+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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Keywords | Human Ebp1 / PA2G4 family / MET-AP homolog / expansion segment ES27L / RIBOSOME | |||||||||
Function / homology | Function and homology information eukaryotic 80S initiation complex / axial mesoderm development / 90S preribosome assembly / 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 / Formation of a pool of free 40S subunits ...eukaryotic 80S initiation complex / axial mesoderm development / 90S preribosome assembly / 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 / 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 / protein-RNA complex assembly / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / cytosolic ribosome / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ossification / ribosomal large subunit biogenesis / 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 / rRNA processing / transcription corepressor activity / cellular response to UV / azurophil granule lumen / regulation of translation / cytoplasmic translation / cytosolic large ribosomal subunit / nucleic acid binding / postsynaptic density / structural constituent of ribosome / ribonucleoprotein complex / translation / focal adhesion / negative regulation of DNA-templated transcription / mRNA binding / ubiquitin protein ligase binding / Neutrophil degranulation / synapse / negative regulation of apoptotic process / nucleolus / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Wild K / Aleksic M | |||||||||
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 | 25.6 KB 25.6 KB | Display Display | EMDB header |
Images | emd_10344.png | 244.3 KB | ||
Filedesc metadata | emd-10344.cif.gz | 8.8 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-10344 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-10344 | HTTPS FTP |
-Validation report
Summary document | emd_10344_validation.pdf.gz | 424.9 KB | Display | EMDB validaton report |
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Full document | emd_10344_full_validation.pdf.gz | 424.4 KB | Display | |
Data in XML | emd_10344_validation.xml.gz | 7.9 KB | Display | |
Data in CIF | emd_10344_validation.cif.gz | 9.1 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-10344 ftp://ftp.pdbj.org/pub/emdb/validation_reports/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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Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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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Specialist optics | Energy filter - Name: GIF Bioquantum / Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number real images: 3370 / Average electron dose: 38.0 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: 3.0 µm / Nominal defocus min: 0.5 µm |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |