+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-12189 | |||||||||
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Title | Cryo-EM structure of the human Ebp1 - 80S ribosome | |||||||||
Map data | ||||||||||
Sample |
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Keywords | EBP1 / PAG2G4 / MetAP2 / metalloprotease / ribosome / ES27 / ribosomal tunnel exit | |||||||||
Function / homology | Function and homology information 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 / TORC2 complex binding / GAIT complex / middle ear morphogenesis / A band ...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 / TORC2 complex binding / GAIT complex / middle ear morphogenesis / A band / alpha-beta T cell differentiation / cytoplasmic side of rough endoplasmic reticulum membrane / exit from mitosis / 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 / negative regulation of ubiquitin protein ligase activity / optic nerve development / response to aldosterone / retinal ganglion cell axon guidance / homeostatic process / macrophage chemotaxis / lung morphogenesis / male meiosis I / Protein hydroxylation / Peptide chain elongation / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / blastocyst development / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / protein localization to nucleus / 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 targeting / protein-RNA complex assembly / cellular response to interleukin-4 / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of ubiquitin-dependent protein catabolic process / rough endoplasmic reticulum / MDM2/MDM4 family protein binding / Maturation of protein E / Maturation of protein E / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / ER Quality Control Compartment (ERQC) / maturation of LSU-rRNA / Myoclonic epilepsy of Lafora / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Glycogen synthesis / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TICAM1,TRAF6-dependent induction of TAK1 complex / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Membrane binding and targetting of GAG proteins / Endosomal Sorting Complex Required For Transport (ESCRT) / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / cytosolic ribosome / Regulation of FZD by ubiquitination / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / VLDLR internalisation and degradation / embryo implantation / Downregulation of ERBB4 signaling / TRAF6-mediated induction of TAK1 complex within TLR4 complex / TRAF6 mediated IRF7 activation in TLR7/8 or 9 signaling / APC-Cdc20 mediated degradation of Nek2A / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Regulation of innate immune responses to cytosolic DNA / InlA-mediated entry of Listeria monocytogenes into host cells / NF-kB is activated and signals survival / Regulation of pyruvate metabolism / Downregulation of ERBB2:ERBB3 signaling / NRIF signals cell death from the nucleus / Pexophagy / Regulation of PTEN localization / ossification / Activated NOTCH1 Transmits Signal to the Nucleus / Regulation of BACH1 activity / Translesion synthesis by REV1 / TICAM1, RIP1-mediated IKK complex recruitment / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / MAP3K8 (TPL2)-dependent MAPK1/3 activation / Translesion synthesis by POLK / ribosomal large subunit biogenesis Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.3 Å | |||||||||
Authors | Desogus J / Bhaskar V | |||||||||
Funding support | Switzerland, 2 items
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Citation | Journal: RNA / Year: 2021 Title: Dynamic association of human Ebp1 with the ribosome. Authors: Varun Bhaskar / Jessica Desogus / Alexandra Graff-Meyer / Andreas D Schenk / Simone Cavadini / Jeffrey A Chao / Abstract: Ribosomes are the macromolecular machines at the heart of protein synthesis; however, their function can be modulated by a variety of additional protein factors that directly interact with them. ...Ribosomes are the macromolecular machines at the heart of protein synthesis; however, their function can be modulated by a variety of additional protein factors that directly interact with them. Here, we report the cryo-EM structure of human Ebp1 (p48 isoform) bound to the human 80S ribosome at 3.3 Å resolution. Ebp1 binds in the vicinity of the peptide exit tunnel on the 80S ribosome, and this binding is enhanced upon puromycin-mediated translational inhibition. The association of Ebp1 with the 80S ribosome centers around its interaction with ribosomal proteins eL19 and uL23 and the 28S rRNA. Further analysis of the Ebp1-ribosome complex suggests that Ebp1 can rotate around its insert domain, which may enable it to assume a wide range of conformations while maintaining its interaction with the ribosome. Structurally, Ebp1 shares homology with the methionine aminopeptidase 2 family of enzymes; therefore, this inherent flexibility may also be conserved. | |||||||||
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_12189.map.gz | 52.6 MB | EMDB map data format | |
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Header (meta data) | emd-12189-v30.xml emd-12189.xml | 61.9 KB 61.9 KB | Display Display | EMDB header |
Images | emd_12189.png | 42.6 KB | ||
Filedesc metadata | emd-12189.cif.gz | 13.8 KB | ||
Others | emd_12189_additional_1.map.gz | 55.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-12189 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-12189 | HTTPS FTP |
-Validation report
Summary document | emd_12189_validation.pdf.gz | 407.3 KB | Display | EMDB validaton report |
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Full document | emd_12189_full_validation.pdf.gz | 406.9 KB | Display | |
Data in XML | emd_12189_validation.xml.gz | 8.3 KB | Display | |
Data in CIF | emd_12189_validation.cif.gz | 9.7 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12189 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-12189 | HTTPS FTP |
-Related structure data
Related structure data | 7bhpMC 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_12189.map.gz / Format: CCP4 / Size: 824 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: 0.86 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: #1
File | emd_12189_additional_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Complex of human EBP1 and 80S ribosome
+Supramolecule #1: Complex of human EBP1 and 80S ribosome
+Macromolecule #1: 28S ribosomal RNA
+Macromolecule #2: 5S ribosomal RNA
+Macromolecule #3: 5.8S ribosomal RNA
+Macromolecule #45: Poly GC double helix strand modeled for ES27L density next to EBP...
+Macromolecule #4: 60S ribosomal protein L8
+Macromolecule #5: 60S ribosomal protein L3
+Macromolecule #6: 60S ribosomal protein L4
+Macromolecule #7: 60S ribosomal protein L5
+Macromolecule #8: 60S ribosomal protein L6
+Macromolecule #9: 60S ribosomal protein L7
+Macromolecule #10: 60S ribosomal protein L7a
+Macromolecule #11: 60S ribosomal protein L9
+Macromolecule #12: 60S ribosomal protein L10-like
+Macromolecule #13: 60S ribosomal protein L11
+Macromolecule #14: 60S ribosomal protein L13
+Macromolecule #15: 60S ribosomal protein L14
+Macromolecule #16: 60S ribosomal protein L15
+Macromolecule #17: 60S ribosomal protein L13a
+Macromolecule #18: 60S ribosomal protein L17
+Macromolecule #19: 60S ribosomal protein L18
+Macromolecule #20: 60S ribosomal protein L19
+Macromolecule #21: 60S ribosomal protein L18a
+Macromolecule #22: 60S ribosomal protein L21
+Macromolecule #23: 60S ribosomal protein L22
+Macromolecule #24: 60S ribosomal protein L24
+Macromolecule #25: 60S ribosomal protein L23a
+Macromolecule #26: 60S ribosomal protein L26
+Macromolecule #27: 60S ribosomal protein L27
+Macromolecule #28: 60S ribosomal protein L27a
+Macromolecule #29: 60S ribosomal protein L29
+Macromolecule #30: 60S ribosomal protein L30
+Macromolecule #31: 60S ribosomal protein L31
+Macromolecule #32: 60S ribosomal protein L32
+Macromolecule #33: 60S ribosomal protein L35a
+Macromolecule #34: 60S ribosomal protein L34
+Macromolecule #35: 60S ribosomal protein L35
+Macromolecule #36: 60S ribosomal protein L36
+Macromolecule #37: 60S ribosomal protein L37
+Macromolecule #38: 60S ribosomal protein L38
+Macromolecule #39: 60S ribosomal protein L39
+Macromolecule #40: Ubiquitin-60S ribosomal protein L40
+Macromolecule #41: 60S ribosomal protein L36a
+Macromolecule #42: 60S ribosomal protein L37a
+Macromolecule #43: 60S ribosomal protein L28
+Macromolecule #44: Proliferation-associated protein 2G4
+Macromolecule #46: MAGNESIUM ION
+Macromolecule #47: ZINC ION
+Macromolecule #48: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Average electron dose: 40.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Startup model | Type of model: PDB ENTRY |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.3 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 44556 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |
-Atomic model buiding 1
Initial model |
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Refinement | Protocol: RIGID BODY FIT | ||||||||
Output model | PDB-7bhp: |