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- EMDB-1762: Cryo-EM structure of the E. coli translating ribosome in complex ... -

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Basic information

Entry
Database: EMDB / ID: EMD-1762
TitleCryo-EM structure of the E. coli translating ribosome in complex with SRP and its receptor
Map dataE. coli translating ribosome in complex with SRP and its receptor
Sample
  • Sample: Ribosome-nascent chain-SRP-FtsY complex
  • Complex: 70S ribosomeRibosome
  • Protein or peptide: Signal Recognition Particle Protein
  • Protein or peptide: Cell division protein FtsY
KeywordsRibosome / Co-translational Targeting / Signal Recognition Particle / FtsY
Function / homology
Function and homology information


signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / protein targeting to membrane / ribonucleoprotein complex / GTPase activity / GTP binding / ATP hydrolysis activity / plasma membrane ...signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / protein targeting to membrane / ribonucleoprotein complex / GTPase activity / GTP binding / ATP hydrolysis activity / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Signal-recognition particle receptor FtsY / Signal recognition particle protein / SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily ...Signal-recognition particle receptor FtsY / Signal recognition particle protein / SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit / Signal recognition particle, SRP54 subunit, M-domain / Signal recognition particle, SRP54 subunit, M-domain superfamily / Signal peptide binding domain / SRP54-type proteins GTP-binding domain signature. / Signal recognition particle SRP54, helical bundle / Signal recognition particle SRP54, N-terminal domain superfamily / SRP54-type protein, helical bundle domain / SRP54-type protein, helical bundle domain / Signal recognition particle, SRP54 subunit, GTPase domain / SRP54-type protein, GTPase domain / SRP54-type protein, GTPase domain / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Signal recognition particle protein / Signal recognition particle protein / Signal recognition particle receptor FtsY
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 13.5 Å
AuthorsEstrozi LF / Boehringer D / Shan S-O / Ban N / Schaffitzel C
CitationJournal: Nat Struct Mol Biol / Year: 2011
Title: Cryo-EM structure of the E. coli translating ribosome in complex with SRP and its receptor.
Authors: Leandro F Estrozi / Daniel Boehringer / Shu-Ou Shan / Nenad Ban / Christiane Schaffitzel /
Abstract: We report the 'early' conformation of the Escherichia coli signal recognition particle (SRP) and its receptor FtsY bound to the translating ribosome, as determined by cryo-EM. FtsY binds to the ...We report the 'early' conformation of the Escherichia coli signal recognition particle (SRP) and its receptor FtsY bound to the translating ribosome, as determined by cryo-EM. FtsY binds to the tetraloop of the SRP RNA, whereas the NG domains of the SRP protein and FtsY interact weakly in this conformation. Our results suggest that optimal positioning of the SRP RNA tetraloop and the Ffh NG domain leads to FtsY recruitment.
History
DepositionJul 13, 2010-
Header (metadata) releaseNov 16, 2010-
Map releaseMar 23, 2011-
UpdateDec 11, 2013-
Current statusDec 11, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2xkv
  • Surface level: 0.009
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2xkv
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1762.png

Downloads & links

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Map

FileDownload / File: emd_1762.map.gz / Format: CCP4 / Size: 3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationE. coli translating ribosome in complex with SRP and its receptor
Voxel sizeX=Y=Z: 3.81 Å
Density
Contour LevelBy EMDB: 0.009 / Movie #1: 0.009
Minimum - Maximum-0.0657185 - 0.100835
Average (Standard dev.)0.00020288 (±0.00988419)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions939393
Spacing939393
CellA=B=C: 354.33 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.813.813.81
M x/y/z939393
origin x/y/z0.0000.0000.000
length x/y/z354.330354.330354.330
α/β/γ90.00090.00090.000
start NX/NY/NZ000
NX/NY/NZ454586
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS939393
D min/max/mean-0.0660.1010.000

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Supplemental data

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Sample components

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Entire : Ribosome-nascent chain-SRP-FtsY complex

EntireName: Ribosome-nascent chain-SRP-FtsY complex
Components
  • Sample: Ribosome-nascent chain-SRP-FtsY complex
  • Complex: 70S ribosomeRibosome
  • Protein or peptide: Signal Recognition Particle Protein
  • Protein or peptide: Cell division protein FtsY

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Supramolecule #1000: Ribosome-nascent chain-SRP-FtsY complex

SupramoleculeName: Ribosome-nascent chain-SRP-FtsY complex / type: sample / ID: 1000
Oligomeric state: One SRP-FtsY complex bound to 70S ribosome
Number unique components: 3
Molecular weightTheoretical: 2.65 MDa

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Supramolecule #1: 70S ribosome

SupramoleculeName: 70S ribosome / type: complex / ID: 1 / Name.synonym: 70S ribosome / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 2.5 MDa

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Macromolecule #1: Signal Recognition Particle Protein

MacromoleculeName: Signal Recognition Particle Protein / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 145 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Signal recognition particle protein

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Macromolecule #2: Cell division protein FtsY

MacromoleculeName: Cell division protein FtsY / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Oligomeric state: Monomer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightTheoretical: 145 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceUniProtKB: Signal recognition particle receptor FtsY

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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

Concentration0.32 mg/mL
BufferpH: 7.5 / Details: 50 mM Hepes-KOH, 100 mM KOAc, 8 mM Mg(OAc)2
GridDetails: Carbon-coated lacey formvar grids
VitrificationCryogen name: ETHANE / Instrument: HOMEMADE PLUNGER / Details: Vitrification instrument: Plunger

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Electron microscopy

MicroscopeFEI TECNAI F20
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 50000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 3.5 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 50000
Sample stageSpecimen holder: Eucentric / Specimen holder model: GATAN LIQUID NITROGEN
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: NIKON SUPER COOLSCAN 9000
Tilt angle min0
Tilt angle max0
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 13.5 Å / Resolution method: FSC 0.5 CUT-OFF / Number images used: 28822

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Atomic model buiding 1

Initial modelPDB ID:

1dul

SoftwareName: CNS
RefinementSpace: REAL
Output model

PDB-2xkv:
Atomic Model of the SRP-FtsY Early Conformation

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Atomic model buiding 2

Initial modelPDB ID:

1okk

SoftwareName: CNS
RefinementSpace: REAL
Output model

PDB-2xkv:
Atomic Model of the SRP-FtsY Early Conformation

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