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- PDB-7kao: Cryo-EM structure of the Sec complex from S. cerevisiae, Sec61 po... -
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Basic information
Entry | Database: PDB / ID: 7kao | ||||||
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Title | Cryo-EM structure of the Sec complex from S. cerevisiae, Sec61 pore mutant, class without Sec62 | ||||||
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![]() | PROTEIN TRANSPORT / Sec61 / translocon / endoplasmic reticulum / protein translocation / Sec62 / Sec63 / channel | ||||||
Function / homology | ![]() misfolded protein transport / Sec62/Sec63 complex / translocon complex / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / cytosol to endoplasmic reticulum transport / rough endoplasmic reticulum membrane / Ssh1 translocon complex / Sec61 translocon complex / protein-transporting ATPase activity / post-translational protein targeting to endoplasmic reticulum membrane ...misfolded protein transport / Sec62/Sec63 complex / translocon complex / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / cytosol to endoplasmic reticulum transport / rough endoplasmic reticulum membrane / Ssh1 translocon complex / Sec61 translocon complex / protein-transporting ATPase activity / post-translational protein targeting to endoplasmic reticulum membrane / filamentous growth / SRP-dependent cotranslational protein targeting to membrane / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / post-translational protein targeting to membrane, translocation / peptide transmembrane transporter activity / nuclear inner membrane / retrograde protein transport, ER to cytosol / protein transmembrane transporter activity / ERAD pathway / guanyl-nucleotide exchange factor activity / cell periphery / ribosome binding / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum / mitochondrion / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4 Å | ||||||
![]() | Itskanov, S. / Park, E. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Stepwise gating of the Sec61 protein-conducting channel by Sec63 and Sec62. Authors: Samuel Itskanov / Katie M Kuo / James C Gumbart / Eunyong Park / ![]() Abstract: Many proteins are transported into the endoplasmic reticulum by the universally conserved Sec61 channel. Post-translational transport requires two additional proteins, Sec62 and Sec63, but their ...Many proteins are transported into the endoplasmic reticulum by the universally conserved Sec61 channel. Post-translational transport requires two additional proteins, Sec62 and Sec63, but their functions are poorly defined. In the present study, we determined cryo-electron microscopy (cryo-EM) structures of several variants of Sec61-Sec62-Sec63 complexes from Saccharomyces cerevisiae and Thermomyces lanuginosus and show that Sec62 and Sec63 induce opening of the Sec61 channel. Without Sec62, the translocation pore of Sec61 remains closed by the plug domain, rendering the channel inactive. We further show that the lateral gate of Sec61 must first be partially opened by interactions between Sec61 and Sec63 in cytosolic and luminal domains, a simultaneous disruption of which completely closes the channel. The structures and molecular dynamics simulations suggest that Sec62 may also prevent lipids from invading the channel through the open lateral gate. Our study shows how Sec63 and Sec62 work together in a hierarchical manner to activate Sec61 for post-translational protein translocation. | ||||||
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 | ![]() | 250.4 KB | Display | ![]() |
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PDB format | ![]() | 194.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 22778MC ![]() 7kahC ![]() 7kaiC ![]() 7kajC ![]() 7kakC ![]() 7kalC ![]() 7kamC ![]() 7kanC ![]() 7kapC ![]() 7kaqC ![]() 7karC ![]() 7kasC ![]() 7katC ![]() 7kauC ![]() 7kb5C 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
-Protein transport protein ... , 3 types, 3 molecules ACB
#1: Protein | Mass: 52936.086 Da / Num. of mol.: 1 / Mutation: M90L, T185I, M294I, M450L Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: ATCC 204508 / S288c / Gene: SEC61, YLR378C, L3502.5 / Plasmid details: SEC63 is chromosomally tagged with TEV-GFP / Production host: ![]() ![]() |
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#2: Protein | Mass: 8958.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Plasmid details: SEC63 is chromosomally tagged with TEV-GFP / Strain: ATCC 204508 / S288c / References: UniProt: P35179 |
#3: Protein | Mass: 8723.155 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Plasmid details: SEC63 is chromosomally tagged with TEV-GFP / Strain: ATCC 204508 / S288c / References: UniProt: P52870 |
-Protein , 1 types, 1 molecules D
#4: Protein | Mass: 75301.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Plasmid details: SEC63 is chromosomally tagged with TEV-GFP / Strain: ATCC 204508 / S288c / References: UniProt: P14906 |
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-Translocation protein ... , 2 types, 2 molecules EF
#5: Protein | Mass: 24263.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Plasmid details: SEC63 is chromosomally tagged with TEV-GFP / Strain: ATCC 204508 / S288c / References: UniProt: P33754 |
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#6: Protein | Mass: 21631.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) ![]() ![]() Plasmid details: SEC63 is chromosomally tagged with TEV-GFP / Strain: ATCC 204508 / S288c / References: UniProt: P39742 |
-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
Component | Name: Endoplasmic reticulum protein-transport machinery Sec complex from yeast with Sec61 pore ring mutated. Type: COMPLEX Details: Sec61 has the following mutations: M90L/T185I/M294I/M450L Entity ID: all / Source: MULTIPLE SOURCES |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: ![]() ![]() |
Buffer solution | pH: 7.5 |
Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Grid material: GOLD / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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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 |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Calibrated magnification: 43478 X / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 48.8 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
EM imaging optics | Energyfilter name: GIF Quantum LS / Energyfilter slit width: 20 eV |
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Processing
Software | Name: PHENIX / Version: 1.16_3549: / Classification: refinement | ||||||||||||||||||||||||||||||||
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EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 195915 / Details: autopicked particles | ||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 35573 / Algorithm: FOURIER SPACE / Symmetry type: POINT | ||||||||||||||||||||||||||||||||
Refine LS restraints |
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