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Yorodumi- EMDB-2316: Structural Basis of Signal Sequence Surveillance and Selection by... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-2316 | |||||||||
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Title | Structural Basis of Signal Sequence Surveillance and Selection by the SRP-SR Complex | |||||||||
Map data | RNCEspP-SRP-FtsY | |||||||||
Sample |
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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 / signal-recognition-particle GTPase / 7S RNA binding / SRP-dependent cotranslational protein targeting to membrane / dipeptidyl-peptidase activity / fungal-type vacuole membrane / 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 / dipeptidyl-peptidase activity / fungal-type vacuole membrane / 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 | |||||||||
Biological species | Escherichia coli (E. coli) / Sulfolobus solfataricus (archaea) / Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 12.0 Å | |||||||||
Authors | von Loeffelholz O / Knoops K / Ariosa A / Zhang X / Karuppasamy M / Huard K / Schoehn G / Berger I / Shan SO / Schaffitzel C | |||||||||
Citation | 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 |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_2316.map.gz | 1.6 MB | EMDB map data format | |
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Header (meta data) | emd-2316-v30.xml emd-2316.xml | 13.9 KB 13.9 KB | Display Display | EMDB header |
Images | 2316-view_2.png | 168.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-2316 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-2316 | HTTPS FTP |
-Validation report
Summary document | emd_2316_validation.pdf.gz | 241.5 KB | Display | EMDB validaton report |
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Full document | emd_2316_full_validation.pdf.gz | 240.6 KB | Display | |
Data in XML | emd_2316_validation.xml.gz | 4.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2316 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-2316 | HTTPS FTP |
-Related structure data
Related structure data | 3zn8MC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_2316.map.gz / Format: CCP4 / Size: 12.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | RNCEspP-SRP-FtsY | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 3.75 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : Ribosome-SRP-FtsY complex with EspP nascent chain
Entire | Name: Ribosome-SRP-FtsY complex with EspP nascent chain |
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Components |
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-Supramolecule #1000: Ribosome-SRP-FtsY complex with EspP nascent chain
Supramolecule | Name: Ribosome-SRP-FtsY complex with EspP nascent chain / type: sample / ID: 1000 / Details: monodisperse / Oligomeric state: monomer / Number unique components: 6 |
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Molecular weight | Experimental: 2.65 MDa / Theoretical: 2.65 MDa |
-Supramolecule #1: 70S ribosome
Supramolecule | Name: 70S ribosome / type: complex / ID: 1 / Details: EspP nascent chain construct translating ribosome / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: ALL |
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Source (natural) | Organism: Escherichia coli (E. coli) / Location in cell: cytosol |
Molecular weight | Experimental: 2.5 MDa / Theoretical: 2.5 MDa |
-Macromolecule #1: SIGNAL RECOGNITION PARTICLE PROTEIN
Macromolecule | Name: SIGNAL RECOGNITION PARTICLE PROTEIN / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) / Recombinant strain: star |
-Macromolecule #2: SIGNAL RECOGNITION PARTICLE RECEPTOR FTSY
Macromolecule | Name: SIGNAL RECOGNITION PARTICLE RECEPTOR FTSY / type: protein_or_peptide / ID: 2 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Molecular weight | Experimental: 145 KDa / Theoretical: 145 KDa |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) / Recombinant strain: star |
-Macromolecule #3: 4.5 S RNA
Macromolecule | Name: 4.5 S RNA / type: protein_or_peptide / ID: 3 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Escherichia coli (E. coli) |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) / Recombinant strain: star |
-Macromolecule #4: SIGNAL RECOGNITION PARTICLE 54 KDA PROTEIN
Macromolecule | Name: SIGNAL RECOGNITION PARTICLE 54 KDA PROTEIN / type: protein_or_peptide / ID: 4 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Sulfolobus solfataricus (archaea) |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) / Recombinant strain: star |
-Macromolecule #5: DIPEPTIDYL AMINOPEPTIDASE B
Macromolecule | Name: DIPEPTIDYL AMINOPEPTIDASE B / type: protein_or_peptide / ID: 5 / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: Yes |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Recombinant expression | Organism: Escherichia coli BL21 (bacteria) / Recombinant strain: star |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 Details: 50 mM Hepes-KOH, 100 mM KOAc, 8 mM Mg(OAc)2, pH 7.5 |
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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 |
-Electron microscopy
Microscope | FEI POLARA 300 |
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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 |
Electron optics | Calibrated magnification: 76000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.3 mm / Nominal defocus max: 5.0 µm / Nominal defocus min: 0.7 µm / Nominal magnification: 76000 |
Sample stage | Specimen holder: Nitrogen cooled, Polara multi-specimen holder Specimen holder model: OTHER |
Experimental equipment | Model: Tecnai Polara / Image courtesy: FEI Company |
-Image processing
Details | semi automatic particle picking from phase flipped images |
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CTF correction | Details: phase flipping |
Final reconstruction | Applied 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 |