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- EMDB-6211: Cryo-EM structure of ribosomal protein S1 on the ribosome -

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Basic information

Entry
Database: EMDB / ID: EMD-6211
TitleCryo-EM structure of ribosomal protein S1 on the ribosome
Map dataReconstruction of ErmCL-stalled E. coli ribosome containing density for the first domains of ribosomal protein S1
Sample
  • Sample: Reconstruction of ErmCL-stalled E. coli ribosome containing density for the first domains of ribosomal protein S1
  • Complex: ErmCL-stalled ribosome
KeywordsRibosome / Ribosomal protein S1 / Cryo-EM
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.5 Å
AuthorsByrgazov K / Grishkovskaya I / Arenz S / Coudevylle N / Temmel H / Wilson DN / Djinovic-Carugo K / Moll I
CitationJournal: Nucleic Acids Res / Year: 2015
Title: Structural basis for the interaction of protein S1 with the Escherichia coli ribosome.
Authors: Konstantin Byrgazov / Irina Grishkovskaya / Stefan Arenz / Nicolas Coudevylle / Hannes Temmel / Daniel N Wilson / Kristina Djinovic-Carugo / Isabella Moll /
Abstract: In Gram-negative bacteria, the multi-domain protein S1 is essential for translation initiation, as it recruits the mRNA and facilitates its localization in the decoding centre. In sharp contrast to ...In Gram-negative bacteria, the multi-domain protein S1 is essential for translation initiation, as it recruits the mRNA and facilitates its localization in the decoding centre. In sharp contrast to its functional importance, S1 is still lacking from the high-resolution structures available for Escherichia coli and Thermus thermophilus ribosomes and thus the molecular mechanism governing the S1-ribosome interaction has still remained elusive. Here, we present the structure of the N-terminal S1 domain D1 when bound to the ribosome at atomic resolution by using a combination of NMR, X-ray crystallography and cryo-electron microscopy. Together with biochemical assays, the structure reveals that S1 is anchored to the ribosome primarily via a stabilizing π-stacking interaction within the short but conserved N-terminal segment that is flexibly connected to domain D1. This interaction is further stabilized by salt bridges involving the zinc binding pocket of protein S2. Overall, this work provides one hitherto enigmatic piece in the 'ribosome puzzle', namely the detailed molecular insight into the topology of the S1-ribosome interface. Moreover, our data suggest novel mechanisms that have the potential to modulate protein synthesis in response to environmental cues by changing the affinity of S1 for the ribosome.
History
DepositionDec 5, 2014-
Header (metadata) releaseDec 24, 2014-
Map releaseDec 24, 2014-
UpdateJan 21, 2015-
Current statusJan 21, 2015Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.0006
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.0006
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

emd_6211.png

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Map

FileDownload / File: emd_6211.map.gz / Format: CCP4 / Size: 185.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationReconstruction of ErmCL-stalled E. coli ribosome containing density for the first domains of ribosomal protein S1
Voxel sizeX=Y=Z: 1.0489 Å
Density
Contour LevelBy AUTHOR: 0.0006 / Movie #1: 0.0006
Minimum - Maximum-0.00085958 - 0.00166435
Average (Standard dev.)0.00001144 (±0.00015951)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions368368368
Spacing368368368
CellA=B=C: 385.9952 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.04889945652171.04889945652171.0488994565217
M x/y/z368368368
origin x/y/z0.0000.0000.000
length x/y/z385.995385.995385.995
α/β/γ90.00090.00090.000
start NX/NY/NZ-72-72-72
NX/NY/NZ145145145
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS368368368
D min/max/mean-0.0010.0020.000

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Supplemental data

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Sample components

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Entire : Reconstruction of ErmCL-stalled E. coli ribosome containing densi...

EntireName: Reconstruction of ErmCL-stalled E. coli ribosome containing density for the first domains of ribosomal protein S1
Components
  • Sample: Reconstruction of ErmCL-stalled E. coli ribosome containing density for the first domains of ribosomal protein S1
  • Complex: ErmCL-stalled ribosome

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Supramolecule #1000: Reconstruction of ErmCL-stalled E. coli ribosome containing densi...

SupramoleculeName: Reconstruction of ErmCL-stalled E. coli ribosome containing density for the first domains of ribosomal protein S1
type: sample / ID: 1000 / Number unique components: 1

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Supramolecule #1: ErmCL-stalled ribosome

SupramoleculeName: ErmCL-stalled ribosome / type: complex / ID: 1 / Name.synonym: 70S ribosome / Recombinant expression: No / Database: NCBI / Ribosome-details: ribosome-prokaryote: ALL
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

BufferpH: 7.4 / Details: 50 mM HEPES, 100 mM KOAc, 20 mM MgOAc
GridDetails: 2 nm pre-coated Quantifoil R3/3 holey carbon supported grids
VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 200 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.5 µm / Nominal defocus min: 1.2 µm / Nominal magnification: 75000
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
DateMay 21, 2012
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) / Number real images: 6902 / Average electron dose: 20 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: Defocus groups
Final reconstructionResolution.type: BY AUTHOR / Resolution: 9.5 Å / Resolution method: OTHER / Software - Name: SPIDER / Details: Final map was filtered to 9.5 Angstrom resolution. / Number images used: 128846
DetailsCTF-parameter estimation in SPIDER TF ED, particle picking in Signature, image processing in SPIDER

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