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Basic information
Entry | Database: EMDB / ID: EMD-1143 | |||||||||
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Title | Structure of the E. coli protein-conducting channel bound to a translating ribosome. | |||||||||
![]() | EM map of the E.coli proten-conducting channel bound to a translating ribosome | |||||||||
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Function / homology | ![]() protein insertion into membrane from inner side / cell envelope Sec protein transport complex / protein transport by the Sec complex / intracellular protein transmembrane transport / protein-transporting ATPase activity / signal sequence binding / SRP-dependent cotranslational protein targeting to membrane, translocation / stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity ...protein insertion into membrane from inner side / cell envelope Sec protein transport complex / protein transport by the Sec complex / intracellular protein transmembrane transport / protein-transporting ATPase activity / signal sequence binding / SRP-dependent cotranslational protein targeting to membrane, translocation / stringent response / mRNA base-pairing translational repressor activity / ornithine decarboxylase inhibitor activity / transcription antitermination factor activity, RNA binding / misfolded RNA binding / Group I intron splicing / RNA folding / protein secretion / protein transmembrane transporter activity / transcriptional attenuation / endoribonuclease inhibitor activity / RNA-binding transcription regulator activity / protein targeting / positive regulation of ribosome biogenesis / negative regulation of cytoplasmic translation / translational termination / DnaA-L2 complex / four-way junction DNA binding / translation repressor activity / negative regulation of translational initiation / negative regulation of DNA-templated DNA replication initiation / regulation of mRNA stability / ribosome assembly / mRNA regulatory element binding translation repressor activity / positive regulation of RNA splicing / assembly of large subunit precursor of preribosome / transcription elongation factor complex / DNA endonuclease activity / cytosolic ribosome assembly / regulation of DNA-templated transcription elongation / transcription antitermination / response to reactive oxygen species / regulation of cell growth / DNA-templated transcription termination / maintenance of translational fidelity / intracellular protein transport / response to radiation / ribosomal large subunit assembly / mRNA 5'-UTR binding / large ribosomal subunit / ribosome biogenesis / ribosome binding / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / transferase activity / 5S rRNA binding / large ribosomal subunit rRNA binding / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / membrane => GO:0016020 / tRNA binding / molecular adaptor activity / cytoplasmic translation / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / translation / response to antibiotic / negative regulation of DNA-templated transcription / mRNA binding / protein homodimerization activity / DNA binding / RNA binding / zinc ion binding / membrane / plasma membrane / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 14.9 Å | |||||||||
![]() | Mitra K / Schaffitzel C / Shaikh T / Tama F / Jenni S / Brooks III CL / Ban N / Frank J | |||||||||
![]() | ![]() Title: Structure of the E. coli protein-conducting channel bound to a translating ribosome. Authors: Kakoli Mitra / Christiane Schaffitzel / Tanvir Shaikh / Florence Tama / Simon Jenni / Charles L Brooks / Nenad Ban / Joachim Frank / ![]() Abstract: Secreted and membrane proteins are translocated across or into cell membranes through a protein-conducting channel (PCC). Here we present a cryo-electron microscopy reconstruction of the Escherichia ...Secreted and membrane proteins are translocated across or into cell membranes through a protein-conducting channel (PCC). Here we present a cryo-electron microscopy reconstruction of the Escherichia coli PCC, SecYEG, complexed with the ribosome and a nascent chain containing a signal anchor. This reconstruction shows a messenger RNA, three transfer RNAs, the nascent chain, and detailed features of both a translocating PCC and a second, non-translocating PCC bound to mRNA hairpins. The translocating PCC forms connections with ribosomal RNA hairpins on two sides and ribosomal proteins at the back, leaving a frontal opening. Normal mode-based flexible fitting of the archaeal SecYEbeta structure into the PCC electron microscopy densities favours a front-to-front arrangement of two SecYEG complexes in the PCC, and supports channel formation by the opening of two linked SecY halves during polypeptide translocation. On the basis of our observation in the translocating PCC of two segregated pores with different degrees of access to bulk lipid, we propose a model for co-translational protein translocation. | |||||||||
History |
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Structure visualization
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 6.2 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 14.3 KB 14.3 KB | Display Display | ![]() |
Images | ![]() | 67.6 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 317.4 KB | Display | ![]() |
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Full document | ![]() | 317 KB | Display | |
Data in XML | ![]() | 5.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2akhMC ![]() 2akiMC ![]() 4v4wM M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | EM map of the E.coli proten-conducting channel bound to a translating ribosome | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size |
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Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
-Entire : co-translational E. coli 70S ribosome-nascent chain complexed wit...
Entire | Name: co-translational E. coli 70S ribosome-nascent chain complexed with SecYEG |
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Components |
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-Supramolecule #1000: co-translational E. coli 70S ribosome-nascent chain complexed wit...
Supramolecule | Name: co-translational E. coli 70S ribosome-nascent chain complexed with SecYEG type: sample / ID: 1000 / Number unique components: 8 |
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-Supramolecule #1: 30S
Supramolecule | Name: 30S / type: complex / ID: 1 / Name.synonym: small subunit / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: SSU 30S |
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Source (natural) | Organism: ![]() ![]() |
-Supramolecule #2: 50S
Supramolecule | Name: 50S / type: complex / ID: 2 / Name.synonym: large subunit / Recombinant expression: No / Ribosome-details: ribosome-prokaryote: LSU 50S |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #1: A-site tRNA
Macromolecule | Name: A-site tRNA / type: rna / ID: 1 / Classification: OTHER / Structure: DOUBLE HELIX / Synthetic?: No |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #2: P-site tRNA
Macromolecule | Name: P-site tRNA / type: rna / ID: 2 / Classification: OTHER / Structure: DOUBLE HELIX / Synthetic?: No |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #3: E-site tRNA
Macromolecule | Name: E-site tRNA / type: rna / ID: 3 / Classification: OTHER / Structure: DOUBLE HELIX / Synthetic?: No |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #4: mRNA
Macromolecule | Name: mRNA / type: rna / ID: 4 / Classification: OTHER / Structure: SINGLE STRANDED / Synthetic?: Yes |
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Source (natural) | Organism: ![]() ![]() |
-Macromolecule #5: protein-conducting channel
Macromolecule | Name: protein-conducting channel / type: protein_or_peptide / ID: 5 / Name.synonym: translocon, SecYEG / Number of copies: 2 / Oligomeric state: dimer of heterotrimer / Recombinant expression: Yes |
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Source (natural) | Organism: ![]() ![]() |
Recombinant expression | Organism: ![]() ![]() |
-Macromolecule #6: nascent chain
Macromolecule | Name: nascent chain / type: protein_or_peptide / ID: 6 / Details: Strep-II-FtsQ-SecM construct / Recombinant expression: Yes |
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Source (natural) | Organism: unidentified (others) / synonym: translocon |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Vitrification | Cryogen name: ETHANE / Chamber humidity: 90 % / Chamber temperature: 93 K / Instrument: HOMEMADE PLUNGER Details: Vitrification instrument: two sided blotting plunger Method: Blot for 2 seconds before plunging |
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Electron microscopy
Microscope | FEI TECNAI F30 |
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Temperature | Average: 93 K |
Date | Mar 9, 2004 |
Image recording | Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: ZEISS SCAI / Digitization - Sampling interval: 14 µm / Number real images: 385 / Average electron dose: 11 e/Å2 / Od range: 1.2 / Bits/pixel: 12 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 39000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.26 mm / Nominal defocus max: 4.3 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 39000 |
Sample stage | Specimen holder: Cryo stage / Specimen holder model: OTHER |
Experimental equipment | ![]() Model: Tecnai F30 / Image courtesy: FEI Company |
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Image processing
CTF correction | Details: defocus groups |
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Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 14.9 Å / Resolution method: FSC 0.5 CUT-OFF / Software - Name: SPIDER package Details: The falloff of Fourier amplitudes toward higher spatial frequencies was corrected using the x-ray solution scattering intensity distribution of 70S ribosomes from E. coli during each round of refinement Number images used: 53325 |
Final angle assignment | Details: SPIDER: theta 15 degrees, phi 15 degrees |
-Atomic model buiding 1
Details | Protocol: normal mode-based flexible fitting. Fitting of SecYEG atomic model into isolated EM density of protein-conducting channels |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: correlation coefficient |
Output model | ![]() PDB-2akh: ![]() PDB-2aki: ![]() PDB-4v4w: |
-Atomic model buiding 2
Details | Protocol: normal mode-based flexible fitting. Fitting of SecYEG atomic model into isolated EM density of protein-conducting channels |
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Refinement | Space: REAL / Protocol: FLEXIBLE FIT / Target criteria: correlation coefficient |
Output model | ![]() PDB-2akh: ![]() PDB-2aki: ![]() PDB-4v4w: |
-Atomic model buiding 3
Software | Name: RSR2000 |
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Details | Protocol: real space refinement |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: R-factor |
Output model | ![]() PDB-2akh: ![]() PDB-2aki: ![]() PDB-4v4w: |
-Atomic model buiding 4
Software | Name: RSR2000 |
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Details | Protocol: real space refinement |
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: R-factor |
Output model | ![]() PDB-2akh: ![]() PDB-2aki: ![]() PDB-4v4w: |