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- EMDB-1217: Signal recognition particle receptor exposes the ribosomal transl... -

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Basic information

Entry
Database: EMDB / ID: EMD-1217
TitleSignal recognition particle receptor exposes the ribosomal translocon binding site.
Map dataa
Sample
  • Sample: ribosome-SRP-SR
  • Complex: 80s
  • Protein or peptide: SRP
  • Protein or peptide: SRP receptorSignal recognition particle receptor
Function / homology
Function and homology information


SRP-dependent cotranslational protein targeting to membrane / signal recognition particle receptor complex / 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 / cotranslational protein targeting to membrane / signal-recognition-particle GTPase / protein targeting to ER ...SRP-dependent cotranslational protein targeting to membrane / signal recognition particle receptor complex / 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 / cotranslational protein targeting to membrane / signal-recognition-particle GTPase / protein targeting to ER / XBP1(S) activates chaperone genes / SRP-dependent cotranslational protein targeting to membrane, translocation / 7S RNA binding / exocrine pancreas development / SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane / ribonucleoprotein complex binding / cytoplasmic microtubule / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / chloroplast / neutrophil chemotaxis / GDP binding / cytosolic large ribosomal subunit / ribosome / rRNA binding / structural constituent of ribosome / nuclear speck / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / ubiquitin protein ligase binding / GTP binding / endoplasmic reticulum membrane / endoplasmic reticulum / ATP hydrolysis activity / RNA binding / extracellular exosome / membrane / nucleus / cytosol / cytoplasm
Similarity search - Function
Signal recognition particle receptor, alpha subunit, N-terminal / Signal recognition particle, alpha subunit, N-terminal / Signal recognition particle receptor, beta subunit / Signal recognition particle receptor beta subunit / Signal recognition particle, SRP54 subunit, eukaryotic / Signal recognition particle, SRP19 subunit / Signal recognition particle, subunit SRP19-like superfamily / SRP19 protein / SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit ...Signal recognition particle receptor, alpha subunit, N-terminal / Signal recognition particle, alpha subunit, N-terminal / Signal recognition particle receptor, beta subunit / Signal recognition particle receptor beta subunit / Signal recognition particle, SRP54 subunit, eukaryotic / Signal recognition particle, SRP19 subunit / Signal recognition particle, subunit SRP19-like superfamily / SRP19 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 / Longin-like domain superfamily / Ribosomal protein L23 / 60S ribosomal protein L35 / Ribosomal protein L31e / Ribosomal protein L31e domain superfamily / Ribosomal protein L31e / Ribosomal_L31e / Ribosomal protein L23/L25, conserved site / Ribosomal protein L23 signature. / Ribosomal L29 protein / Ribosomal protein L29/L35 / Ribosomal protein L29/L35 superfamily / Ribosomal protein L23 / Ribosomal protein L25/L23 / Ribosomal protein L23/L15e core domain superfamily / Nucleotide-binding alpha-beta plait domain superfamily / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Ribosomal protein L25 / Signal recognition particle receptor subunit alpha / Signal recognition particle receptor subunit beta / Signal recognition particle subunit SRP54 / Signal recognition particle 19 kDa protein / Putative 60S ribosomal protein L31 / Large ribosomal subunit protein uL29
Similarity search - Component
Biological speciesTriticum sp. (plant) / Canis sp. (mammal)
Methodsingle particle reconstruction / cryo EM / Resolution: 7.4 Å
AuthorsHalic M
CitationJournal: Science / Year: 2006
Title: Signal recognition particle receptor exposes the ribosomal translocon binding site.
Authors: Mario Halic / Marco Gartmann / Oliver Schlenker / Thorsten Mielke / Martin R Pool / Irmgard Sinning / Roland Beckmann /
Abstract: Signal sequences of secretory and membrane proteins are recognized by the signal recognition particle (SRP) as they emerge from the ribosome. This results in their targeting to the membrane by ...Signal sequences of secretory and membrane proteins are recognized by the signal recognition particle (SRP) as they emerge from the ribosome. This results in their targeting to the membrane by docking with the SRP receptor, which facilitates transfer of the ribosome to the translocon. Here, we present the 8 angstrom cryo-electron microscopy structure of a "docking complex" consisting of a SRP-bound 80S ribosome and the SRP receptor. Interaction of the SRP receptor with both SRP and the ribosome rearranged the S domain of SRP such that a ribosomal binding site for the translocon, the L23e/L35 site, became exposed, whereas Alu domain-mediated elongation arrest persisted.
History
DepositionApr 18, 2006-
Header (metadata) releaseApr 18, 2006-
Map releaseApr 30, 2008-
UpdateOct 24, 2012-
Current statusOct 24, 2012Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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  • Surface view colored by height
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-2go5
  • Surface level: 0.15
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2go5
  • 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_1217.map.gz / Format: CCP4 / Size: 185.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Annotationa
Voxel sizeX=Y=Z: 1.23 Å
Density
Contour Level1: 0.173 / Movie #1: 0.15
Minimum - Maximum-0.551018 - 1.54614
Average (Standard dev.)0.0147826 (±0.124948)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderYXZ
Origin-184-184-183
Dimensions368368368
Spacing368368368
CellA=B=C: 452.64 Å
α=β=γ: 90 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.231.231.23
M x/y/z368368368
origin x/y/z0.0000.0000.000
length x/y/z452.640452.640452.640
α/β/γ90.00090.00090.000
start NX/NY/NZ-184-184-183
NX/NY/NZ368368368
MAP C/R/S213
start NC/NR/NS-184-184-183
NC/NR/NS368368368
D min/max/mean-0.5511.5460.015

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Supplemental data

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Sample components

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Entire : ribosome-SRP-SR

EntireName: ribosome-SRP-SR
Components
  • Sample: ribosome-SRP-SR
  • Complex: 80s
  • Protein or peptide: SRP
  • Protein or peptide: SRP receptorSignal recognition particle receptor

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Supramolecule #1000: ribosome-SRP-SR

SupramoleculeName: ribosome-SRP-SR / type: sample / ID: 1000 / Number unique components: 3

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Supramolecule #1: 80s

SupramoleculeName: 80s / type: complex / ID: 1 / Name.synonym: 80s / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL
Source (natural)Organism: Triticum sp. (plant) / synonym: Bread wheat

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Macromolecule #1: SRP

MacromoleculeName: SRP / type: protein_or_peptide / ID: 1 / Name.synonym: SRP / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No
Source (natural)Organism: Canis sp. (mammal) / synonym: dog

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Macromolecule #2: SRP receptor

MacromoleculeName: SRP receptor / type: protein_or_peptide / ID: 2 / Name.synonym: SR / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No
Source (natural)Organism: Canis sp. (mammal) / synonym: 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

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Electron microscopy

MicroscopeFEI TECNAI F30
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELDBright-field microscopy
Sample stageSpecimen holder: gg / Specimen holder model: GATAN HELIUM
Image recordingDigitization - Scanner: PRIMESCAN / Digitization - Sampling interval: 1.23 µm
Experimental equipment
Model: Tecnai F30 / Image courtesy: FEI Company

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Image processing

Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 7.4 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: spider

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Atomic model buiding 1

SoftwareName: situs
DetailsProtocol: Rigid Body
RefinementProtocol: RIGID BODY FIT
Output model

PDB-2go5:
Structure of signal recognition particle receptor (SR) in complex with signal recognition particle (SRP) and ribosome nascent chain complex

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