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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: EMD-1003
TitleSolution structure of the E. coli 70S ribosome at 11.5 A resolution.
Map dataE. coli 70S Ribosome
Sample
  • Sample: FMet-tRNAMet 70S Ribosome from E.coli
  • Complex: 70S ribosome Escherichia coli
  • RNA: fMet-tRNA
  • RNA: MF-mRNA
Function / homology
Function and homology information


ribosomal small subunit biogenesis / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / regulation of translation / large ribosomal subunit / cytosolic large ribosomal subunit / small ribosomal subunit / tRNA binding / ribosome / rRNA binding ...ribosomal small subunit biogenesis / cytosolic small ribosomal subunit / large ribosomal subunit rRNA binding / regulation of translation / large ribosomal subunit / cytosolic large ribosomal subunit / small ribosomal subunit / tRNA binding / ribosome / rRNA binding / structural constituent of ribosome / translation / ribonucleoprotein complex / response to antibiotic / cytoplasm
Similarity search - Function
Ribosomal protein L1, bacterial-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site ...Ribosomal protein L1, bacterial-type / Ribosomal protein L1, conserved site / Ribosomal protein L1 / Ribosomal protein L1 signature. / Ribosomal protein L1, 3-layer alpha/beta-sandwich / Ribosomal protein L1-like / Ribosomal protein L1/ribosomal biogenesis protein / Ribosomal protein L1p/L10e family / Ribosomal protein L11, bacterial-type / Ribosomal protein L11, conserved site / Ribosomal protein L11 signature. / Ribosomal protein L6, conserved site / Ribosomal protein L6 signature 1. / Ribosomal protein L11, N-terminal / Ribosomal protein L11, N-terminal domain / Ribosomal protein L11/L12 / Ribosomal protein L11, C-terminal / Ribosomal protein L11, C-terminal domain superfamily / Ribosomal protein L11/L12, N-terminal domain superfamily / Ribosomal protein L11, RNA binding domain / Ribosomal protein L11/L12 / Ribosomal protein L6, bacterial-type / Ribosomal protein S6, conserved site / Ribosomal protein S6 signature. / Ribosomal protein S7, bacterial/organellar-type / Ribosomal protein S4, bacterial-type / 30S ribosomal protein S17 / Ribosomal protein S5, bacterial-type / Ribosomal protein S6, plastid/chloroplast / Ribosomal protein S15, bacterial-type / Ribosomal protein S6 / Ribosomal protein S6 / Ribosomal protein S6 superfamily / Translation elongation factor EF1B/ribosomal protein S6 / : / Ribosomal protein S5, N-terminal, conserved site / Ribosomal protein S5 signature. / Ribosomal protein S7, conserved site / Ribosomal protein S7 signature. / Ribosomal protein S17, conserved site / Ribosomal protein S17 signature. / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S5 / Ribosomal protein S5, N-terminal / Ribosomal protein S5, N-terminal domain / S5 double stranded RNA-binding domain profile. / Ribosomal protein S8 signature. / Ribosomal protein S5, C-terminal / Ribosomal protein S5, C-terminal domain / Ribosomal protein S4/S9 N-terminal domain / Ribosomal protein S4/S9, N-terminal / Ribosomal protein S4, conserved site / Ribosomal protein S4 signature. / Ribosomal protein L6, alpha-beta domain / Ribosomal protein L6 / Ribosomal protein L6 / Ribosomal protein S15 signature. / Ribosomal protein L6, alpha-beta domain superfamily / Ribosomal protein S4/S9 / S4 RNA-binding domain profile. / Ribosomal protein S8 / Ribosomal protein S8 superfamily / Ribosomal protein S8 / S4 RNA-binding domain / S4 domain / RNA-binding S4 domain / Ribosomal protein S5/S7 / Ribosomal protein S7 domain / Ribosomal protein S7 domain superfamily / RNA-binding S4 domain superfamily / Ribosomal protein S7p/S5e / Ribosomal protein S17/S11 / Ribosomal protein S17 / Ribosomal protein S15 / Ribosomal_S15 / Ribosomal protein S15 / S15/NS1, RNA-binding / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Nucleic acid-binding, OB-fold
Similarity search - Domain/homology
Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein uL11 ...Small ribosomal subunit protein uS5 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS8 / Small ribosomal subunit protein uS7 / Small ribosomal subunit protein uS4 / Small ribosomal subunit protein uS5 / Small ribosomal subunit protein bS6 / Small ribosomal subunit protein uS17 / Large ribosomal subunit protein uL1 / Large ribosomal subunit protein uL11 / Small ribosomal subunit protein uS15 / Small ribosomal subunit protein uS4 / Large ribosomal subunit protein uL6 / Small ribosomal subunit protein uS15 / Large ribosomal subunit protein uL1 / Small ribosomal subunit protein bS6
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 11.5 Å
AuthorsGabashvili IS
CitationJournal: Cell / 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 /
Abstract: Over 73,000 projections of the E. coli ribosome bound with formyl-methionyl initiator tRNAf(Met) were used to obtain an 11.5 A cryo-electron microscopy map of the complex. This map allows ...Over 73,000 projections of the E. coli ribosome bound with formyl-methionyl initiator tRNAf(Met) were used to obtain an 11.5 A cryo-electron microscopy map of the complex. This map allows identification of RNA helices, peripheral proteins, and intersubunit bridges. Comparison of double-stranded RNA regions and positions of proteins identified in both cryo-EM and X-ray maps indicates good overall agreement but points to rearrangements of ribosomal components required for the subunit association. Fitting of known components of the 50S stalk base region into the map defines the architecture of the GTPase-associated center and reveals a major change in the orientation of the alpha-sarcin-ricin loop. Analysis of the bridging connections between the subunits provides insight into the dynamic signaling mechanism between the ribosomal subunits.
History
DepositionJun 26, 2002-
Header (metadata) releaseAug 22, 2002-
Map releaseAug 22, 2002-
UpdateOct 17, 2012-
Current statusOct 17, 2012Processing site: PDBe / Status: Released

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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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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-1eg0
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_1003.map.gz / Format: CCP4 / Size: 7.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationE. coli 70S Ribosome
Voxel sizeX=Y=Z: 2.93 Å
Density
Contour Level1: 82.799999999999997 / Movie #1: 50
Minimum - Maximum-141.974999999999994 - 339.987000000000023
Average (Standard dev.)1.85585 (±38.046700000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-62-62-62
Dimensions125125125
Spacing125125125
CellA=B=C: 366.25 Å
α=β=γ: 90 °

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
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
Components
  • Sample: FMet-tRNAMet 70S Ribosome from E.coli
  • Complex: 70S ribosome Escherichia coli
  • RNA: fMet-tRNA
  • RNA: MF-mRNA

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Supramolecule #1000: FMet-tRNAMet 70S Ribosome from E.coli

SupramoleculeName: FMet-tRNAMet 70S Ribosome from E.coli / type: sample / ID: 1000
Details: preparation and buffer conditions are as described in Malhotra et al., J. Mol. Biol. (1998) 280, 103-116
Number unique components: 3
Molecular weightTheoretical: 2.5 MDa

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Supramolecule #1: 70S ribosome Escherichia coli

SupramoleculeName: 70S ribosome Escherichia coli / type: complex / ID: 1 / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: LSU 50S
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #1: fMet-tRNA

MacromoleculeName: fMet-tRNA / type: rna / ID: 1 / Classification: OTHER / Structure: DOUBLE HELIX / Synthetic?: No
Source (natural)Organism: Escherichia coli (E. coli)

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Macromolecule #2: MF-mRNA

MacromoleculeName: MF-mRNA / type: rna / ID: 2 / Details: 46 nucleotides / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: No
Source (natural)Organism: Escherichia coli (E. coli)

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

Concentration0.09 mg/mL
BufferpH: 7.6
Details: 20 mM Hepes, 6 mM Mg(CH3COO)2 150 mM NH4Cl, 4 mM beta-Mercaptoethanol, 0.5 mM Spermine, 2 mM Spermidine.
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: 2 side blotting plunger / Method: Blot and plunge

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Electron microscopy

MicroscopeFEI/PHILIPS CM200FEG/ST
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 51200 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.0 mm / Nominal defocus max: 4.34 µm / Nominal defocus min: 2.17 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Cryo Transfer / Specimen holder model: GATAN LIQUID NITROGEN
TemperatureAverage: 93 K
Details25 % of data from Philips EM420 with LaB6 at 100kV
DateOct 4, 1997
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PERKIN ELMER / Digitization - Sampling interval: 15 µm / Number real images: 239 / Average electron dose: 10 e/Å2 / Bits/pixel: 12
Tilt angle min0
Tilt angle max0

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Image processing

CTF correctionDetails: Wiener filtration of defocus group volumes
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 11.5 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER/WEB / Number images used: 73523

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Atomic model buiding 1

SoftwareName: O
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
RefinementProtocol: RIGID BODY FIT
Output model

PDB-1eg0:
FITTING OF COMPONENTS WITH KNOWN STRUCTURE INTO AN 11.5 A CRYO-EM MAP OF THE E.COLI 70S RIBOSOME

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