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- EMDB-1310: Scaffolding as an organizing principle in trans-translation. The ... -

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Basic information

Entry
Database: EMDB / ID: EMD-1310
TitleScaffolding as an organizing principle in trans-translation. The roles of small protein B and ribosomal protein S1.
Map dataCryo-EM map of Thermus thermophilus 70S ribosome bound with small protein B
Sample
  • Sample: Thermus thermophilus 70S ribosome
  • Complex: 70S Ribosome
  • Protein or peptide: small protein B
  • RNA: tRNA
  • RNA: rRNA
Function / homologytrans-translation / SsrA-binding protein / SsrA-binding protein, conserved site / Small protein B / SmpB protein / SsrA-binding protein. / RNA binding / cytosol / SsrA-binding protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
Methodsingle particle reconstruction / cryo EM / negative staining / Resolution: 11.8 Å
AuthorsGillet R / Kaur S / Li W / Hallier M / Felden B / Frank J
CitationJournal: J Biol Chem / Year: 2007
Title: Scaffolding as an organizing principle in trans-translation. The roles of small protein B and ribosomal protein S1.
Authors: Reynald Gillet / Sukhjit Kaur / Wen Li / Marc Hallier / Brice Felden / Joachim Frank /
Abstract: A eubacterial ribosome stalled on a defective mRNA can be released through a quality control mechanism referred to as trans-translation, which depends on the coordinating binding actions of transfer- ...A eubacterial ribosome stalled on a defective mRNA can be released through a quality control mechanism referred to as trans-translation, which depends on the coordinating binding actions of transfer-messenger RNA, small protein B, and ribosome protein S1. By means of cryo-electron microscopy, we obtained a map of the complex composed of a stalled ribosome and small protein B, which appears near the decoding center. This result suggests that, when lacking a codon, the A-site on the small subunit is a target for small protein B. To investigate the role of S1 played in trans-translation, we obtained a cryo-electron microscopic map, including a stalled ribosome, transfer-messenger RNA, and small protein Bs but in the absence of S1. In this complex, several connections between the 30 S subunit and transfer-messenger RNA that appear in the +S1 complex are no longer found. We propose the unifying concept of scaffolding for the roles of small protein B and S1 in binding of transfer-messenger RNA to the ribosome during trans-translation, and we infer a pathway of sequential binding events in the initial phase of trans-translation.
History
DepositionDec 12, 2006-
Header (metadata) releaseDec 14, 2006-
Map releaseJun 12, 2007-
UpdateMay 26, 2011-
Current statusMay 26, 2011Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 35
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 35
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2ob7
  • Surface level: 35
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2ob7
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

1310.gif

Downloads & links

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Map

FileDownload / File: emd_1310.map.gz / Format: CCP4 / Size: 8.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationCryo-EM map of Thermus thermophilus 70S ribosome bound with small protein B
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
2.82 Å/pix.
x 130 pix.
= 366.6 Å		2.82 Å/pix.
x 130 pix.
= 366.6 Å		2.82 Å/pix.
x 130 pix.
= 366.6 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 2.82 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 60.200000000000003 / Movie #1: 35
Minimum - Maximum-105.753 - 255.685000000000002
Average (Standard dev.)5.9479 (±25.539000000000001)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin-65-65-65
Dimensions130130130
Spacing130130130
CellA=B=C: 366.6 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z2.822.822.82
M x/y/z130130130
origin x/y/z0.0000.0000.000
length x/y/z366.600366.600366.600
α/β/γ90.00090.00090.000
start NX/NY/NZ-63-63-63
NX/NY/NZ128128128
MAP C/R/S123
start NC/NR/NS-65-65-65
NC/NR/NS130130130
D min/max/mean-105.753255.6855.948

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Supplemental data

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Sample components

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Entire : Thermus thermophilus 70S ribosome

EntireName: Thermus thermophilus 70S ribosome
Components
  • Sample: Thermus thermophilus 70S ribosome
  • Complex: 70S Ribosome
  • Protein or peptide: small protein B
  • RNA: tRNA
  • RNA: rRNA

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Supramolecule #1000: Thermus thermophilus 70S ribosome

SupramoleculeName: Thermus thermophilus 70S ribosome / type: sample / ID: 1000 / Details: the sample was monodisperse / Number unique components: 4
Molecular weightTheoretical: 2.3 MDa

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Supramolecule #1: 70S Ribosome

SupramoleculeName: 70S Ribosome / type: complex / ID: 1 / Ribosome-details: ribosome-prokaryote: ALL
Molecular weightExperimental: 2.3 MDa

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Macromolecule #1: small protein B

MacromoleculeName: small protein B / type: protein_or_peptide / ID: 1 / Recombinant expression: No
Source (natural)Organism: Thermus thermophilus (bacteria)
Molecular weightExperimental: 19 KDa

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Macromolecule #2: tRNA

MacromoleculeName: tRNA / type: rna / ID: 2 / Classification: TRANSFER / Structure: OTHER / Synthetic?: No
Source (natural)Organism: Thermus thermophilus (bacteria) / synonym: tRNA

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Macromolecule #3: rRNA

MacromoleculeName: rRNA / type: rna / ID: 3 / Classification: TRANSFER / Structure: OTHER / Synthetic?: No
Source (natural)Organism: Thermus thermophilus (bacteria)

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Experimental details

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Structure determination

Methodnegative staining, cryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5 / Details: see Methods
StainingType: NEGATIVE / Details: No staining (Cryo-EM)
GridDetails: Quanti-foil grids coated with a thin carbon layer
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 279 K / Instrument: OTHER / Details: Vitrification instrument: Vitrobot
Method: Blot for 5 seconds before plunging Rapid plunge freezing in liquid ethane

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Electron microscopy

MicroscopeFEI TECNAI F20
TemperatureMin: 93 K / Max: 93 K / Average: 93 K
Alignment procedureLegacy - Electron beam tilt params: 0
DateAug 3, 2004
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 28 / Average electron dose: 15 e/Å2 / Bits/pixel: 8
Tilt angle min0
Tilt angle max0
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 49696 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.0 mm / Nominal defocus max: 3.12 µm / Nominal defocus min: 1.3 µm / Nominal magnification: 50000
Sample stageSpecimen holder: cryo transfer / Specimen holder model: GATAN LIQUID NITROGEN
Experimental equipment
Model: Tecnai F20 / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: CTF correctionn of 3D map
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 11.8 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER package / Number images used: 37000

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Atomic model buiding 1

Initial modelPDB ID:

1pv6


Chain - Chain ID: A
SoftwareName: O
DetailsPDBEntryID_givenInChain. Protocol: Rigid Body. manual fitting with O
RefinementProtocol: RIGID BODY FIT
Output model

PDB-2ob7:
Structure of tmRNA-(SmpB)2 complex as inferred from cryo-EM

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