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Open data
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Basic information
Entry | Database: PDB / ID: 6swa | |||||||||||||||
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Title | Mus musculus brain neocortex ribosome 60S bound to Ebp1 | |||||||||||||||
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![]() | RIBOSOME / 60S / EBP1 / neurodevelopment / neocortex / 80S / peptide tunnel exit | |||||||||||||||
Function / homology | ![]() 5.8S rRNA binding / Protein hydroxylation / translation at postsynapse / Formation of a pool of free 40S subunits / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit ...5.8S rRNA binding / Protein hydroxylation / translation at postsynapse / Formation of a pool of free 40S subunits / SRP-dependent cotranslational protein targeting to membrane / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / selenocysteine insertion sequence binding / embryonic brain development / eukaryotic 80S initiation complex / negative regulation of protein neddylation / translation at presynapse / axial mesoderm development / negative regulation of formation of translation preinitiation complex / 90S preribosome assembly / aminoacyl-tRNA synthetase multienzyme complex / TORC2 complex binding / GAIT complex / middle ear morphogenesis / peroxisome proliferator activated receptor binding / A band / regulation of G1 to G0 transition / exit from mitosis / alpha-beta T cell differentiation / protein-DNA complex disassembly / optic nerve development / response to aldosterone / retinal ganglion cell axon guidance / G1 to G0 transition / positive regulation of axonogenesis / homeostatic process / lung morphogenesis / cell-substrate adhesion / macrophage chemotaxis / growth factor binding / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / blastocyst development / protein localization to nucleus / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / protein-RNA complex assembly / positive regulation of G1/S transition of mitotic cell cycle / protein targeting / cellular response to interleukin-4 / positive regulation of axon extension / translation regulator activity / cellular response to actinomycin D / cytosolic ribosome / ribonucleoprotein complex binding / rough endoplasmic reticulum / negative regulation of ubiquitin-dependent protein catabolic process / Neutrophil degranulation / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ossification / cellular response to dexamethasone stimulus / maturation of LSU-rRNA / ribosomal large subunit biogenesis / skeletal system development / liver regeneration / positive regulation of cell differentiation / sensory perception of sound / bone development / multicellular organism growth / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / cellular response to type II interferon / rRNA processing / large ribosomal subunit / antimicrobial humoral immune response mediated by antimicrobial peptide / transcription corepressor activity / presynapse / retina development in camera-type eye / regulation of translation / heparin binding / cell body / fibroblast proliferation / 5S rRNA binding / large ribosomal subunit rRNA binding / postsynapse / response to ethanol / defense response to Gram-negative bacterium / killing of cells of another organism / response to lipopolysaccharide / cytosolic large ribosomal subunit / nucleic acid binding / tRNA binding / cytoplasmic translation / postsynaptic density / protein stabilization / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / ribonucleoprotein complex / translation / negative regulation of DNA-templated transcription / mRNA binding Similarity search - Function | |||||||||||||||
Biological species | ![]() ![]() | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||||||||
![]() | Kraushar, M.L. / Sprink, T. | |||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Protein Synthesis in the Developing Neocortex at Near-Atomic Resolution Reveals Ebp1-Mediated Neuronal Proteostasis at the 60S Tunnel Exit. Authors: Matthew L Kraushar / Ferdinand Krupp / Dermot Harnett / Paul Turko / Mateusz C Ambrozkiewicz / Thiemo Sprink / Koshi Imami / Manuel Günnigmann / Ulrike Zinnall / Carlos H Vieira-Vieira / ...Authors: Matthew L Kraushar / Ferdinand Krupp / Dermot Harnett / Paul Turko / Mateusz C Ambrozkiewicz / Thiemo Sprink / Koshi Imami / Manuel Günnigmann / Ulrike Zinnall / Carlos H Vieira-Vieira / Theres Schaub / Agnieszka Münster-Wandowski / Jörg Bürger / Ekaterina Borisova / Hiroshi Yamamoto / Mladen-Roko Rasin / Uwe Ohler / Dieter Beule / Thorsten Mielke / Victor Tarabykin / Markus Landthaler / Günter Kramer / Imre Vida / Matthias Selbach / Christian M T Spahn / ![]() ![]() ![]() Abstract: Protein synthesis must be finely tuned in the developing nervous system as the final essential step of gene expression. This study investigates the architecture of ribosomes from the neocortex during ...Protein synthesis must be finely tuned in the developing nervous system as the final essential step of gene expression. This study investigates the architecture of ribosomes from the neocortex during neurogenesis, revealing Ebp1 as a high-occupancy 60S peptide tunnel exit (TE) factor during protein synthesis at near-atomic resolution by cryoelectron microscopy (cryo-EM). Ribosome profiling demonstrated Ebp1-60S binding is highest during start codon initiation and N-terminal peptide elongation, regulating ribosome occupancy of these codons. Membrane-targeting domains emerging from the 60S tunnel, which recruit SRP/Sec61 to the shared binding site, displace Ebp1. Ebp1 is particularly abundant in the early-born neural stem cell (NSC) lineage and regulates neuronal morphology. Ebp1 especially impacts the synthesis of membrane-targeted cell adhesion molecules (CAMs), measured by pulsed stable isotope labeling by amino acids in cell culture (pSILAC)/bioorthogonal noncanonical amino acid tagging (BONCAT) mass spectrometry (MS). Therefore, Ebp1 is a central component of protein synthesis, and the ribosome TE is a focal point of gene expression control in the molecular specification of neuronal morphology during development. | |||||||||||||||
History |
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Structure visualization
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Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 3 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1.1 MB | Display | |
Data in XML | ![]() | 205.3 KB | Display | |
Data in CIF | ![]() | 350.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 10321MC M: map data used to model this data C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Components
+60S ribosomal protein ... , 38 types, 38 molecules ABCDEFGHIJKLMNOPQRSTUVXYZabcde...
-Ribosomal protein ... , 4 types, 4 molecules Wjmn
#23: Protein | Mass: 15161.899 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#36: Protein/peptide | Mass: 6295.562 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#39: Protein | Mass: 12345.776 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
#40: Protein | Mass: 10168.153 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
-RNA chain , 3 types, 3 molecules qrs
#43: RNA chain | Mass: 1170200.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: We used the Oryctolagus cuniculus sequence to model the Mus musculus 28S ribosomal RNA Source: (natural) ![]() ![]() |
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#44: RNA chain | Mass: 50449.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: We used the Oryctolagus cuniculus sequence to model the Mus musculus 5.8S ribosomal RNA Source: (natural) ![]() ![]() |
#45: RNA chain | Mass: 38385.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: We used the Oryctolagus cuniculus sequence to model the Mus musculus 5S ribosomal RNA Source: (natural) ![]() ![]() |
-Protein , 1 types, 1 molecules t
#46: Protein | Mass: 39388.098 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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-Non-polymers , 2 types, 250 molecules ![](data/chem/img/MG.gif)
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#47: Chemical | ChemComp-MG / #48: Chemical | |
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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 |
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Sample preparation
Component | Name: Mus musculus postnatal day 0 brain neocortex 80S ribosome bound to Ebp1 Type: RIBOSOME / Entity ID: #1-#46 / Source: NATURAL | ||||||||||||||||||||||||||||||||||||||||
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Molecular weight | Value: 3.2 MDa / Experimental value: NO | ||||||||||||||||||||||||||||||||||||||||
Source (natural) | Organism: ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 100 divisions/in. / Grid type: Quantifoil R3/3 | ||||||||||||||||||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K |
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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: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 31000 X / Nominal defocus max: 2500 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Average exposure time: 20 sec. / Electron dose: 31.78 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Num. of real images: 5379 |
EM imaging optics | Energyfilter name: GIF Quantum LS |
Image scans | Movie frames/image: 40 |
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Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||
Particle selection | Num. of particles selected: 208206 | |||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | |||||||||||||||||||||
3D reconstruction | Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 208206 / Symmetry type: POINT |