A Grassucci, D I Svergun, J Frank, P Penczek Howard Hughes Medical Institute, Health Research, Inc., Albany, New York 11201-0509, USA.
Keywords	Bacterial Proteins (ultrastructure), Cryoelectron Microscopy, Escherichia coli (ultrastructure), GTP Phosphohydrolases (ultrastructure, 3.6.1.-), Image Processing, Computer-Assisted, Macromolecular Substances, Peptide Elongation Factor G (ultrastructure), RNA, Bacterial (ultrastructure), RNA, Ribosomal (ultrastructure), RNA, Transfer, Met (ultrastructure), Ribosomal Proteins (ultrastructure), Ribosomes (ultrastructure), Solutions, tRNA, formylmethionine-
Links	PubMed: 10721991, PII: S0092-8674(00)80690-X

Map

File

EMD-1003.map ( map file in CCP4 format, 7814 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:	82.8, 50 (movie #1):
Minimum - Maximum:	-141.975 - 339.987
Average (Standard dev.):	1.85585 (38.0467)

Data Type

float (32-bit)

Space Group Number

Map Geometry

Axis Order :	X	Y	Z
Dimensions :	125	125	125
Origin :	-62	-62	-62
Limit :	62	62	62
Spacing :	125	125	125

Unit Cell

A = 366.25 A , B = 366.25 A , C = 366.25 A ,
alpha = 90 degrees , beta = 90 degrees , gamma = 90 degrees

Pixel Spacing

X = 2.93 A , Y = 2.93 A , Z = 2.93 A

CCP4 map header info

mode	Image stored as Reals
A/pix X/Y/Z	2.93	2.93	2.93
M x/y/z	125	125	125
origin x/y/z	0.000	0.000	0.000
length x/y/z	366.250	366.250	366.250
alpha/beta/gamma	90.000	90.000	90.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S	1	2	3
start NC/NR/NS	-62	-62	-62
NC/NR/NS	125	125	125
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean	-141.975	339.987	1.856

Annotation Details

E. coli 70S Ribosome

Supplement
Images
Images	1003.gif

Sample
Name	FMet-tRNAMet 70S Ribosome from E.coli
Number of Components	3
Theoretical Mass	2.5 MDa
Details	preparation and buffer conditions are as described in Malhotra et al., J. Mol. Biol. (1998) 280, 103-116
Component #1: ribosome-prokaryote - 70S ribosome Escherichia coli
Scientific name	70S ribosome Escherichia coli
Scientific Name of Species	Escherichia coli (NCBI Taxonomy: 562)
Prokaryote	LSU 50S
Recombinant expression	No
Component #2: nucleic-acid - fMet-tRNA
Scientific name	fMet-tRNA
Scientific Name of Species	Escherichia coli (NCBI Taxonomy: 562)
Class	RNA
Structure	DOUBLE HELIX
Synthetic	No
Component #3: nucleic-acid - MF-mRNA
Scientific name	MF-mRNA
Details	46 nucleotides
Scientific Name of Species	Escherichia coli (NCBI Taxonomy: 562)
Class	RNA
Structure	SINGLE STRANDED
Synthetic	No

Experiment
Sample Preparation
Specimen Conc	0.09 mg/ml
Specimen State	particle
Buffer	Details: 20 mM Hepes, 6 mM Mg(CH3COO)2 150 mM NH4Cl, 4 mM beta-Mercaptoethanol, 0.5 mM Spermine, 2 mM Spermidine. pH: 7.6
Vitrification
Cryogen Name	ETHANE
Instrument	HOMEMADE PLUNGER
Method	Blot and plunge
Details	Vitrification instrument: 2 side blotting plunger
Imaging
Microscope	FEI/PHILIPS CM200FEG/ST
Date	1997-
Details	25 % of data from Philips EM420 with LaB6 at 100kV
Electron Gun
Electron Source	FIELD EMISSION GUN
Accelerating Voltage	200 kV
Electron Dose	10 e/A**2
Illumination Mode	FLOOD BEAM
Lens
Magnification	Nominal: 50000 X, Calibrated: 51200 X
Nominal Cs	2.0 mm
Imaging Mode	BRIGHT FIELD
Defocus	2170 nm - 4340 nm
Specimen Holder
Holder	Cryo Transfer ( GATAN LIQUID NITROGEN )
Tilt Angle	0 degrees - 0 degrees
Temperature	93 Kelvin
Camera
Detector	Kodak SO163
Image Acquisition
Number of Digital Images	239
Sampling Size	15 microns
Quant Bit Number	12
Scanner	PERKIN ELMER

Processing
Method	single particle reconstruction
3 D reconstruction
Algorithm	Projection Matching
Software	SPIDER/WEB
CTF Correction	Wiener filtration of defocus group volumes
Resolution By Author	11.5
Resolution Method	FSC at 0.5 cut-off
Single Particle
Number of Projections	73523
Atomic Model Fitting
Model #0
Refinement Protocol	rigid body
Software	O
Details	manual fitting using O Mol_Id: 1; Molecule: S4 Ribosomal Protein; Chain: A; Other_Details: Modeled By Analogous Protein Of B. Stearothermophilus Taken From Pdb Entry 1C06 Mol_Id: 2; Molecule: S5 Ribosomal Protein; Chain: B; Other_Details: Modeled By Analogous Protein Of B. Stearothermophilus Taken From Pdb Entry 1Pkp Mol_Id: 3; Molecule: S6 Ribosomal Protein; Chain: C; Other_Details: Modeled By Analogous Protein Of T. Thermophilus Taken From Pdb Entry 1Ris Mol_Id: 4; Molecule: S7 Ribosomal Protein; Chain: D; Other_Details: Modeled By Analogous Protein Of T. Thermophilus Taken From Pdb Entry 1Rss Mol_Id: 5; Molecule: S8 Ribosomal Protein; Chain: E; Other_Details: Modeled By Analogous Protein Of T. Thermophilus Taken From Pdb Entry 1An7 Mol_Id: 6; Molecule: S15 Ribosomal Protein; Chain: F; Other_Details: Modeled By Analogous Protein Of B. Stearothermophilus Taken From Pdb Entry 1A32 Mol_Id: 7; Molecule: S17 Ribosomal Protein; Chain: G; Other_Details: Modeled By Analogous Protein Of B. Stearothermophilus Taken From Pdb Entries 1Rip and 1Qd7 Mol_Id: 8; Molecule: S20 Ribosomal Protein; Chain: H; Other_Details: Modeled By Analogous Protein Of T. Thermophilus Taken From Pdb Entry 1Qd7 Mol_Id: 9; Molecule: Ribosomal Protein L1; Chain: N; Other_Details: Modeled By Analogous Protein Of T. Thermophilus Taken From Pdb Entry 1Ad2 Mol_Id: 10; Molecule: Ribosomal Protein L6; Chain: J; Mutation: Yes; Other_Details: Modeled By Analogous Protein Of T. Stearothermophilus Taken From Pdb Entry 1Rl6 Mol_Id: 11; Molecule: Ribosomal Protein L11; Chain: K; Other_Details: Modeled By Analogous Protein Of T. Maritima Taken From Pdb Entry 1Mms Mol_Id: 12; Molecule: Fragment Of 16S Rrna Helix 23; Chain: I; Fragment: Residues 673-713; Other_Details: Modeled As Analogous Fragment Of T. Thermophilus Taken From Pdb Entry 1Qd7 Mol_Id: 13; Molecule: Fragment Of 23S Rrna; Chain: L; Fragment: Residues 1051-1108; Other_Details: T. Maritima RNA Sequence and Model Taken From Pdb Entry 1Mms Mol_Id: 14; Molecule: Helix 95 Of 23S Rrna; Chain: M; Other_Details: E. Coli RNA Sequence and Model Taken From Pdb Entry 480D Mol_Id: 15; Molecule: Formyl-Methionyl-tRNA; Chain: O; Synonym: Fmet-tRNA; Other_Details: E. Coli Fmet-tRNA Sequence and Model Taken From Pdb Entry 2Fmt
Fitted Coordinate
PDB entry ID	PDB-1eg0

Download

Data from EMDB

Header (meta data in XML format)

emd-1003.xml (10.3 KB)

Map data

emd_1003.map.gz (6.7 MB)

Images

1003.gif (81.7 KB)

FTP directory

ftp://ftp.pdbj.org/pub/emdb/structures/EMD-1003

Movie files

movie #1

	.mp4 (H.264/MPEG-4 AVC format), 3.6 MB .webm (WebM/VP8 format), 5.5 MB Session file for UCSF-Chimera, 26.4 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, 26.4 KB

movie #3

	.mp4 (H.264/MPEG-4 AVC format), 3.6 MB .webm (WebM/VP8 format), 5 MB Session file for UCSF-Chimera, 347.9 KB

movie #4

	.mp4 (H.264/MPEG-4 AVC format), 3.5 MB .webm (WebM/VP8 format), 4.6 MB