+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3245 | |||||||||
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Title | Density map of the Sec61 channel opened by a signal sequence | |||||||||
Map data | This is the final postprocessed, sharpened, and masked map. | |||||||||
Sample |
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Keywords | ribosome / Sec61 / translocation / signal sequence | |||||||||
Function / homology | Function and homology information : / Growth hormone receptor signaling / long-day photoperiodism / response to external biotic stimulus / negative regulation of nitric oxide mediated signal transduction / peptide hormone secretion / prolactin receptor binding / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / membrane docking / positive regulation of lactation ...: / Growth hormone receptor signaling / long-day photoperiodism / response to external biotic stimulus / negative regulation of nitric oxide mediated signal transduction / peptide hormone secretion / prolactin receptor binding / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / membrane docking / positive regulation of lactation / regulation of meiotic cell cycle process involved in oocyte maturation / pronephric nephron development / response to L-arginine / cotranslational protein targeting to membrane / Ssh1 translocon complex / Sec61 translocon complex / protein targeting to ER / protein insertion into ER membrane / positive regulation of fatty acid biosynthetic process / mammary gland development / signal transduction involved in regulation of gene expression / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / post-translational protein targeting to membrane, translocation / blastocyst formation / response to food / biosynthetic process / positive regulation of endocytosis / protein transmembrane transporter activity / response to mechanical stimulus / lactation / response to nutrient levels / female pregnancy / positive regulation of receptor signaling pathway via JAK-STAT / positive regulation of non-canonical NF-kappaB signal transduction / hormone activity / phospholipid binding / positive regulation of nitric oxide biosynthetic process / ribosome binding / positive regulation of NF-kappaB transcription factor activity / endoplasmic reticulum lumen / negative regulation of gene expression / positive regulation of cell population proliferation / endoplasmic reticulum membrane / positive regulation of gene expression / negative regulation of apoptotic process / extracellular space / extracellular region / cytosol Similarity search - Function | |||||||||
Biological species | Canis lupus (gray wolf) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.6 Å | |||||||||
Authors | Voorhees RM / Hegde RS | |||||||||
Citation | Journal: Science / Year: 2016 Title: Structure of the Sec61 channel opened by a signal sequence. Authors: Rebecca M Voorhees / Ramanujan S Hegde / Abstract: Secreted and integral membrane proteins compose up to one-third of the biological proteome. These proteins contain hydrophobic signals that direct their translocation across or insertion into the ...Secreted and integral membrane proteins compose up to one-third of the biological proteome. These proteins contain hydrophobic signals that direct their translocation across or insertion into the lipid bilayer by the Sec61 protein-conducting channel. The molecular basis of how hydrophobic signals within a nascent polypeptide trigger channel opening is not understood. Here, we used cryo-electron microscopy to determine the structure of an active Sec61 channel that has been opened by a signal sequence. The signal supplants helix 2 of Sec61α, which triggers a rotation that opens the central pore both axially across the membrane and laterally toward the lipid bilayer. Comparisons with structures of Sec61 in other states suggest a pathway for how hydrophobic signals engage the channel to gain access to the lipid bilayer. | |||||||||
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_3245.map.gz | 31.1 MB | EMDB map data format | |
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Header (meta data) | emd-3245-v30.xml emd-3245.xml | 10.8 KB 10.8 KB | Display Display | EMDB header |
Images | EMD-3245_overview_map.png | 631.8 KB | ||
Others | emd_3245_half_map_1.map.gz emd_3245_half_map_2.map.gz | 225 MB 225 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3245 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3245 | HTTPS FTP |
-Validation report
Summary document | emd_3245_validation.pdf.gz | 339.9 KB | Display | EMDB validaton report |
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Full document | emd_3245_full_validation.pdf.gz | 339.5 KB | Display | |
Data in XML | emd_3245_validation.xml.gz | 7.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3245 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-3245 | HTTPS FTP |
-Related structure data
Related structure data | 3jc2MC 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_3245.map.gz / Format: CCP4 / Size: 276 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This is the final postprocessed, sharpened, and masked map. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Supplemental map: emd 3245 half map 1.map
File | emd_3245_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Supplemental map: emd 3245 half map 2.map
File | emd_3245_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : The stalled mammalian Sec61 complex opened by the pre-prolactin s...
Entire | Name: The stalled mammalian Sec61 complex opened by the pre-prolactin signal sequence. |
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Components |
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-Supramolecule #1000: The stalled mammalian Sec61 complex opened by the pre-prolactin s...
Supramolecule | Name: The stalled mammalian Sec61 complex opened by the pre-prolactin signal sequence. type: sample / ID: 1000 / Details: The sample was monodisperse / Oligomeric state: monomer / Number unique components: 2 |
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-Supramolecule #1: mammalian ribosome
Supramolecule | Name: mammalian ribosome / type: complex / ID: 1 / Name.synonym: 80S ribosome / Recombinant expression: No / Ribosome-details: ribosome-eukaryote: ALL |
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Source (natural) | Organism: Canis lupus (gray wolf) / synonym: Dog / Tissue: pancreas / Organelle: Endoplasmic Reticulum / Location in cell: Endoplasmic Reticulum |
-Macromolecule #1: Sec61 channel
Macromolecule | Name: Sec61 channel / type: protein_or_peptide / ID: 1 / Name.synonym: Sec61 translocon / Details: The heterotrimeric mammalian Sec61 channel / Number of copies: 1 / Oligomeric state: monomer / Recombinant expression: No |
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Source (natural) | Organism: Canis lupus (gray wolf) / synonym: Dog / Tissue: pancreas / Organelle: Endoplasmic reticulum / Location in cell: Endoplasmic reticulum |
-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 pH 7.5, 200 mM KOAc, 15 mM MgOAc2, 1 mM DTT, 0.25% digitonin |
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Grid | Details: 400 mesh holey carbon grid coated with a continuous layer of amorphous carbon |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Instrument: FEI VITROBOT MARK II Method: Incubate for 30 seconds at 4 C and blot for 9 seconds before plunging |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Alignment procedure | Legacy - Astigmatism: Objective astigmatism was corrected at 60,000 times magnification |
Date | Mar 9, 2015 |
Image recording | Category: CCD / Film or detector model: FEI FALCON II (4k x 4k) / Number real images: 1489 / Average electron dose: 27 e/Å2 Details: Every image is the average of 17 frames recorded by the direct electron detector. |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 2.0 µm / Nominal magnification: 59000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Details | The particles were selected using the automated particle selection in Relion. |
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CTF correction | Details: Each particle |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Algorithm: OTHER / Resolution.type: BY AUTHOR / Resolution: 3.6 Å / Resolution method: OTHER / Software - Name: Relion / Number images used: 101339 |
Final two d classification | Number classes: 5 |
-Atomic model buiding 1
Initial model | PDB ID: |
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Software | Name: Chimera and Coot |
Refinement | Space: REAL / Protocol: RIGID BODY FIT |
Output model | PDB-3jc2: |
-Atomic model buiding 2
Initial model | PDB ID: |
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Software | Name: Chimera, coot, and Refmac |
Refinement | Space: RECIPROCAL / Protocol: FLEXIBLE FIT |
Output model | PDB-3jc2: |