+Open data
-Basic information
Entry | Database: PDB / ID: 8b6l | ||||||||||||
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Title | Subtomogram average of the human Sec61-TRAP-OSTA-translocon | ||||||||||||
Components |
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Keywords | MEMBRANE PROTEIN / membrane protein complex / protein translocation / N-glycosylation / signal peptide insertion | ||||||||||||
Function / homology | Function and homology information oligosaccharyltransferase complex binding / oligosaccharyltransferase I complex / oligosaccharyltransferase III complex / Asparagine N-linked glycosylation / membrane-bounded organelle / epidermal growth factor binding / endoplasmic reticulum Sec complex / co-translational protein modification / pronephric nephron development / endoplasmic reticulum quality control compartment ...oligosaccharyltransferase complex binding / oligosaccharyltransferase I complex / oligosaccharyltransferase III complex / Asparagine N-linked glycosylation / membrane-bounded organelle / epidermal growth factor binding / endoplasmic reticulum Sec complex / co-translational protein modification / pronephric nephron development / endoplasmic reticulum quality control compartment / oligosaccharyltransferase complex / dolichyl-diphosphooligosaccharide-protein glycotransferase / dolichyl-diphosphooligosaccharide-protein glycotransferase activity / cotranslational protein targeting to membrane / Ssh1 translocon complex / Sec61 translocon complex / protein targeting to ER / protein insertion into ER membrane / XBP1(S) activates chaperone genes / post-translational protein targeting to endoplasmic reticulum membrane / protein N-linked glycosylation via asparagine / SRP-dependent cotranslational protein targeting to membrane, translocation / SRP-dependent cotranslational protein targeting to membrane / signal sequence binding / post-translational protein targeting to membrane, translocation / endoplasmic reticulum organization / protein N-linked glycosylation / epithelial cell apoptotic process / azurophil granule membrane / retrograde protein transport, ER to cytosol / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / protein glycosylation / Advanced glycosylation endproduct receptor signaling / blastocyst development / SRP-dependent cotranslational protein targeting to membrane / protein transmembrane transporter activity / endomembrane system / post-translational protein modification / ERAD pathway / rough endoplasmic reticulum / enzyme activator activity / T cell activation / response to endoplasmic reticulum stress / guanyl-nucleotide exchange factor activity / response to cytokine / protein modification process / regulation of protein stability / calcium channel activity / melanosome / ribosome binding / ER-Phagosome pathway / Maturation of spike protein / membrane => GO:0016020 / nuclear body / inflammatory response / intracellular membrane-bounded organelle / positive regulation of cell population proliferation / endoplasmic reticulum membrane / Neutrophil degranulation / negative regulation of apoptotic process / apoptotic process / endoplasmic reticulum / protein-containing complex / RNA binding / extracellular exosome / membrane / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | ELECTRON MICROSCOPY / subtomogram averaging / cryo EM / Resolution: 7.6 Å | ||||||||||||
Authors | Gemmer, M. / Fedry, J.M.M. / Forster, F.G. | ||||||||||||
Funding support | European Union, Netherlands, 3items
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Citation | Journal: Nature / Year: 2023 Title: Visualization of translation and protein biogenesis at the ER membrane. Authors: Max Gemmer / Marten L Chaillet / Joyce van Loenhout / Rodrigo Cuevas Arenas / Dimitrios Vismpas / Mariska Gröllers-Mulderij / Fujiet A Koh / Pascal Albanese / Richard A Scheltema / Stuart C ...Authors: Max Gemmer / Marten L Chaillet / Joyce van Loenhout / Rodrigo Cuevas Arenas / Dimitrios Vismpas / Mariska Gröllers-Mulderij / Fujiet A Koh / Pascal Albanese / Richard A Scheltema / Stuart C Howes / Abhay Kotecha / Juliette Fedry / Friedrich Förster / Abstract: The dynamic ribosome-translocon complex, which resides at the endoplasmic reticulum (ER) membrane, produces a major fraction of the human proteome. It governs the synthesis, translocation, membrane ...The dynamic ribosome-translocon complex, which resides at the endoplasmic reticulum (ER) membrane, produces a major fraction of the human proteome. It governs the synthesis, translocation, membrane insertion, N-glycosylation, folding and disulfide-bond formation of nascent proteins. Although individual components of this machinery have been studied at high resolution in isolation, insights into their interplay in the native membrane remain limited. Here we use cryo-electron tomography, extensive classification and molecular modelling to capture snapshots of mRNA translation and protein maturation at the ER membrane at molecular resolution. We identify a highly abundant classical pre-translocation intermediate with eukaryotic elongation factor 1a (eEF1a) in an extended conformation, suggesting that eEF1a may remain associated with the ribosome after GTP hydrolysis during proofreading. At the ER membrane, distinct polysomes bind to different ER translocons specialized in the synthesis of proteins with signal peptides or multipass transmembrane proteins with the translocon-associated protein complex (TRAP) present in both. The near-complete atomic model of the most abundant ER translocon variant comprising the protein-conducting channel SEC61, TRAP and the oligosaccharyltransferase complex A (OSTA) reveals specific interactions of TRAP with other translocon components. We observe stoichiometric and sub-stoichiometric cofactors associated with OSTA, which are likely to include protein isomerases. In sum, we visualize ER-bound polysomes with their coordinated downstream machinery. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8b6l.cif.gz | 712.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8b6l.ent.gz | 583.8 KB | Display | PDB format |
PDBx/mmJSON format | 8b6l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8b6l_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 8b6l_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 8b6l_validation.xml.gz | 96.2 KB | Display | |
Data in CIF | 8b6l_validation.cif.gz | 148.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/b6/8b6l ftp://data.pdbj.org/pub/pdb/validation_reports/b6/8b6l | HTTPS FTP |
-Related structure data
Related structure data | 15870MC 8b6zC 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
-Protein transport protein Sec61 subunit ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 52304.406 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P61619 |
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#2: Protein | Mass: 9987.456 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P60468 |
#3: Protein | Mass: 7752.325 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293F / References: UniProt: P60059 |
-Protein/peptide , 1 types, 1 molecules D
#4: Protein/peptide | Mass: 1890.321 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
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-Translocon-associated protein subunit ... , 4 types, 4 molecules EFGH
#5: Protein | Mass: 32263.219 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P43307 |
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#6: Protein | Mass: 20154.986 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P43308 |
#7: Protein | Mass: 21106.465 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UNL2 |
#8: Protein | Mass: 19015.547 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P51571 |
-Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit ... , 5 types, 5 molecules IKMOP
#9: Protein | Mass: 80607.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) References: UniProt: P46977, dolichyl-diphosphooligosaccharide-protein glycotransferase |
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#11: Protein/peptide | Mass: 4196.004 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P0C6T2 |
#13: Protein | Mass: 12503.631 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61803 |
#15: Protein | Mass: 68656.156 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P04843 |
#16: Protein | Mass: 69347.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P04844 |
-Protein , 3 types, 3 molecules JLN
#10: Protein | Mass: 16844.215 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9NRP0 |
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#12: Protein | Mass: 9083.804 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P61165 |
#14: Protein | Mass: 50854.578 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P39656 |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: subtomogram averaging |
-Sample preparation
Component | Name: Sec61-TRAP-OSTA translocon complex / Type: ORGANELLE OR CELLULAR COMPONENT Details: Translocon complex embedded in its native membrane and bound to cytosolic ribosomes Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
Specimen | Conc.: 2 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES Details: ER-derived vesicles decorated with cytosolic ribosomes. |
Specimen support | Grid material: COPPER / Grid type: Quantifoil |
Vitrification | Cryogen name: ETHANE-PROPANE / Details: Manual plunger |
-Electron microscopy imaging
Experimental equipment | Model: Talos Arctica / Image courtesy: FEI Company |
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Microscopy | Model: FEI TALOS ARCTICA |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 200 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 79000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 3000 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN |
Image recording | Average exposure time: 0.7 sec. / Electron dose: 2.3 e/Å2 / Avg electron dose per subtomogram: 80 e/Å2 / Detector mode: COUNTING / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of grids imaged: 8 |
Image scans | Movie frames/image: 7 / Used frames/image: 7-7 |
-Processing
EM software |
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EM 3D crystal entity | ∠α: 90 ° / ∠β: 90 ° / ∠γ: 90 ° / A: 600 Å / B: 600 Å / C: 600 Å / Space group name: C1 / Space group num: 1 | ||||||||||||||||||||||||||||||||||||||||||||
CTF correction | Details: Estimation and correction in WARP/M / Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | ||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 7.6 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 42215 / Algorithm: BACK PROJECTION / Symmetry type: 3D CRYSTAL | ||||||||||||||||||||||||||||||||||||||||||||
EM volume selection | Method: Template matching / Num. of tomograms: 869 / Num. of volumes extracted: 134350 Reference model: Subtomogram average of ER membrane-associated ribosome | ||||||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL |