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- PDB-3jc2: The structure of the mammalian Sec61 channel opened by a signal s... -
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Basic information
Entry | Database: PDB / ID: 3jc2 | ||||||
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Title | The structure of the mammalian Sec61 channel opened by a signal sequence | ||||||
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![]() | TRANSPORT PROTEIN / Sec61 / translocation / signal sequence | ||||||
Function / homology | ![]() : / 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 / blastocyst formation / signal sequence binding / post-translational protein targeting to membrane, translocation / SRP-dependent cotranslational protein targeting to membrane, translocation / 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 / hormone activity / phospholipid binding / positive regulation of non-canonical NF-kappaB signal transduction / 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 / positive regulation of gene expression / endoplasmic reticulum membrane / negative regulation of apoptotic process / extracellular space / extracellular region / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.6 Å | ||||||
![]() | Voorhees, R.M. / Hegde, R.S. | ||||||
![]() | ![]() 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
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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PDBx/mmCIF format | ![]() | 106.5 KB | Display | ![]() |
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PDB format | ![]() | 85.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 751.6 KB | Display | ![]() |
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Full document | ![]() | 764.1 KB | Display | |
Data in XML | ![]() | 23.5 KB | Display | |
Data in CIF | ![]() | 33.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3245MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
#1: Protein | Mass: 52279.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: purified from native canine microsomes / Source: (natural) ![]() ![]() |
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#2: Protein | Mass: 7019.456 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: purified from native canine microsomes / Source: (natural) ![]() ![]() |
#3: Protein/peptide | Mass: 2053.576 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() Tissue fraction (production host): reticulocyte translation extract in the presence of canine microsomes References: UniProt: Q6VMP1, UniProt: P01239*PLUS |
#4: Protein/peptide | Mass: 2741.370 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: purified from native canine microsomes / Source: (natural) ![]() ![]() |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
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Buffer solution | Name: 50 mM HEPES, 200 mM potassium acetate, 15 mM magnesium acetate, 1 mM DTT, 0.25% Digitonin pH: 7.5 Details: 50 mM HEPES, 200 mM potassium acetate, 15 mM magnesium acetate, 1 mM DTT, 0.25% Digitonin | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Specimen support | Details: Quantifoil (R2/2) holey carbon grid covered in a 70 Angstrom-thick layer of amorphous carbon | ||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK I / Cryogen name: ETHANE / Humidity: 100 % Details: 3 uL sample was added to the grid, incubated for 30 seconds at 4 C, blotted for 9 seconds, and then plunged into liquid ethane (FEI VITROBOT). Method: 3 uL sample was added to the grid, incubated for 30 seconds at 4 C, blotted for 9 seconds |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Mar 6, 2015 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Calibrated magnification: 104478 X / Nominal defocus max: 3500 nm / Nominal defocus min: 2000 nm |
Image recording | Electron dose: 27 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
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Processing
EM software |
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Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||
3D reconstruction | Resolution: 3.6 Å / Num. of particles: 101339 / Nominal pixel size: 1.34 Å / Actual pixel size: 1.34 Å / Symmetry type: POINT | |||||||||||||||
Atomic model building | Space: REAL / Target criteria: R-factor Details: DETAILS--Real-space fitting using Chimera and Coot followed by reciprocal-space refinement using REFMAC | |||||||||||||||
Atomic model building |
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Refinement step | Cycle: LAST
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