+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 / 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 / peroxisome proliferator activated receptor binding / middle ear morphogenesis / A band / alpha-beta T cell differentiation / regulation of G1 to G0 transition / exit from mitosis / protein-DNA complex disassembly / optic nerve development / positive regulation of axonogenesis / response to aldosterone / retinal ganglion cell axon guidance / G1 to G0 transition / homeostatic process / cell-substrate adhesion / lung morphogenesis / growth factor binding / macrophage chemotaxis / 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 / positive regulation of axon extension / protein targeting / cellular response to interleukin-4 / translation regulator activity / cellular response to actinomycin D / ribonucleoprotein complex binding / cytosolic ribosome / rough endoplasmic reticulum / negative regulation of ubiquitin-dependent protein catabolic process / Neutrophil degranulation / cellular response to dexamethasone stimulus / ossification / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 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 / cellular response to type II interferon / cytoplasmic ribonucleoprotein granule / rRNA processing / antimicrobial humoral immune response mediated by antimicrobial peptide / transcription corepressor activity / large ribosomal subunit / 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 / nucleic acid binding / cytosolic large ribosomal subunit / 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 | 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 |
-Validation report
Summary document | emd_10321_validation.pdf.gz | 269.7 KB | Display | EMDB validaton report |
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Full document | emd_10321_full_validation.pdf.gz | 268.8 KB | Display | |
Data in XML | emd_10321_validation.xml.gz | 7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10321 ftp://ftp.pdbj.org/pub/emdb/validation_reports/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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Specialist optics | Energy filter - Name: GIF Quantum LS |
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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 31000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |