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Yorodumi- PDB-7aft: Cryo-EM structure of the signal sequence-engaged post-translation... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7aft | ||||||
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Title | Cryo-EM structure of the signal sequence-engaged post-translational Sec translocon | ||||||
Components |
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Keywords | MEMBRANE PROTEIN / Post-translational translocation / Protein translocation / Sec complex / Signal sequence | ||||||
Function / homology | Function and homology information mating pheromone activity / mating / protein transmembrane import into intracellular organelle / misfolded protein transport / pheromone-dependent signal transduction involved in conjugation with cellular fusion / Sec62/Sec63 complex / translocon complex / cytosol to endoplasmic reticulum transport / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / rough endoplasmic reticulum membrane ...mating pheromone activity / mating / protein transmembrane import into intracellular organelle / misfolded protein transport / pheromone-dependent signal transduction involved in conjugation with cellular fusion / Sec62/Sec63 complex / translocon complex / cytosol to endoplasmic reticulum transport / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / 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, translocation / peptide transmembrane transporter activity / signal sequence binding / SRP-dependent cotranslational protein targeting to membrane / post-translational protein targeting to membrane, translocation / cupric ion binding / nuclear inner membrane / retrograde protein transport, ER to cytosol / protein transmembrane transporter activity / : / guanyl-nucleotide exchange factor activity / cell periphery / ribosome binding / endoplasmic reticulum membrane / structural molecule activity / endoplasmic reticulum / mitochondrion / extracellular region / membrane / cytosol Similarity search - Function | ||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.4 Å | ||||||
Authors | Weng, T.-H. / Beatrix, B. / Berninghausen, O. / Becker, T. / Cheng, J. / Beckmann, R. | ||||||
Citation | Journal: EMBO J / Year: 2021 Title: Architecture of the active post-translational Sec translocon. Authors: Tsai-Hsuan Weng / Wieland Steinchen / Birgitta Beatrix / Otto Berninghausen / Thomas Becker / Gert Bange / Jingdong Cheng / Roland Beckmann / Abstract: In eukaryotes, most secretory and membrane proteins are targeted by an N-terminal signal sequence to the endoplasmic reticulum, where the trimeric Sec61 complex serves as protein-conducting channel ...In eukaryotes, most secretory and membrane proteins are targeted by an N-terminal signal sequence to the endoplasmic reticulum, where the trimeric Sec61 complex serves as protein-conducting channel (PCC). In the post-translational mode, fully synthesized proteins are recognized by a specialized channel additionally containing the Sec62, Sec63, Sec71, and Sec72 subunits. Recent structures of this Sec complex in the idle state revealed the overall architecture in a pre-opened state. Here, we present a cryo-EM structure of the yeast Sec complex bound to a substrate, and a crystal structure of the Sec62 cytosolic domain. The signal sequence is inserted into the lateral gate of Sec61α similar to previous structures, yet, with the gate adopting an even more open conformation. The signal sequence is flanked by two Sec62 transmembrane helices, the cytoplasmic N-terminal domain of Sec62 is more rigidly positioned, and the plug domain is relocated. We crystallized the Sec62 domain and mapped its interaction with the C-terminus of Sec63. Together, we obtained a near-complete and integrated model of the active Sec complex. | ||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 7aft.cif.gz | 214 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7aft.ent.gz | 142.6 KB | Display | PDB format |
PDBx/mmJSON format | 7aft.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/af/7aft ftp://data.pdbj.org/pub/pdb/validation_reports/af/7aft | HTTPS FTP |
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-Related structure data
Related structure data | 11774MC 6zzzC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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-Components
-Protein transport protein ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 52978.148 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P32915 |
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#2: Protein | Mass: 8723.155 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P52870 |
#3: Protein | Mass: 8958.641 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P35179 |
-Protein , 2 types, 2 molecules DH
#4: Protein | Mass: 75432.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P14906 |
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#8: Protein | Mass: 19766.402 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: MF(ALPHA)1, MF-ALPHA-1, MFAL1, YPL187W / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P01149 |
-Translocation protein ... , 3 types, 3 molecules EFG
#5: Protein | Mass: 24263.939 Da / Num. of mol.: 1 / Source method: isolated from a natural source Source: (natural) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) 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) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / References: UniProt: P39742 |
#7: Protein | Mass: 35649.891 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: The residue numbering in chain G is based on the transmembrane helix prediction of Sec62. Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: SEC62, YPL094C, LPG14C / Production host: Saccharomyces cerevisiae (brewer's yeast) / References: UniProt: P21825 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
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Molecular weight | Value: 0.255 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) |
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Buffer solution | pH: 7.4 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||
Specimen support | Grid material: GOLD / Grid type: UltrAuFoil R2/2 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM | ||||||||||||||||||
Electron lens | Mode: BRIGHT FIELDBright-field microscopy | ||||||||||||||||||
Image recording |
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Image scans | Movie frames/image: 40 |
-Processing
Software | Name: PHENIX / Version: 1.17.1_3660: / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Image processing |
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CTF correction |
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3D reconstruction | Algorithm: FOURIER SPACE / Entry-ID: 7AFT / Resolution: 4.4 Å / Resolution method: FSC 0.143 CUT-OFF / Symmetry type: POINT
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Atomic model building | Protocol: RIGID BODY FIT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6N3Q | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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