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

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Basic information

Entry
Database: EMDB / ID: 1003
TitleSolution structure of the E. coli 70S ribosome at 11.5 A resolution.
SampleFMet-tRNAMet 70S Ribosome from E.coli
SourceEscherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /
Map dataE. coli 70S Ribosome
Methodsingle particle reconstruction, at 11.5 Å resolution
AuthorsGabashvili IS
CitationCell, 2000, 100, 537-549

Cell, 2000, 100, 537-549 StrPapers
Solution structure of the E. coli 70S ribosome at 11.5 A resolution.
I S Gabashvili / R K Agrawal / C M Spahn / R A Grassucci / D I Svergun / J Frank / P Penczek

Validation ReportPDB-ID: 1eg0

SummaryFull reportAbout validation report
DateDeposition: Jun 26, 2002 / Header (metadata) release: Aug 22, 2002 / Map release: Aug 22, 2002 / Last update: Jun 26, 2002

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 50
  • Imaged by UCSF CHIMERA
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  • Surface view colored by height
  • Surface level: 50
  • Imaged by UCSF CHIMERA
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  • Surface view with fitted model
  • Atomic models: : PDB-1eg0
  • Surface level: 50
  • Imaged by UCSF CHIMERA
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Supplemental images

Downloads & links

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Map

Fileemd_1003.map.gz (map file in CCP4 format, 7631 KB)
Projections & slices

Image control

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AxesZ (Sec.)Y (Row.)X (Col.)
125 pix
2.93 Å/pix.
= 366.25 Å
125 pix
2.93 Å/pix.
= 366.25 Å
125 pix
2.93 Å/pix.
= 366.25 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider package.

Voxel sizeX=Y=Z: 2.93 Å
Density
Contour Level:82.8, 50 (movie #1):
Minimum - Maximum-141.975 - 339.987
Average (Standard dev.)1.85585 (38.0467)
Details

EMDB XML:

Space Group Number1
Map Geometry
Axis orderXYZ
Dimensions125125125
Origin-62-62-62
Limit626262
Spacing125125125
CellA=B=C: 366.25 Å
α=β=γ: 90 deg.

CCP4 map header:

modeImage stored as Reals
Å/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
α/β/γ90.00090.00090.000
start NX/NY/NZ
NX/NY/NZ
MAP C/R/S123
start NC/NR/NS-62-62-62
NC/NR/NS125125125
D min/max/mean-141.975339.9871.856

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Supplemental data

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Sample components

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Entire FMet-tRNAMet 70S Ribosome from E.coli

EntireName: FMet-tRNAMet 70S Ribosome from E.coli
Details: preparation and buffer conditions are as described in Malhotra et al., J. Mol. Biol. (1998) 280, 103-116
Number of components: 3
MassTheoretical: 2.5 MDa

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Component #1: ribosome-prokaryote, 70S ribosome Escherichia coli

Ribosome-prokaryoteName: 70S ribosome Escherichia coli / Prokaryote: LSU 50S / Recombinant expression: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #2: nucleic-acid, fMet-tRNA

Nucleic-acidName: fMet-tRNA / Class: RNA / Structure: DOUBLE HELIX / Synthetic: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Component #3: nucleic-acid, MF-mRNA

Nucleic-acidName: MF-mRNA / Class: RNA / Details: 46 nucleotides / Structure: SINGLE STRANDED / Synthetic: No
SourceSpecies: Escherichia coli / bacteria / エシェリキア・コリ, 大腸菌 /

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Experimental details

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Sample preparation

Specimen stateparticle
Sample solutionSpecimen conc.: 0.09 mg/ml
Buffer solution: 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
VitrificationInstrument: HOMEMADE PLUNGER / Cryogen name: ETHANE / Method: Blot and plunge / Details: Vitrification instrument: 2 side blotting plunger

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Electron microscopy imaging

ImagingMicroscope: FEI/PHILIPS CM200FEG/ST / Date: 1997- / Details: 25 % of data from Philips EM420 with LaB6 at 100kV
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Electron dose: 10 e/Å2 / Illumination mode: FLOOD BEAM
LensMagnification: 50000 X (nominal), 51200 X (calibrated) / Cs: 2 mm / Imaging mode: BRIGHT FIELD / Defocus: 2170 - 4340 nm
Specimen HolderHolder: Cryo Transfer / Model: GATAN LIQUID NITROGEN / Temperature: 93 K
CameraDetector: KODAK SO-163 FILM

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Image acquisition

Image acquisitionNumber of digital images: 239 / Scanner: PERKIN ELMER / Sampling size: 15 microns / Bit depth: 12

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Image processing

ProcessingMethod: single particle reconstruction / Number of projections: 73523 / Applied symmetry: C1 (asymmetric)
3D reconstructionAlgorithm: Projection Matching / Software: SPIDER/WEB / CTF correction: Wiener filtration of defocus group volumes / Resolution: 11.5 Å / Resolution method: FSC 0.5

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Atomic model buiding

Modeling #1Software: O / Refinement protocol: rigid body
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
Output model

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