[English] 日本語
Yorodumi
- EMDB-1264: Following the signal sequence from ribosomal tunnel exit to signa... -

+
Open data


ID or keywords:

Loading...

-
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 / signal recognition particle / cotranslational protein targeting to membrane / granulocyte differentiation / protein targeting to ER / signal-recognition-particle GTPase / SRP-dependent cotranslational protein targeting to membrane, translocation ...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 / cotranslational protein targeting to membrane / granulocyte differentiation / protein targeting to ER / signal-recognition-particle GTPase / SRP-dependent cotranslational protein targeting to membrane, translocation / 7S RNA binding / exocrine pancreas development / SRP-dependent cotranslational protein targeting to membrane / phototransduction / ribonucleoprotein complex binding / neutrophil chemotaxis / visual perception / chloroplast / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / G protein-coupled receptor activity / GDP binding / cytosolic large ribosomal subunit / rRNA binding / nuclear speck / nuclear body / structural constituent of ribosome / ribosome / translation / ribonucleoprotein complex / GTPase activity / mRNA binding / GTP binding / nucleolus / endoplasmic reticulum / ATP hydrolysis activity / RNA binding / nucleus / 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

-
Structure visualization

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

1264.gif

Downloads & links

-
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

-
Supplemental data

-
Sample components

-
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

-
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

-
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

-
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

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

VitrificationCryogen name: ETHANE

-
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

-
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

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more