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- EMDB-2844: Structural basis for targeting and elongation arrest of Bacillus ... -

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Basic information

Entry
Database: EMDB / ID: EMD-2844
TitleStructural basis for targeting and elongation arrest of Bacillus signal recognition particle
Map datamammalian signal recognition particle bound to ribosome nascent chain complex.
Sample
  • Sample: mammalian signal recognition particle bound to ribosome nascent chain complex
  • Complex: SRP-bound 80S ribosome
  • Protein or peptide: signal recognition particle
KeywordsSignal recognition particle (SRP) / Stalled Ribosome
Function / homology
Function and homology information


SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / signal recognition particle binding / granulocyte differentiation / absorption of visible light / negative regulation of translational elongation / G protein-coupled photoreceptor activity / photoreceptor inner segment membrane ...SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane, signal sequence recognition / endoplasmic reticulum signal peptide binding / signal recognition particle, endoplasmic reticulum targeting / signal recognition particle binding / granulocyte differentiation / absorption of visible light / negative regulation of translational elongation / G protein-coupled photoreceptor activity / photoreceptor inner segment membrane / rhodopsin mediated signaling pathway / 11-cis retinal binding / cellular response to light stimulus / signal-recognition-particle GTPase / protein targeting to ER / SRP-dependent cotranslational protein targeting to membrane, translocation / 7S RNA binding / exocrine pancreas development / : / SRP-dependent cotranslational protein targeting to membrane / photoreceptor outer segment membrane / plasma membrane => GO:0005886 / phototransduction / photoreceptor outer segment / ribonucleoprotein complex binding / visual perception / neutrophil chemotaxis / photoreceptor disc membrane / GDP binding / membrane => GO:0016020 / nuclear speck / G protein-coupled receptor signaling pathway / GTPase activity / GTP binding / nucleolus / endoplasmic reticulum / ATP hydrolysis activity / nucleoplasm / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Signal recognition particle, SRP9 subunit / SRP9 domain / Signal recognition particle SRP9 / Signal recognition particle 9 kDa protein (SRP9) / Signal recognition particle, SRP14 subunit / Signal recognition particle, SRP9/SRP14 subunit / Signal recognition particle 14kD protein / Signal recognition particle subunit SRP68 / Signal recognition particle subunit SRP68, RNA-binding domain / SRP68, N-terminal domain superfamily ...Signal recognition particle, SRP9 subunit / SRP9 domain / Signal recognition particle SRP9 / Signal recognition particle 9 kDa protein (SRP9) / Signal recognition particle, SRP14 subunit / Signal recognition particle, SRP9/SRP14 subunit / Signal recognition particle 14kD protein / Signal recognition particle subunit SRP68 / Signal recognition particle subunit SRP68, RNA-binding domain / SRP68, N-terminal domain superfamily / RNA-binding signal recognition particle 68 / Signal recognition particle, SRP54 subunit, eukaryotic / Signal recognition particle, SRP19 subunit / Signal recognition particle, subunit SRP19-like superfamily / SRP19 protein / Rhodopsin, N-terminal / Amino terminal of the G-protein receptor rhodopsin / Rhodopsin / Opsin / Visual pigments (opsins) retinal binding site / Visual pigments (opsins) retinal binding site. / 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 / G-protein coupled receptors family 1 signature. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Signal recognition particle 19 kDa protein / Signal recognition particle 14 kDa protein / Signal recognition particle 9 kDa protein / Rhodopsin / Signal recognition particle subunit SRP54 / Signal recognition particle subunit SRP68
Similarity search - Component
Biological speciesTriticum (plant) / Canis lupus familiaris (dog)
Methodsingle particle reconstruction / cryo EM / Resolution: 9.0 Å
AuthorsBeckert B / Kedrov A / Sohmen D / Kempf G / Wild K / Sinning I / Stahlberg H / Wilson D N / Beckmann R
CitationJournal: Nat Struct Mol Biol / Year: 2015
Title: Translational arrest by a prokaryotic signal recognition particle is mediated by RNA interactions.
Authors: Bertrand Beckert / Alexej Kedrov / Daniel Sohmen / Georg Kempf / Klemens Wild / Irmgard Sinning / Henning Stahlberg / Daniel N Wilson / Roland Beckmann /
Abstract: The signal recognition particle (SRP) recognizes signal sequences of nascent polypeptides and targets ribosome-nascent chain complexes to membrane translocation sites. In eukaryotes, translating ...The signal recognition particle (SRP) recognizes signal sequences of nascent polypeptides and targets ribosome-nascent chain complexes to membrane translocation sites. In eukaryotes, translating ribosomes are slowed down by the Alu domain of SRP to allow efficient targeting. In prokaryotes, however, little is known about the structure and function of Alu domain-containing SRPs. Here, we report a complete molecular model of SRP from the Gram-positive bacterium Bacillus subtilis, based on cryo-EM. The SRP comprises two subunits, 6S RNA and SRP54 or Ffh, and it facilitates elongation slowdown similarly to its eukaryotic counterpart. However, protein contacts with the small ribosomal subunit observed for the mammalian Alu domain are substituted in bacteria by RNA-RNA interactions of 6S RNA with the α-sarcin-ricin loop and helices H43 and H44 of 23S rRNA. Our findings provide a structural basis for cotranslational targeting and RNA-driven elongation arrest in prokaryotes.
History
DepositionDec 15, 2014-
Header (metadata) releaseJan 21, 2015-
Map releaseSep 9, 2015-
UpdateOct 14, 2015-
Current statusOct 14, 2015Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.119
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.119
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-4ue5
  • Surface level: 0.119
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-4ue5
  • 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_2844.map.gz / Format: CCP4 / Size: 276 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationmammalian signal recognition particle bound to ribosome nascent chain complex.
Voxel sizeX=Y=Z: 1.24 Å
Density
Contour LevelBy AUTHOR: 0.119 / Movie #1: 0.119
Minimum - Maximum-0.32551476 - 0.6513412
Average (Standard dev.)0.00232387 (±0.04317628)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions420420420
Spacing420420420
CellA=B=C: 520.8 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.241.241.24
M x/y/z420420420
origin x/y/z0.0000.0000.000
length x/y/z520.800520.800520.800
α/β/γ90.00090.00090.000
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS420420420
D min/max/mean-0.3260.6510.002

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Supplemental data

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Sample components

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Entire : mammalian signal recognition particle bound to ribosome nascent c...

EntireName: mammalian signal recognition particle bound to ribosome nascent chain complex
Components
  • Sample: mammalian signal recognition particle bound to ribosome nascent chain complex
  • Complex: SRP-bound 80S ribosome
  • Protein or peptide: signal recognition particle

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Supramolecule #1000: mammalian signal recognition particle bound to ribosome nascent c...

SupramoleculeName: mammalian signal recognition particle bound to ribosome nascent chain complex
type: sample / ID: 1000 / Number unique components: 2

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Supramolecule #1: SRP-bound 80S ribosome

SupramoleculeName: SRP-bound 80S ribosome / type: complex / ID: 1 / Name.synonym: 80S ribosome / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL
Source (natural)Organism: Triticum (plant)
Molecular weightExperimental: 3 MDa / Theoretical: 3 MDa

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Macromolecule #1: signal recognition particle

MacromoleculeName: signal recognition particle / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Recombinant expression: No
Source (natural)Organism: Canis lupus familiaris (dog)

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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

VitrificationCryogen name: ETHANE / Instrument: FEI VITROBOT MARK IV

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.7 mm / Nominal defocus max: 4.0 µm / Nominal defocus min: 0.8 µm
Sample stageSpecimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
DateMar 3, 2013
Image recordingCategory: CCD / Film or detector model: TVIPS TEMCAM-F816 (8k x 8k) / Number real images: 3627 / Average electron dose: 20 e/Å2 / Bits/pixel: 16
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionDetails: micrograph
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 9.0 Å / Resolution method: OTHER / Software - Name: Spider / Number images used: 19096
DetailsAutomated particle selection was performed using the program Signature.Three dimensional reconstructions were then performed using the SPIDER software package.

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