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- EMDB-1264: Following the signal sequence from ribosomal tunnel exit to signa... -

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Basic information

Entry
Database: EMDB / ID: EMD-1264
TitleFollowing the signal sequence from ribosomal tunnel exit to signal recognition particle.
Map dataMammalian SRP-RNC complex
Sample
  • Sample: mammalian signal recognition particle bound to ribosome nascent chain complex
  • Complex: ribosome
  • Protein or peptide: signal recognition particle
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 / granulocyte differentiation / signal recognition particle / cotranslational protein targeting to membrane / protein targeting to ER / signal-recognition-particle GTPase / exocrine pancreas development ...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 / granulocyte differentiation / signal recognition particle / cotranslational protein targeting to membrane / protein targeting to ER / signal-recognition-particle GTPase / exocrine pancreas development / SRP-dependent cotranslational protein targeting to membrane, translocation / 7S RNA binding / phototransduction / SRP-dependent cotranslational protein targeting to membrane / neutrophil chemotaxis / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / visual perception / chloroplast / G protein-coupled receptor activity / GDP binding / cytoplasmic translation / cytosolic large ribosomal subunit / nuclear body / rRNA binding / ribosome / structural constituent of ribosome / nuclear speck / ribonucleoprotein complex / translation / GTPase activity / mRNA binding / GTP binding / nucleolus / endoplasmic reticulum / ATP hydrolysis activity / RNA binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Rhodopsin, N-terminal domain superfamily / 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 / SRP/SRP receptor, N-terminal / Signal recognition particle, SRP54 subunit ...Rhodopsin, N-terminal domain superfamily / 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 / 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 / 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. / G protein-coupled receptor, rhodopsin-like / GPCR, rhodopsin-like, 7TM / G-protein coupled receptors family 1 profile. / 7 transmembrane receptor (rhodopsin family) / 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 19 kDa protein / Signal recognition particle subunit SRP54 / Rhodopsin / Putative 60S ribosomal protein L31 / Large ribosomal subunit protein uL29
Similarity search - Component
Biological speciesTriticum sp. (plant)
Methodsingle particle reconstruction / cryo EM / Resolution: 8.7 Å
AuthorsHalic M / Blau M / Becker T / Mielke T / Pool MR / Wild K / Sinning I / Beckmann R
CitationJournal: Nature / Year: 2006
Title: Following the signal sequence from ribosomal tunnel exit to signal recognition particle.
Authors: Mario Halic / Michael Blau / Thomas Becker / Thorsten Mielke / Martin R Pool / Klemens Wild / Irmgard Sinning / Roland Beckmann /
Abstract: Membrane and secretory proteins can be co-translationally inserted into or translocated across the membrane. This process is dependent on signal sequence recognition on the ribosome by the signal ...Membrane and secretory proteins can be co-translationally inserted into or translocated across the membrane. This process is dependent on signal sequence recognition on the ribosome by the signal recognition particle (SRP), which results in targeting of the ribosome-nascent-chain complex to the protein-conducting channel at the membrane. Here we present an ensemble of structures at subnanometre resolution, revealing the signal sequence both at the ribosomal tunnel exit and in the bacterial and eukaryotic ribosome-SRP complexes. Molecular details of signal sequence interaction in both prokaryotic and eukaryotic complexes were obtained by fitting high-resolution molecular models. The signal sequence is presented at the ribosomal tunnel exit in an exposed position ready for accommodation in the hydrophobic groove of the rearranged SRP54 M domain. Upon ribosome binding, the SRP54 NG domain also undergoes a conformational rearrangement, priming it for the subsequent docking reaction with the NG domain of the SRP receptor. These findings provide the structural basis for improving our understanding of the early steps of co-translational protein sorting.
History
DepositionAug 29, 2006-
Header (metadata) releaseAug 30, 2006-
Map releaseAug 30, 2008-
UpdateDec 4, 2013-
Current statusDec 4, 2013Processing site: PDBe / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.1
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  • Surface view colored by height
  • Surface level: 0.1
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  • Surface view with fitted model
  • Atomic models: PDB-2j37
  • Surface level: 0.1
  • Imaged by UCSF Chimera
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  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-2j37
  • Imaged by Jmol
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Movie viewer
Structure viewerEM map:
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Supplemental images

1264.gif

Downloads & links

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Map

FileDownload / File: emd_1264.map.gz / Format: CCP4 / Size: 185.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationMammalian SRP-RNC complex
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)X (Row.)Y (Col.)
1.23 Å/pix.
x 368 pix.
= 452.64 Å		1.23 Å/pix.
x 368 pix.
= 452.64 Å		1.23 Å/pix.
x 368 pix.
= 452.64 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.23 Å
Density

Histogram

Histogram (log scale)
Contour Level1: 0.0602 / Movie #1: 0.1
Minimum - Maximum-0.317222 - 0.706723
Average (Standard dev.)0.00446942 (±0.0542121)
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-0.3170.7070.004

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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: 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: ribosome

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

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Macromolecule #1: signal recognition particle

MacromoleculeName: signal recognition particle / type: protein_or_peptide / ID: 1 / Name.synonym: srp / Recombinant expression: No
Source (natural)Organism: Triticum sp. (plant) / synonym: wheat

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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
Image recordingCategory: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Average electron dose: 20 e/Å2 / Bits/pixel: 16
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.0 µm / Nominal defocus min: 0.9 µm
Sample stageSpecimen holder: f / Specimen holder model: OTHER
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: 8.7 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: spider

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