[English] 日本語
Yorodumi
- EMDB-2316: Structural Basis of Signal Sequence Surveillance and Selection by... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-2316
TitleStructural Basis of Signal Sequence Surveillance and Selection by the SRP-SR Complex
Map dataRNCEspP-SRP-FtsY
Sample
  • Sample: Ribosome-SRP-FtsY complex with EspP nascent chain
  • Complex: 70S ribosomeRibosome
  • Protein or peptide: SIGNAL RECOGNITION PARTICLE PROTEIN
  • Protein or peptide: SIGNAL RECOGNITION PARTICLE RECEPTOR FTSY
  • Protein or peptide: 4.5 S RNA
  • Protein or peptide: SIGNAL RECOGNITION PARTICLE 54 KDA PROTEIN
  • Protein or peptide: DIPEPTIDYL AMINOPEPTIDASE B
KeywordsRibosome / SRP / signal recognition particle / SR / FtsY / cryo-EM
Function / homology
Function and homology information


Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases / signal recognition particle binding / signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / fungal-type vacuole membrane / dipeptidyl-peptidase activity / stringent response ...Synthesis, secretion, and inactivation of Glucagon-like Peptide-1 (GLP-1) / Hydrolases; Acting on peptide bonds (peptidases); Dipeptidyl-peptidases and tripeptidyl-peptidases / signal recognition particle binding / signal recognition particle / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / fungal-type vacuole membrane / dipeptidyl-peptidase activity / stringent response / protein targeting / aminopeptidase activity / cytoplasmic side of plasma membrane / protein processing / serine-type endopeptidase activity / GTPase activity / GTP binding / ATP hydrolysis activity / protein homodimerization activity / proteolysis / plasma membrane / cytosol
Similarity search - Function
Signal-recognition particle receptor FtsY / Signal recognition particle 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 ...Signal-recognition particle receptor FtsY / Signal recognition particle 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 / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Signal recognition particle protein / Signal recognition particle receptor FtsY / Dipeptidyl aminopeptidase B / Signal recognition particle 54 kDa protein
Similarity search - Component
Biological speciesEscherichia coli (E. coli) / Sulfolobus solfataricus (archaea) / Saccharomyces cerevisiae (brewer's yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 12.0 Å
Authorsvon Loeffelholz O / Knoops K / Ariosa A / Zhang X / Karuppasamy M / Huard K / Schoehn G / Berger I / Shan SO / Schaffitzel C
CitationJournal: Nat Struct Mol Biol / Year: 2013
Title: Structural basis of signal sequence surveillance and selection by the SRP-FtsY complex.
Authors: Ottilie von Loeffelholz / Kèvin Knoops / Aileen Ariosa / Xin Zhang / Manikandan Karuppasamy / Karine Huard / Guy Schoehn / Imre Berger / Shu-ou Shan / Christiane Schaffitzel /
Abstract: Signal-recognition particle (SRP)-dependent targeting of translating ribosomes to membranes is a multistep quality-control process. Ribosomes that are translating weakly hydrophobic signal sequences ...Signal-recognition particle (SRP)-dependent targeting of translating ribosomes to membranes is a multistep quality-control process. Ribosomes that are translating weakly hydrophobic signal sequences can be rejected from the targeting reaction even after they are bound to the SRP. Here we show that the early complex, formed by Escherichia coli SRP and its receptor FtsY with ribosomes translating the incorrect cargo EspP, is unstable and rearranges inefficiently into subsequent conformational states, such that FtsY dissociation is favored over successful targeting. The N-terminal extension of EspP is responsible for these defects in the early targeting complex. The cryo-electron microscopy structure of this 'false' early complex with EspP revealed an ordered M domain of SRP protein Ffh making two ribosomal contacts, and the NG domains of Ffh and FtsY forming a distorted, flexible heterodimer. Our results provide a structural basis for SRP-mediated signal-sequence selection during recruitment of the SRP receptor.
History
DepositionFeb 13, 2013-
Header (metadata) releaseFeb 27, 2013-
Map releaseFeb 26, 2014-
UpdateFeb 26, 2014-
Current statusFeb 26, 2014Processing site: PDBe / Status: Released

-
Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.00016
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by height
  • Surface level: 0.00016
  • Imaged by UCSF Chimera
  • Download
  • Surface view with fitted model
  • Atomic models: PDB-3zn8
  • Surface level: 0.00015
  • Imaged by UCSF Chimera
  • Download
  • Simplified surface model + fitted atomic model
  • Atomic modelsPDB-3zn8
  • Imaged by Jmol
  • Download
Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

2316-view_2....

Downloads & links

-
Map

FileDownload / File: emd_2316.map.gz / Format: CCP4 / Size: 12.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationRNCEspP-SRP-FtsY
Voxel sizeX=Y=Z: 3.75 Å
Density
Contour LevelBy EMDB: 0.00015 / Movie #1: 0.00016
Minimum - Maximum-0.00068688 - 0.00097974
Average (Standard dev.)0.00006962 (±0.00004827)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions150150150
Spacing150150150
CellA=B=C: 562.5 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z3.753.753.75
M x/y/z150150150
origin x/y/z0.0000.0000.000
length x/y/z562.500562.500562.500
α/β/γ90.00090.00090.000
start NX/NY/NZ-36-12-40
NX/NY/NZ732581
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS150150150
D min/max/mean-0.0010.0010.000

-
Supplemental data

-
Sample components

-
Entire : Ribosome-SRP-FtsY complex with EspP nascent chain

EntireName: Ribosome-SRP-FtsY complex with EspP nascent chain
Components
  • Sample: Ribosome-SRP-FtsY complex with EspP nascent chain
  • Complex: 70S ribosomeRibosome
  • Protein or peptide: SIGNAL RECOGNITION PARTICLE PROTEIN
  • Protein or peptide: SIGNAL RECOGNITION PARTICLE RECEPTOR FTSY
  • Protein or peptide: 4.5 S RNA
  • Protein or peptide: SIGNAL RECOGNITION PARTICLE 54 KDA PROTEIN
  • Protein or peptide: DIPEPTIDYL AMINOPEPTIDASE B

-
Supramolecule #1000: Ribosome-SRP-FtsY complex with EspP nascent chain

SupramoleculeName: Ribosome-SRP-FtsY complex with EspP nascent chain / type: sample / ID: 1000 / Details: monodisperse / Oligomeric state: monomer / Number unique components: 6
Molecular weightExperimental: 2.65 MDa / Theoretical: 2.65 MDa

-
Supramolecule #1: 70S ribosome

SupramoleculeName: 70S ribosome / type: complex / ID: 1 / Details: EspP nascent chain construct translating ribosome / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL
Source (natural)Organism: Escherichia coli (E. coli) / Location in cell: cytosol
Molecular weightExperimental: 2.5 MDa / Theoretical: 2.5 MDa

-
Macromolecule #1: SIGNAL RECOGNITION PARTICLE PROTEIN

MacromoleculeName: SIGNAL RECOGNITION PARTICLE PROTEIN / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria) / Recombinant strain: star

-
Macromolecule #2: SIGNAL RECOGNITION PARTICLE RECEPTOR FTSY

MacromoleculeName: SIGNAL RECOGNITION PARTICLE RECEPTOR FTSY / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli)
Molecular weightExperimental: 145 KDa / Theoretical: 145 KDa
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria) / Recombinant strain: star

-
Macromolecule #3: 4.5 S RNA

MacromoleculeName: 4.5 S RNA / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Escherichia coli (E. coli)
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria) / Recombinant strain: star

-
Macromolecule #4: SIGNAL RECOGNITION PARTICLE 54 KDA PROTEIN

MacromoleculeName: SIGNAL RECOGNITION PARTICLE 54 KDA PROTEIN / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Sulfolobus solfataricus (archaea)
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria) / Recombinant strain: star

-
Macromolecule #5: DIPEPTIDYL AMINOPEPTIDASE B

MacromoleculeName: DIPEPTIDYL AMINOPEPTIDASE B / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes
Source (natural)Organism: Saccharomyces cerevisiae (brewer's yeast)
Recombinant expressionOrganism: Escherichia coli BL21 (bacteria) / Recombinant strain: star

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.5
Details: 50 mM Hepes-KOH, 100 mM KOAc, 8 mM Mg(OAc)2, pH 7.5
VitrificationCryogen name: NITROGEN / Chamber humidity: 100 % / Chamber temperature: 77 K / Instrument: FEI VITROBOT MARK IV
Method: grids were glow discharged on both sides for 30 s, blottime 1s, blotforce 1

-
Electron microscopy

MicroscopeFEI POLARA 300
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsCalibrated magnification: 76000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Cs: 2.3 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 76000
Sample stageSpecimen holder: Nitrogen cooled, Polara multi-specimen holder
Specimen holder model: OTHER
TemperatureMin: 77 K / Max: 80 K / Average: 78 K
Alignment procedureLegacy - Astigmatism: correction based on power spectrum from images taken at 100000 x magnification
Detailslow dose
DateJan 11, 2011
Image recordingCategory: CCD / Film or detector model: GENERIC GATAN (4k x 4k) / Digitization - Sampling interval: 15 µm / Number real images: 1974 / Average electron dose: 15 e/Å2 / Camera length: 61.44 / Details: Images recorded on CCD camera / Bits/pixel: 32
Tilt angle min0
Experimental equipment
Model: Tecnai Polara / Image courtesy: FEI Company

-
Image processing

CTF correctionDetails: phase flipping
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 12.0 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: Spider / Number images used: 46945
Detailssemi automatic particle picking from phase flipped images

+
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