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Yorodumi- EMDB-26133: Structure of the rabbit 80S ribosome stalled on a 4-TMD Rhodopsin... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-26133 | ||||||||||||
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Title | Structure of the rabbit 80S ribosome stalled on a 4-TMD Rhodopsin intermediate in complex with the multipass translocon | ||||||||||||
Map data | Reference map | ||||||||||||
Sample |
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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 / SRP-dependent cotranslational protein targeting to membrane, translocation / signal sequence binding / endoplasmic reticulum calcium ion homeostasis / post-translational protein targeting to membrane, translocation / protein folding chaperone complex / 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 / protein-RNA complex assembly / regulation of signal transduction / ERAD pathway / cellular response to actinomycin D / 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 / protein tag activity / antimicrobial humoral immune response mediated by antimicrobial peptide / ribosome binding / retina development in camera-type eye / regulation of translation / heparin binding / 5S rRNA binding / large ribosomal subunit rRNA binding / nuclear membrane / killing of cells of another organism / cytosolic large ribosomal subunit / defense response to Gram-negative bacterium / cytoplasmic translation / tRNA binding / postsynaptic density / protein stabilization / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / translation / mRNA binding / synapse / ubiquitin protein ligase binding / 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 | single particle reconstruction / cryo EM / Resolution: 3.88 Å | ||||||||||||
Authors | Kim MK / Lewis AJO / Keenan RJ / Hegde RS | ||||||||||||
Funding support | United States, 3 items
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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
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_26133.map.gz | 218.7 MB | EMDB map data format | |
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Header (meta data) | emd-26133-v30.xml emd-26133.xml | 69.2 KB 69.2 KB | Display Display | EMDB header |
Images | emd_26133.png | 87.4 KB | ||
Filedesc metadata | emd-26133.cif.gz | 15.9 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-26133 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-26133 | HTTPS FTP |
-Related structure data
Related structure data | 7tutMC 7tm3C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_26133.map.gz / Format: CCP4 / Size: 266.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Annotation | Reference map | ||||||||||||||||||||
Voxel size | X=Y=Z: 1.34 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Sample components
+Entire : 80S ribosome translating a stalled, four-TMD nascent chain (deriv...
+Supramolecule #1: 80S ribosome translating a stalled, four-TMD nascent chain (deriv...
+Macromolecule #1: uL2
+Macromolecule #2: uL4
+Macromolecule #3: uL18
+Macromolecule #4: eL6
+Macromolecule #5: uL30
+Macromolecule #6: eL8
+Macromolecule #7: uL6
+Macromolecule #8: uL16
+Macromolecule #9: uL5
+Macromolecule #10: eL13
+Macromolecule #11: eL14
+Macromolecule #12: eL15
+Macromolecule #13: uL13
+Macromolecule #14: uL22
+Macromolecule #15: eL18
+Macromolecule #16: eL19
+Macromolecule #17: eL20
+Macromolecule #18: eL21
+Macromolecule #19: eL22
+Macromolecule #20: uL14
+Macromolecule #21: eL24
+Macromolecule #22: eL23
+Macromolecule #23: uL24
+Macromolecule #24: eL27
+Macromolecule #25: uL15
+Macromolecule #26: eL29
+Macromolecule #27: eL30
+Macromolecule #28: eL31
+Macromolecule #29: eL32
+Macromolecule #30: eL33
+Macromolecule #31: eL34
+Macromolecule #32: eL35
+Macromolecule #33: eL36
+Macromolecule #34: eL37
+Macromolecule #35: eL38
+Macromolecule #36: eL39
+Macromolecule #37: eL40
+Macromolecule #38: eL41
+Macromolecule #39: eL42
+Macromolecule #40: eL43
+Macromolecule #42: eL28
+Macromolecule #45: uL3
+Macromolecule #46: Nascent chain
+Macromolecule #47: Protein transport protein Sec61 subunit alpha isoform 1
+Macromolecule #48: Protein transport protein Sec61 subunit beta
+Macromolecule #49: Protein transport protein Sec61 gamma
+Macromolecule #50: Coiled-coil domain containing 47
+Macromolecule #51: PAT complex subunit Asterix
+Macromolecule #52: Nicalin
+Macromolecule #53: Transmembrane protein 147
+Macromolecule #54: Calcium load-activated calcium channel
+Macromolecule #56: Obligate partner of TMCO1 insertase
+Macromolecule #41: P-site tRNA
+Macromolecule #43: 5S ribosomal RNA
+Macromolecule #44: 5.8S ribosomal RNA
+Macromolecule #55: 28S ribosomal RNA
+Macromolecule #57: MAGNESIUM ION
+Macromolecule #58: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | 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 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV Details: Blot for 4 seconds with Whatman filter papers at a blot force of -15 before plunging.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.7 µm / Nominal defocus min: 1.9000000000000001 µm |
Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Number grids imaged: 1 / Number real images: 13755 / Average electron dose: 54.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: OTHER |
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Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.88 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 136812 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | PDB-7tut: |