+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10321 | |||||||||||||||
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Title | Mus musculus brain neocortex ribosome 60S bound to Ebp1 | |||||||||||||||
Map data | ex vivo derived mus musculus P0 brain neocortex ribosome containing eEF2 and EBP1 | |||||||||||||||
Sample |
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Function / homology | Function and homology information 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 / aminoacyl-tRNA synthetase multienzyme complex / embryonic brain development / eukaryotic 80S initiation complex / negative regulation of protein neddylation / translation at presynapse / axial mesoderm development / regulation of G1 to G0 transition / negative regulation of formation of translation preinitiation complex / exit from mitosis / protein-DNA complex disassembly / 90S preribosome assembly / optic nerve development / TORC2 complex binding / GAIT complex / G1 to G0 transition / retinal ganglion cell axon guidance / middle ear morphogenesis / peroxisome proliferator activated receptor binding / A band / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / alpha-beta T cell differentiation / response to aldosterone / positive regulation of axonogenesis / homeostatic process / lung morphogenesis / macrophage chemotaxis / cell-substrate adhesion / smooth endoplasmic reticulum / growth factor binding / protein-RNA complex assembly / blastocyst development / translation regulator activity / protein localization to nucleus / cellular response to actinomycin D / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / protein targeting / positive regulation of G1/S transition of mitotic cell cycle / positive regulation of axon extension / MDM2/MDM4 family protein binding / ribonucleoprotein complex binding / rough endoplasmic reticulum / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / negative regulation of ubiquitin-dependent protein catabolic process / ribosomal large subunit biogenesis / cellular response to interleukin-4 / Neutrophil degranulation / ossification / cytosolic ribosome / : / positive regulation of translation / regulation of signal transduction by p53 class mediator / innate immune response in mucosa / mRNA 3'-UTR binding / skeletal system development / positive regulation of cell differentiation / sensory perception of sound / multicellular organism growth / mRNA 5'-UTR binding / bone development / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / rRNA processing / cellular response to type II interferon / ribosomal large subunit assembly / transcription corepressor activity / large ribosomal subunit rRNA binding / antimicrobial humoral immune response mediated by antimicrobial peptide / large ribosomal subunit / presynapse / regulation of translation / retina development in camera-type eye / heparin binding / cell body / 5S rRNA binding / cytosolic large ribosomal subunit / cytoplasmic translation / antibacterial humoral response / fibroblast proliferation / postsynapse / killing of cells of another organism / defense response to Gram-negative bacterium / tRNA binding / negative regulation of translation / response to lipopolysaccharide / postsynaptic density / nucleic acid binding / rRNA binding Similarity search - Function | |||||||||||||||
Biological species | Mus musculus (house mouse) / Mouse (mice) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | |||||||||||||||
Authors | Kraushar ML / Sprink T | |||||||||||||||
Funding support | Germany, 4 items
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Citation | Journal: Mol Cell / Year: 2021 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
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_10321.map.gz | 33.7 MB | EMDB map data format | |
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Header (meta data) | emd-10321-v30.xml emd-10321.xml | 60 KB 60 KB | Display Display | EMDB header |
Images | emd_10321.png | 269.1 KB | ||
Others | emd_10321_additional_1.map.gz | 21.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10321 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10321 | HTTPS FTP |
-Related structure data
Related structure data | 6swaMC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_10321.map.gz / Format: CCP4 / Size: 178 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | ex vivo derived mus musculus P0 brain neocortex ribosome containing eEF2 and EBP1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.3267 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Supplemental map: emd 10321 additional 1.map
File | emd_10321_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Mus musculus postnatal day 0 brain neocortex 80S ribosome bound t...
+Supramolecule #1: Mus musculus postnatal day 0 brain neocortex 80S ribosome bound t...
+Macromolecule #1: 60S ribosomal protein L8
+Macromolecule #2: 60S ribosomal protein L3
+Macromolecule #3: 60S ribosomal protein L4
+Macromolecule #4: 60S ribosomal protein L5
+Macromolecule #5: 60S ribosomal protein L6
+Macromolecule #6: 60S ribosomal protein L7
+Macromolecule #7: 60S ribosomal protein L7a
+Macromolecule #8: 60S ribosomal protein L9
+Macromolecule #9: 60S ribosomal protein L10
+Macromolecule #10: 60S ribosomal protein L11
+Macromolecule #11: 60S ribosomal protein L13
+Macromolecule #12: 60S ribosomal protein L14
+Macromolecule #13: 60S ribosomal protein L15
+Macromolecule #14: 60S ribosomal protein L13a
+Macromolecule #15: 60S ribosomal protein L17
+Macromolecule #16: 60S ribosomal protein L18
+Macromolecule #17: 60S ribosomal protein L18a
+Macromolecule #18: 60S ribosomal protein L21
+Macromolecule #19: 60S ribosomal protein L22
+Macromolecule #20: 60S ribosomal protein L23
+Macromolecule #21: 60S ribosomal protein L24
+Macromolecule #22: 60S ribosomal protein L23a
+Macromolecule #23: Ribosomal protein L26
+Macromolecule #24: 60S ribosomal protein L27
+Macromolecule #25: 60S ribosomal protein L27a
+Macromolecule #26: 60S ribosomal protein L29
+Macromolecule #27: 60S ribosomal protein L30
+Macromolecule #28: 60S ribosomal protein L31
+Macromolecule #29: 60S ribosomal protein L32
+Macromolecule #30: 60S ribosomal protein L35a
+Macromolecule #31: 60S ribosomal protein L34
+Macromolecule #32: 60S ribosomal protein L35
+Macromolecule #33: 60S ribosomal protein L36
+Macromolecule #34: 60S ribosomal protein L37
+Macromolecule #35: 60S ribosomal protein L38
+Macromolecule #36: Ribosomal protein L39
+Macromolecule #37: 60S ribosomal protein L40
+Macromolecule #38: 60S ribosomal protein L41
+Macromolecule #39: Ribosomal protein L36A
+Macromolecule #40: Ribosomal protein L37a
+Macromolecule #41: 60S ribosomal protein L19
+Macromolecule #42: 60S ribosomal protein L28
+Macromolecule #46: Proliferation-associated protein 2G4
+Macromolecule #43: 28S ribosomal RNA
+Macromolecule #44: 5.8S ribosomal RNA
+Macromolecule #45: 5S ribosomal RNA
+Macromolecule #47: MAGNESIUM ION
+Macromolecule #48: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 Component:
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Grid | Model: Quantifoil R3/3 / Material: COPPER / Mesh: 100 / Support film - Material: CARBON / Support film - topology: HOLEY / Support film - Film thickness: 2.0 nm / Pretreatment - Type: GLOW DISCHARGE | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II |
-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 / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 31000 |
Specialist optics | Energy filter - Name: GIF Quantum LS |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Number real images: 5379 / Average exposure time: 20.0 sec. / Average electron dose: 31.78 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Particle selection | Number selected: 208206 |
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CTF correction | Software - Name: CTFFIND |
Initial angle assignment | Type: COMMON LINE / Software - Name: SPHIRE |
Final 3D classification | Software - Name: SPARX |
Final angle assignment | Type: COMMON LINE / Software - Name: SPARX |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.1 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: SPARX / Number images used: 208206 |