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Solution structure of the E. coli 70S ribosome at 11.5 A resolution.

by single particle reconstruction, at 11.5 A resolution

Movie

Orientation:

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

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

#3: Surface view with fitted model, atomic models: PDB-1eg0, Surface level: 50, Image by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-1eg0, Image by Jmol

Entry
Summary
Database / IDEM DATA BANK (EMDB) / 1003
TitleSolution structure of the E. coli 70S ribosome at 11.5 A resolution.
MapE. coli 70S Ribosome
SampleFMet-tRNAMet 70S Ribosome from E.coli
AuthorsGabashvili IS
DateDeposition: 2002-06-26, Header release: 2002-08-22, Map release: 2002-08-22, Last update: 2012-10-17
EMDB SitesEMDB @PDBe (EU), EMDB @RCSB (USA)
Structure Visualization
MoviesMovie Page

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

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

#3: Surface view with fitted model, atomic models: PDB-1eg0, Surface level: 50, Image by UCSF CHIMERA

#4: Simplified surface model with fitted atomic model: PDB-1eg0, Image by Jmol

Supplemental images
Structure viewersYorodumi, 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)
List of similar structure data about Omokage system
Article
Citation - Primary
ArticleCell, Vol. 100, Issue 5, Page 537-49, Year 2000
TitleSolution structure of the E. coli 70S ribosome at 11.5 A resolution.
AuthorsI 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.
KeywordsBacterial 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-
LinksPubMed: 10721991, PII: S0092-8674(00)80690-X
Map
Fileemd_1003.map.gz ( map file in CCP4 format, 7631 KB )
Projections & SlicesSize of images:
AxesZ (Sec.)Y (Row.)X (Col.)
125 pix
2.93 A/pix
= 366.25 A
125 pix
2.93 A/pix
= 366.25 A
125 pix
2.93 A/pix
= 366.25 A

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Density
Contour Level:82.8, 50 (movie #1):
Minimum - Maximum: -141.975 - 339.987
Average (Standard dev.): 1.85585 (38.0467)
Data TypeImage stored as Reals
Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions125125125
Origin-62-62-62
Limit626262
Spacing125125125
Unit CellA= B= C: 366.25 A
Alpha=beta=gamma: 90 degrees
Pixel SpacingX= Y= Z: 2.93 A
CCP4 map header info
modeImage stored as Reals
A/pix X/Y/Z2.932.932.93
M x/y/z125125125
origin x/y/z0.0000.0000.000
length x/y/z366.250366.250366.250
alpha/beta/gamma90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-62-62-62
NC/NR/NS125125125
start NC,NX/NR,NY/NS,NZ
NC,NX/NR,NY/NS,NZ
D min/max/mean-141.975339.9871.856
Annotation DetailsE. coli 70S Ribosome
Supplement
Images
Images
Sample
NameFMet-tRNAMet 70S Ribosome from E.coli
Number of Components3
Theoretical Mass2.5MDa
Detailspreparation 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 name70S ribosome Escherichia coli
Scientific Name of SpeciesEscherichia coli

NCBI taxonomy562
ProkaryoteLSU 50S
Recombinant expressionNo
Component #2: nucleic-acid - fMet-tRNA
Scientific namefMet-tRNA
Scientific Name of SpeciesEscherichia coli
NCBI taxonomy562
ClassRNA
StructureDOUBLE HELIX
SyntheticNo
Component #3: nucleic-acid - MF-mRNA
Scientific nameMF-mRNA
Details46 nucleotides
Scientific Name of SpeciesEscherichia coli
NCBI taxonomy562
ClassRNA
StructureSINGLE STRANDED
SyntheticNo
Experiment
Sample Preparation
Specimen Conc0.09 mg/ml
Specimen Stateparticle
BufferDetails: 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 NameETHANE
InstrumentHOMEMADE PLUNGER
MethodBlot and plunge
DetailsVitrification instrument: 2 side blotting plunger
Imaging
MicroscopeFEI/PHILIPS CM200FEG/ST
Date1997-
Details25 % of data from Philips EM420 with LaB6 at 100kV
Electron Gun
Electron SourceFIELD EMISSION GUN
Accelerating Voltage200 kV
Electron Dose10 e/A**2
Illumination ModeFLOOD BEAM
Lens
MagnificationNominal: 50000, Calibrated: 51200
Nominal Cs2 mm
Imaging ModeBRIGHT FIELD
Defocus2170 nm - 4340 nm
Specimen Holder
HolderCryo Transfer
ModelGATAN LIQUID NITROGEN
Tilt Angle0 degrees - 0 degrees
Temperature93 K
Camera
DetectorKODAK SO-163 FILM
Image Acquisition
Number of Digital Images239
Sampling Size15
Quant Bit Number12
ScannerPERKIN ELMER
Processing
Methodsingle particle reconstruction
3D reconstruction
AlgorithmProjection Matching
SoftwareSPIDER/WEB
CTF CorrectionWiener filtration of defocus group volumes
Resolution By Author11.5 A
Resolution MethodFSC 0.5
Single Particle
Number of Projections73523
Applied SymmetryC1 (asymmetric)
Atomic Model Fitting
Model #0
Refinement Protocolrigid body
SoftwareO
Detailsmanual 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
Download
Data from EMDB
Header (meta data in XML format)emd-1003.xml (10.4 KB)
Map dataemd_1003.map.gz (6.7 MB)
Images1003.gif (81.7 KB)
FTP directoryftp://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) [no file]
.webm (WebM/VP8 format) [no file]