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Yorodumi- PDB-7tut: Structure of the rabbit 80S ribosome stalled on a 4-TMD Rhodopsin... -
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-Basic information
Entry | Database: PDB / ID: 7tut | ||||||||||||
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Title | Structure of the rabbit 80S ribosome stalled on a 4-TMD Rhodopsin intermediate in complex with the multipass translocon | ||||||||||||
Components |
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Keywords | RIBOSOME / Membrane protein / translocon | ||||||||||||
Function / homology | Function and homology information multi-pass transmembrane protein insertion into ER membrane / multi-pass translocon complex / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / endoplasmic reticulum Sec complex / protein localization to nuclear inner membrane / pronephric nephron development / rough endoplasmic reticulum membrane / cotranslational protein targeting to membrane / Sec61 translocon complex / protein targeting to ER ...multi-pass transmembrane protein insertion into ER membrane / multi-pass translocon complex / Insertion of tail-anchored proteins into the endoplasmic reticulum membrane / endoplasmic reticulum Sec complex / protein localization to nuclear inner membrane / pronephric nephron development / rough endoplasmic reticulum membrane / cotranslational protein targeting to membrane / Sec61 translocon complex / protein targeting to ER / protein-transporting ATPase activity / protein insertion into ER membrane / signal sequence binding / endoplasmic reticulum calcium ion homeostasis / post-translational protein targeting to membrane, translocation / protein folding chaperone complex / SRP-dependent cotranslational protein targeting to membrane, translocation / regulation of G1 to G0 transition / exit from mitosis / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / optic nerve development / retinal ganglion cell axon guidance / G1 to G0 transition / ER overload response / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / protein transmembrane transporter activity / regulation of signal transduction / protein-RNA complex assembly / cellular response to actinomycin D / ERAD pathway / rough endoplasmic reticulum / protein folding chaperone / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / negative regulation of ubiquitin-dependent protein catabolic process / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / post-embryonic development / maturation of LSU-rRNA / ribosomal large subunit biogenesis / positive regulation of translation / cellular response to gamma radiation / mRNA 5'-UTR binding / transcription coactivator binding / modification-dependent protein catabolic process / rRNA processing / antimicrobial humoral immune response mediated by antimicrobial peptide / protein tag activity / ribosome binding / retina development in camera-type eye / regulation of translation / heparin binding / 5S rRNA binding / large ribosomal subunit rRNA binding / nuclear membrane / defense response to Gram-negative bacterium / killing of cells of another organism / cytosolic large ribosomal subunit / tRNA binding / cytoplasmic translation / postsynaptic density / protein stabilization / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / ubiquitin protein ligase binding / synapse / calcium ion binding / positive regulation of cell population proliferation / positive regulation of gene expression / endoplasmic reticulum membrane / nucleolus / negative regulation of transcription by RNA polymerase II / endoplasmic reticulum / RNA binding / nucleoplasm / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Oryctolagus cuniculus (rabbit) Canis lupus (gray wolf) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.88 Å | ||||||||||||
Authors | Kim, M.K. / Lewis, A.J.O. / Keenan, R.J. / Hegde, R.S. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: Nature / Year: 2022 Title: Mechanism of an intramembrane chaperone for multipass membrane proteins. Authors: Luka Smalinskaitė / Min Kyung Kim / Aaron J O Lewis / Robert J Keenan / Ramanujan S Hegde / Abstract: Multipass membrane proteins play numerous roles in biology and include receptors, transporters, ion channels and enzymes. How multipass proteins are co-translationally inserted and folded at the ...Multipass membrane proteins play numerous roles in biology and include receptors, transporters, ion channels and enzymes. How multipass proteins are co-translationally inserted and folded at the endoplasmic reticulum is not well understood. The prevailing model posits that each transmembrane domain (TMD) of a multipass protein successively passes into the lipid bilayer through a front-side lateral gate of the Sec61 protein translocation channel. The PAT complex, an intramembrane chaperone comprising Asterix and CCDC47, engages early TMDs of multipass proteins to promote their biogenesis by an unknown mechanism. Here, biochemical and structural analysis of intermediates during multipass protein biogenesis showed that the nascent chain is not engaged with Sec61, which is occluded and latched closed by CCDC47. Instead, Asterix binds to and redirects the substrate to a location behind Sec61, where the PAT complex contributes to a multipass translocon surrounding a semi-enclosed, lipid-filled cavity. Detection of multiple TMDs in this cavity after their emergence from the ribosome suggests that multipass proteins insert and fold behind Sec61. Accordingly, biogenesis of several multipass proteins was unimpeded by inhibitors of the Sec61 lateral gate. These findings elucidate the mechanism of an intramembrane chaperone and suggest a new framework for multipass membrane protein biogenesis at the endoplasmic reticulum. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7tut.cif.gz | 5.5 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7tut.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7tut.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7tut_validation.pdf.gz | 1.2 MB | Display | wwPDB validaton report |
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Full document | 7tut_full_validation.pdf.gz | 1.3 MB | Display | |
Data in XML | 7tut_validation.xml.gz | 232.1 KB | Display | |
Data in CIF | 7tut_validation.cif.gz | 413.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tu/7tut ftp://data.pdbj.org/pub/pdb/validation_reports/tu/7tut | HTTPS FTP |
-Related structure data
Related structure data | 26133MC 7tm3C C: citing same article (ref.) M: map data used to model this data |
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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 , 49 types, 49 molecules ACDEFGHIJLMNOPQRSTUVWXYZabcdef...
-Protein/peptide , 1 types, 1 molecules n
#38: Protein/peptide | Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A087WNH4 |
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-RNA chain , 4 types, 4 molecules quvK
#41: RNA chain | Mass: 24632.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
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#43: RNA chain | Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: GenBank: X06789.1 |
#44: RNA chain | Mass: 50143.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
#55: RNA chain | Mass: 1148115.375 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
-Protein transport protein Sec61 subunit ... , 2 types, 2 molecules 12
#47: Protein | Mass: 52279.379 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus (gray wolf) / References: UniProt: P38377 |
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#48: Protein | Mass: 9987.456 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Canis lupus (gray wolf) / References: UniProt: P60467 |
-Non-polymers , 2 types, 225 molecules
#57: Chemical | ChemComp-MG / #58: Chemical | ChemComp-ZN / |
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-Details
Has ligand of interest | N |
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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: 80S ribosome translating a stalled, four-TMD nascent chain (derived from rhodopsin), and bound to components of the multi-pass translocon Type: RIBOSOME / Details: Sample prepared by in vitro translation / Entity ID: #1-#56 / Source: MULTIPLE SOURCES |
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Molecular weight | Experimental value: NO |
Buffer solution | pH: 7.5 Details: 50 mM HEPES-KOH, pH 7.5, 200 mM potassium acetate, 5 mM magnesium acetate, 0.25% digitonin, 50 mM biotin |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K Details: Blot for 4 seconds with Whatman filter papers at a blot force of -15 before plunging. |
-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 FIELD / Nominal defocus max: 2700 nm / Nominal defocus min: 1900 nm |
Image recording | Electron dose: 54 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Num. of grids imaged: 1 / Num. of real images: 13755 |
-Processing
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 136812 / Symmetry type: POINT | ||||||||||||||||||||||||
Atomic model building | Protocol: FLEXIBLE FIT / Space: REAL | ||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||
Displacement parameters | Biso mean: 276.11 Å2 | ||||||||||||||||||||||||
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