+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-10344 | |||||||||
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Title | Cryo-EM structure of the human Ebp1-ribosome complex | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information eukaryotic 80S initiation complex / axial mesoderm development / 90S preribosome assembly / TORC2 complex binding / middle ear morphogenesis / 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 / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / Peptide chain elongation / Selenocysteine synthesis ...eukaryotic 80S initiation complex / axial mesoderm development / 90S preribosome assembly / TORC2 complex binding / middle ear morphogenesis / 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 / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / Peptide chain elongation / Selenocysteine synthesis / protein-RNA complex assembly / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / ribosomal large subunit biogenesis / ossification / skeletal system development / positive regulation of translation / : / positive regulation of cell differentiation / sensory perception of sound / cellular response to gamma radiation / mRNA 5'-UTR binding / Regulation of expression of SLITs and ROBOs / transcription corepressor activity / cellular response to UV / azurophil granule lumen / rRNA processing / regulation of translation / ribosomal large subunit assembly / cytosolic large ribosomal subunit / cytoplasmic translation / postsynaptic density / nucleic acid binding / rRNA binding / structural constituent of ribosome / cadherin binding / translation / ribonucleoprotein complex / focal adhesion / mRNA binding / negative regulation of DNA-templated transcription / synapse / ubiquitin protein ligase binding / Neutrophil degranulation / nucleolus / negative regulation of apoptotic process / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Wild K / Aleksic M / Pfeffer M / Sinning I | |||||||||
Funding support | Germany, 1 items
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Citation | Journal: Nat Commun / Year: 2020 Title: MetAP-like Ebp1 occupies the human ribosomal tunnel exit and recruits flexible rRNA expansion segments. Authors: Klemens Wild / Milan Aleksić / Karine Lapouge / Keven D Juaire / Dirk Flemming / Stefan Pfeffer / Irmgard Sinning / Abstract: Human Ebp1 is a member of the proliferation-associated 2G4 (PA2G4) family and plays an important role in cancer regulation. Ebp1 shares the methionine aminopeptidase (MetAP) fold and binds to mature ...Human Ebp1 is a member of the proliferation-associated 2G4 (PA2G4) family and plays an important role in cancer regulation. Ebp1 shares the methionine aminopeptidase (MetAP) fold and binds to mature 80S ribosomes for translational control. Here, we present a cryo-EM single particle analysis reconstruction of Ebp1 bound to non-translating human 80S ribosomes at a resolution range from 3.3 to ~8 Å. Ebp1 blocks the tunnel exit with major interactions to the general uL23/uL29 docking site for nascent chain-associated factors complemented by eukaryote-specific eL19 and rRNA helix H59. H59 is defined as dynamic adaptor undergoing significant remodeling upon Ebp1 binding. Ebp1 recruits rRNA expansion segment ES27L to the tunnel exit via specific interactions with rRNA consensus sequences. The Ebp1-ribosome complex serves as a template for MetAP binding and provides insights into the structural principles for spatial coordination of co-translational events and molecular triage at the ribosomal tunnel exit. | |||||||||
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_10344.map.gz | 50.6 MB | EMDB map data format | |
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Header (meta data) | emd-10344-v30.xml emd-10344.xml | 25.3 KB 25.3 KB | Display Display | EMDB header |
Images | emd_10344.png | 244.3 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10344 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10344 | HTTPS FTP |
-Related structure data
Related structure data | 6sxoMC C: citing same article (ref.) M: atomic model generated by this map |
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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_10344.map.gz / Format: CCP4 / Size: 512 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.07 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
+Entire : Human Ebp1-ribosome complex
+Supramolecule #1: Human Ebp1-ribosome complex
+Supramolecule #2: Proliferation-associated protein 2G4
+Supramolecule #3: ribosomal components
+Macromolecule #1: Proliferation-associated protein 2G4
+Macromolecule #2: 60S ribosomal protein L35
+Macromolecule #3: 60S ribosomal protein L38
+Macromolecule #4: 60S ribosomal protein L19
+Macromolecule #5: 60S ribosomal protein L23a
+Macromolecule #6: 60S ribosomal protein L26
+Macromolecule #7: 28S ribosomal RNA including ES27L-B (2839-3265)
+Macromolecule #8: 5.8S ribosomal RNA
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 / Component - Formula: MgOAc2 / Component - Name: KOAc |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 293 K / Instrument: FEI VITROBOT MARK IV |
Details | 100 nM ribosome, 800 nM Ebp1 |
-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: 3.0 µm / Nominal defocus min: 0.5 µm |
Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 3370 / Average electron dose: 38.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: Gctf |
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Startup model | Type of model: PDB ENTRY PDB model - PDB ID: 6ek0 Details: 6EK0 for the ribosome and 2Q8K for Ebp1 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0) |
Final 3D classification | Software - Name: RELION (ver. 3.0) |
Final angle assignment | Type: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.0) |
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.0) Details: Ebp1-60S density segment after 2-body multibody refinement; filtered to global resolution Number images used: 34467 |