- EMDB-3245: Density map of the Sec61 channel opened by a signal sequence -
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Basic information
Entry
Database: EMDB / ID: EMD-3245
Title
Density map of the Sec61 channel opened by a signal sequence
Map data
This is the final postprocessed, sharpened, and masked map.
Sample
Sample: The stalled mammalian Sec61 complex opened by the pre-prolactin signal sequence.
Complex: mammalian ribosome
Protein or peptide: Sec61 channel
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 / signal sequence binding / blastocyst formation / SRP-dependent cotranslational protein targeting to membrane, translocation / post-translational 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 / endoplasmic reticulum membrane / positive regulation of gene expression / negative regulation of apoptotic process / extracellular space / extracellular region / cytosol Similarity search - Function
Somatotropin/prolactin / Somatotropin hormone, conserved site / Somatotropin hormone family / Somatotropin, prolactin and related hormones signature 1. / Somatotropin, prolactin and related hormones signature 2. / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Protein secE/sec61-gamma signature. ...Somatotropin/prolactin / Somatotropin hormone, conserved site / Somatotropin hormone family / Somatotropin, prolactin and related hormones signature 1. / Somatotropin, prolactin and related hormones signature 2. / Protein translocase SEC61 complex, gamma subunit / Protein translocase SecE domain superfamily / Translocon Sec61/SecY, plug domain / Plug domain of Sec61p / Protein secE/sec61-gamma signature. / Protein secY signature 1. / Protein secY signature 2. / SecE/Sec61-gamma subunits of protein translocation complex / Protein translocase complex, SecE/Sec61-gamma subunit / SecY/SEC61-alpha family / SecY domain superfamily / SecY conserved site / SecY / Four-helical cytokine-like, core Similarity search - Domain/homology
Prolactin / Protein transport protein Sec61 subunit alpha isoform 1 / Protein transport protein Sec61 subunit gamma / Prolactin Similarity search - Component
Biological species
Canis lupus (gray wolf)
Method
single particle reconstruction / cryo EM / Resolution: 3.6 Å
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
Deposition
Nov 14, 2015
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Header (metadata) release
Nov 25, 2015
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Map release
Jan 13, 2016
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Update
Jan 13, 2016
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Current status
Jan 13, 2016
Processing site: PDBe / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
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.
Components
Sample: The stalled mammalian Sec61 complex opened by the pre-prolactin signal sequence.
Complex: mammalian ribosome
Protein or peptide: Sec61 channel
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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
pH: 7.5 Details: 50 mM HEPES pH 7.5, 200 mM KOAc, 15 mM MgOAc2, 1 mM DTT, 0.25% digitonin
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
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Electron microscopy
Microscope
FEI TITAN KRIOS
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
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