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Yorodumi- PDB-8bf9: Molecular view of ER membrane remodeling by the Sec61/TRAP translocon. -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bf9 | |||||||||
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Title | Molecular view of ER membrane remodeling by the Sec61/TRAP translocon. | |||||||||
Components |
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Keywords | TRANSPORT PROTEIN / Membrane protein / protein translocation / protein biogenesis. | |||||||||
Function / homology | Function and homology information Ssh1 translocon complex / SRP-dependent cotranslational protein targeting to membrane / post-translational protein targeting to membrane, translocation / protein transmembrane transporter activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / rRNA binding ...Ssh1 translocon complex / SRP-dependent cotranslational protein targeting to membrane / post-translational protein targeting to membrane, translocation / protein transmembrane transporter activity / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ribosomal large subunit biogenesis / ribosomal large subunit assembly / cytoplasmic translation / cytosolic large ribosomal subunit / rRNA binding / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / endoplasmic reticulum membrane / RNA binding / metal ion binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Ovis aries (sheep) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.69 Å | |||||||||
Authors | Karki, S. / Javanainen, M. / Tranter, D. / Rehan, S. / Huiskonen, J. / Happonen, L. / Paavilainen, V. | |||||||||
Funding support | Finland, 2items
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Citation | Journal: EMBO Rep / Year: 2023 Title: Molecular view of ER membrane remodeling by the Sec61/TRAP translocon. Authors: Sudeep Karki / Matti Javanainen / Shahid Rehan / Dale Tranter / Juho Kellosalo / Juha T Huiskonen / Lotta Happonen / Ville Paavilainen / Abstract: Protein translocation across the endoplasmic reticulum (ER) membrane is an essential step during protein entry into the secretory pathway. The conserved Sec61 protein-conducting channel facilitates ...Protein translocation across the endoplasmic reticulum (ER) membrane is an essential step during protein entry into the secretory pathway. The conserved Sec61 protein-conducting channel facilitates polypeptide translocation and coordinates cotranslational polypeptide-processing events. In cells, the majority of Sec61 is stably associated with a heterotetrameric membrane protein complex, the translocon-associated protein complex (TRAP), yet the mechanism by which TRAP assists in polypeptide translocation remains unknown. Here, we present the structure of the core Sec61/TRAP complex bound to a mammalian ribosome by cryogenic electron microscopy (cryo-EM). Ribosome interactions anchor the Sec61/TRAP complex in a conformation that renders the ER membrane locally thinner by significantly curving its lumenal leaflet. We propose that TRAP stabilizes the ribosome exit tunnel to assist nascent polypeptide insertion through Sec61 and provides a ratcheting mechanism into the ER lumen mediated by direct polypeptide interactions. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bf9.cif.gz | 1.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb8bf9.ent.gz | 1 MB | Display | PDB format |
PDBx/mmJSON format | 8bf9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8bf9_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 8bf9_full_validation.pdf.gz | 1.6 MB | Display | |
Data in XML | 8bf9_validation.xml.gz | 97.4 KB | Display | |
Data in CIF | 8bf9_validation.cif.gz | 165.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bf/8bf9 ftp://data.pdbj.org/pub/pdb/validation_reports/bf/8bf9 | HTTPS FTP |
-Related structure data
Related structure data | 16017MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 2 types, 2 molecules 58
#1: RNA chain | Mass: 1186579.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) |
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#2: RNA chain | Mass: 50143.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) |
-Translocon-associated protein subunit ... , 4 types, 4 molecules ABDG
#3: Protein | Mass: 39381.430 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) |
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#4: Protein | Mass: 20478.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5P572 |
#5: Protein | Mass: 18901.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5P940 |
#6: Protein | Mass: 21100.504 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5NYA9 |
-Large ribosomal subunit protein ... , 4 types, 4 molecules Pdhk
#7: Protein | Mass: 21414.129 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5Q9T9 |
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#14: Protein | Mass: 14494.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PUU0 |
#16: Protein | Mass: 14591.649 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A6P3TAC5 |
#18: Protein | Mass: 8238.948 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) |
-Ribosomal protein ... , 3 types, 3 molecules RXj
#8: Protein | Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5PLN0 |
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#10: Protein | Mass: 17740.193 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A6P3CX48 |
#17: Protein | Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: W5P472 |
-Protein , 5 types, 5 molecules UYCgl
#9: Protein | Mass: 14784.962 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A6P7EJM7 |
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#11: Protein | Mass: 15891.787 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A7K9BN74 |
#12: Protein | Mass: 52034.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) |
#15: Protein | Mass: 9352.173 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) / References: UniProt: A0A836CVU8 |
#19: Protein | Mass: 6426.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) |
-Protein/peptide , 1 types, 1 molecules b
#13: Protein/peptide | Mass: 2486.056 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Ovis aries (sheep) |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Mammlian Ribosome Sec61 TRAP complex / Type: RIBOSOME / Details: Mammlian ribosome-Sec61 TRAP complex / Entity ID: #3-#6, #1-#2, #7-#11, #13-#19 / Source: NATURAL | ||||||||||||||||||||||||||||||
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Molecular weight | Value: 3.2 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||
Source (natural) | Organism: Ovis aries (sheep) | ||||||||||||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Conc.: 0.1 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES / Details: Purified Ribosome Sec61/TRAP complex | ||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 400 divisions/in. / Grid type: Quantifoil R1.2/1.3 | ||||||||||||||||||||||||||||||
Vitrification | Instrument: LEICA PLUNGER / Cryogen name: ETHANE / Humidity: 90 % / Chamber temperature: 298 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: OTHER / Nominal defocus max: 1200 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 47 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of real images: 30294 |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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Particle selection | Num. of particles selected: 1098031 |
3D reconstruction | Resolution: 2.69 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 61177 / Symmetry type: POINT |
Atomic model building | Protocol: BACKBONE TRACE |