+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-3770 | |||||||||
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Title | Human 40S-eIF2D-re-initiation complex | |||||||||
Map data | This map was used for refinement (boxed and map origin re-set to 0). | |||||||||
Sample |
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Keywords | translation re-initiation complex / small ribosomal subunit / RNA binding protein / eukaryotic translation initiation factor / TRANSLATION | |||||||||
Function / homology | Function and homology information IRES-dependent viral translational initiation / ribosome disassembly / formation of translation preinitiation complex / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein tyrosine kinase inhibitor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage ...IRES-dependent viral translational initiation / ribosome disassembly / formation of translation preinitiation complex / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein tyrosine kinase inhibitor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of respiratory burst involved in inflammatory response / positive regulation of gastrulation / IRE1-RACK1-PP2A complex / nucleolus organization / : / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of RNA splicing / negative regulation of DNA repair / laminin receptor activity / oxidized purine DNA binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / supercoiled DNA binding / neural crest cell differentiation / negative regulation of phagocytosis / NF-kappaB complex / rRNA modification in the nucleus and cytosol / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / positive regulation of ubiquitin-protein transferase activity / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / pigmentation / protein kinase A binding / Ribosomal scanning and start codon recognition / negative regulation of ubiquitin protein ligase activity / ion channel inhibitor activity / Translation initiation complex formation / phagocytic cup / positive regulation of mitochondrial depolarization / negative regulation of Wnt signaling pathway / positive regulation of T cell receptor signaling pathway / fibroblast growth factor binding / positive regulation of activated T cell proliferation / regulation of cell division / Protein hydroxylation / TOR signaling / iron-sulfur cluster binding / BH3 domain binding / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Selenocysteine synthesis / monocyte chemotaxis / Formation of a pool of free 40S subunits / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of cyclic-nucleotide phosphodiesterase activity / Eukaryotic Translation Termination / ribosomal small subunit export from nucleus / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / translation regulator activity / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of respiratory burst involved in inflammatory response / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / L13a-mediated translational silencing of Ceruloplasmin expression / gastrulation / Major pathway of rRNA processing in the nucleolus and cytosol / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rough endoplasmic reticulum / regulation of translational fidelity / spindle assembly / MDM2/MDM4 family protein binding / laminin binding / Protein methylation / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Nuclear events stimulated by ALK signaling in cancer / rescue of stalled ribosome / signaling adaptor activity / negative regulation of smoothened signaling pathway / positive regulation of cell cycle / translation initiation factor binding / stress granule assembly / negative regulation of peptidyl-serine phosphorylation / maturation of SSU-rRNA / positive regulation of intrinsic apoptotic signaling pathway / Mitotic Prometaphase / positive regulation of apoptotic signaling pathway / EML4 and NUDC in mitotic spindle formation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / class I DNA-(apurinic or apyrimidinic site) endonuclease activity Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Hepatitis C virus / Saccharomyces cerevisiae (brewer's yeast) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 4.2 Å | |||||||||
Authors | Weisser M / Schaefer T | |||||||||
Citation | Journal: Mol Cell / Year: 2017 Title: Structural and Functional Insights into Human Re-initiation Complexes. Authors: Melanie Weisser / Tanja Schäfer / Marc Leibundgut / Daniel Böhringer / Christopher Herbert Stanley Aylett / Nenad Ban / Abstract: After having translated short upstream open reading frames, ribosomes can re-initiate translation on the same mRNA. This process, referred to as re-initiation, controls the translation of a large ...After having translated short upstream open reading frames, ribosomes can re-initiate translation on the same mRNA. This process, referred to as re-initiation, controls the translation of a large fraction of mammalian cellular mRNAs, many of which are important in cancer. Key ribosomal binding proteins involved in re-initiation are the eukaryotic translation initiation factor 2D (eIF2D) or the homologous complex of MCT-1/DENR. We determined the structures of these factors bound to the human 40S ribosomal subunit in complex with initiator tRNA positioned on an mRNA start codon in the P-site using a combination of cryoelectron microscopy and X-ray crystallography. The structures, supported by biochemical experiments, reveal how eIF2D emulates the function of several canonical translation initiation factors by using three independent, flexibly connected RNA binding domains to simultaneously monitor codon-anticodon interactions in the ribosomal P-site and position the initiator tRNA. | |||||||||
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_3770.map.gz | 7.8 MB | EMDB map data format | |
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Header (meta data) | emd-3770-v30.xml emd-3770.xml | 62.8 KB 62.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_3770_fsc.xml | 11.2 KB | Display | FSC data file |
Images | emd_3770.png | 167.5 KB | ||
Filedesc metadata | emd-3770.cif.gz | 12.4 KB | ||
Others | emd_3770_additional.map.gz emd_3770_half_map_1.map.gz emd_3770_half_map_2.map.gz | 27 MB 98.2 MB 97.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-3770 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-3770 | HTTPS FTP |
-Related structure data
Related structure data | 5oa3MC 5oa9C 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_3770.map.gz / Format: CCP4 / Size: 28.7 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | This map was used for refinement (boxed and map origin re-set to 0). | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.4 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: This map was low-pass filtered to 8 Angstroem...
File | emd_3770_additional.map | ||||||||||||
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Annotation | This map was low-pass filtered to 8 Angstroem and used for the visualization of secondary structure elements (boxed and map origin re-set to 0). | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: unboxed, unfiltered half-map; origin not re-set.
File | emd_3770_half_map_1.map | ||||||||||||
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Annotation | unboxed, unfiltered half-map; origin not re-set. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: unboxed, unfiltered half-map; origin not re-set.
File | emd_3770_half_map_2.map | ||||||||||||
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Annotation | unboxed, unfiltered half-map; origin not re-set. | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : human translation re-initiation complex of eIFD, initiator tRNA a...
+Supramolecule #1: human translation re-initiation complex of eIFD, initiator tRNA a...
+Supramolecule #2: eIF2D
+Supramolecule #3: small ribosomal subunit
+Supramolecule #4: HCV IRES mRNA
+Supramolecule #5: initiator Met-tRNA-i
+Macromolecule #1: Eukaryotic translation initiation factor 2D
+Macromolecule #5: 40S ribosomal protein SA
+Macromolecule #6: 40S ribosomal protein S3a
+Macromolecule #7: 40S ribosomal protein S2
+Macromolecule #8: 40S ribosomal protein S3
+Macromolecule #9: 40S ribosomal protein S4, X isoform
+Macromolecule #10: 40S ribosomal protein S5
+Macromolecule #11: 40S ribosomal protein S6
+Macromolecule #12: 40S ribosomal protein S7
+Macromolecule #13: 40S ribosomal protein S8
+Macromolecule #14: 40S ribosomal protein S9
+Macromolecule #15: 40S ribosomal protein S10
+Macromolecule #16: 40S ribosomal protein S11
+Macromolecule #17: 40S ribosomal protein S12
+Macromolecule #18: 40S ribosomal protein S13
+Macromolecule #19: 40S ribosomal protein S14
+Macromolecule #20: 40S ribosomal protein S15
+Macromolecule #21: 40S ribosomal protein S16
+Macromolecule #22: 40S ribosomal protein S17
+Macromolecule #23: 40S ribosomal protein S18
+Macromolecule #24: 40S ribosomal protein S19
+Macromolecule #25: 40S ribosomal protein S20
+Macromolecule #26: 40S ribosomal protein S21
+Macromolecule #27: 40S ribosomal protein S15a
+Macromolecule #28: 40S ribosomal protein S23
+Macromolecule #29: 40S ribosomal protein S24
+Macromolecule #30: 40S ribosomal protein S25
+Macromolecule #31: 40S ribosomal protein S26
+Macromolecule #32: 40S ribosomal protein S27
+Macromolecule #33: 40S ribosomal protein S28
+Macromolecule #34: 40S ribosomal protein S29
+Macromolecule #35: 40S ribosomal protein S30
+Macromolecule #36: Ribosomal protein S27a
+Macromolecule #37: Receptor of activated protein C kinase 1
+Macromolecule #38: RIBOSOMAL PROTEIN EL41
+Macromolecule #2: initiator Met-tRNA-i
+Macromolecule #3: 18S ribosomal RNA
+Macromolecule #4: IRES mRNA
+Macromolecule #39: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 0.11 mg/mL | |||||||||||||||
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Buffer | pH: 7.6 Component:
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Grid | Model: Quantifoil R2/2 / Pretreatment - Type: GLOW DISCHARGE | |||||||||||||||
Vitrification | Cryogen name: ETHANE-PROPANE |
-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 |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Average electron dose: 40.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |