- EMDB-2316: Structural Basis of Signal Sequence Surveillance and Selection by... -
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Open data
ID or keywords:
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Basic information
Entry
Database: EMDB / ID: EMD-2316
Title
Structural Basis of Signal Sequence Surveillance and Selection by the SRP-SR Complex
Map data
RNCEspP-SRP-FtsY
Sample
Sample: Ribosome-SRP-FtsY complex with EspP nascent chain
Complex: 70S ribosome
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
Keywords
Ribosome / 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 / endoplasmic reticulum signal peptide binding / signal-recognition-particle GTPase / SRP-dependent cotranslational protein targeting to membrane / 7S RNA binding / fungal-type vacuole membrane / SRP-dependent cotranslational protein targeting to membrane, translocation ...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 / endoplasmic reticulum signal peptide binding / signal-recognition-particle GTPase / SRP-dependent cotranslational protein targeting to membrane / 7S RNA binding / fungal-type vacuole membrane / SRP-dependent cotranslational protein targeting to membrane, translocation / dipeptidyl-peptidase activity / stringent response / protein targeting / aminopeptidase activity / protein processing / cytoplasmic side of plasma membrane / serine-type endopeptidase activity / GTPase activity / GTP binding / protein homodimerization activity / ATP hydrolysis 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
Journal: 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
Deposition
Feb 13, 2013
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Header (metadata) release
Feb 27, 2013
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Map release
Feb 26, 2014
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Update
Feb 26, 2014
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Current status
Feb 26, 2014
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
Organism: Escherichia coli BL21 (bacteria) / Recombinant strain: star
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Experimental details
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Structure determination
Method
cryo EM
Processing
single particle reconstruction
Aggregation state
particle
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Sample preparation
Buffer
pH: 7.5 Details: 50 mM Hepes-KOH, 100 mM KOAc, 8 mM Mg(OAc)2, pH 7.5
Vitrification
Cryogen 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
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Electron microscopy
Microscope
FEI POLARA 300
Temperature
Min: 77 K / Max: 80 K / Average: 78 K
Alignment procedure
Legacy - Astigmatism: correction based on power spectrum from images taken at 100000 x magnification
Details
low dose
Date
Jan 11, 2011
Image recording
Category: 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 min
0
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
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