+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-4242 | |||||||||
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Title | Human cap-dependent 48S pre-initiation complex | |||||||||
Map data | human 48S pre-initiation complex, reconstituted in the presence of capped mRNA, eIF4B and eIF4F, displaying eIF2 ternary complex, eIF3 and eIF4B | |||||||||
Sample |
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Function / homology | Function and homology information positive regulation of mRNA binding / viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / methionyl-initiator methionine tRNA binding / eukaryotic translation initiation factor 3 complex, eIF3m / Response of EIF2AK1 (HRI) to heme deficiency / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Recycling of eIF2:GDP / eukaryotic translation initiation factor 2 complex / PERK regulates gene expression ...positive regulation of mRNA binding / viral translational termination-reinitiation / eukaryotic translation initiation factor 3 complex, eIF3e / methionyl-initiator methionine tRNA binding / eukaryotic translation initiation factor 3 complex, eIF3m / Response of EIF2AK1 (HRI) to heme deficiency / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Recycling of eIF2:GDP / eukaryotic translation initiation factor 2 complex / PERK regulates gene expression / eukaryotic translation initiation factor 3 complex / eukaryotic translation initiation factor 4F complex / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / eukaryotic 43S preinitiation complex / protein-synthesizing GTPase / cytoplasmic translational initiation / translation factor activity, RNA binding / formation of translation preinitiation complex / formation of cytoplasmic translation initiation complex / Deadenylation of mRNA / 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 / eukaryotic 48S preinitiation complex / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / IRE1-RACK1-PP2A complex / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / M-decay: degradation of maternal mRNAs by maternally stored factors / negative regulation of RNA splicing / laminin receptor activity / negative regulation of DNA repair / 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 / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / regulation of translational initiation / Formation of the ternary complex, and subsequently, the 43S complex / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / 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 / 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 / Selenocysteine synthesis / 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 phosphatidylinositol 3-kinase/protein kinase B signal transduction / L13a-mediated translational silencing of Ceruloplasmin expression / gastrulation / rough endoplasmic reticulum / regulation of translational fidelity / spindle assembly / Major pathway of rRNA processing in the nucleolus and cytosol / MDM2/MDM4 family protein binding / laminin binding / 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 / negative regulation of smoothened signaling pathway / signaling adaptor activity Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 6.3 Å | |||||||||
Authors | Schaffitzel C | |||||||||
Citation | Journal: Nucleic Acids Res / Year: 2018 Title: Structure of a human cap-dependent 48S translation pre-initiation complex. Authors: Boris Eliseev / Lahari Yeramala / Alexander Leitner / Manikandan Karuppasamy / Etienne Raimondeau / Karine Huard / Elena Alkalaeva / Ruedi Aebersold / Christiane Schaffitzel / Abstract: Eukaryotic translation initiation is tightly regulated, requiring a set of conserved initiation factors (eIFs). Translation of a capped mRNA depends on the trimeric eIF4F complex and eIF4B to load ...Eukaryotic translation initiation is tightly regulated, requiring a set of conserved initiation factors (eIFs). Translation of a capped mRNA depends on the trimeric eIF4F complex and eIF4B to load the mRNA onto the 43S pre-initiation complex comprising 40S and initiation factors 1, 1A, 2, 3 and 5 as well as initiator-tRNA. Binding of the mRNA is followed by mRNA scanning in the 48S pre-initiation complex, until a start codon is recognised. Here, we use a reconstituted system to prepare human 48S complexes assembled on capped mRNA in the presence of eIF4B and eIF4F. The highly purified h-48S complexes are used for cross-linking/mass spectrometry, revealing the protein interaction network in this complex. We report the electron cryo-microscopy structure of the h-48S complex at 6.3 Å resolution. While the majority of eIF4B and eIF4F appear to be flexible with respect to the ribosome, additional density is detected at the entrance of the 40S mRNA channel which we attribute to the RNA-recognition motif of eIF4B. The eight core subunits of eIF3 are bound at the 40S solvent-exposed side, as well as the subunits eIF3d, eIF3b and eIF3i. elF2 and initiator-tRNA bound to the start codon are present at the 40S intersubunit side. This cryo-EM structure represents a molecular snap-shot revealing the h-48S complex following start codon recognition. | |||||||||
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_4242.map.gz | 32.1 MB | EMDB map data format | |
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Header (meta data) | emd-4242-v30.xml emd-4242.xml | 71.1 KB 71.1 KB | Display Display | EMDB header |
Images | emd_4242.png | 56.4 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-4242 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-4242 | HTTPS FTP |
-Related structure data
Related structure data | 6fecMC 4265C 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_4242.map.gz / Format: CCP4 / Size: 34.3 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | human 48S pre-initiation complex, reconstituted in the presence of capped mRNA, eIF4B and eIF4F, displaying eIF2 ternary complex, eIF3 and eIF4B | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 2.5 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 cap-dependent 48S translation pre-initiation complex
+Supramolecule #1: human cap-dependent 48S translation pre-initiation complex
+Supramolecule #2: human cap-dependent 48S translation pre-initiation complex
+Supramolecule #3: mRNA
+Supramolecule #4: Eukaryotic translation initiation factor 4B
+Macromolecule #1: Eukaryotic translation initiation factor 3 subunit A
+Macromolecule #2: Eukaryotic translation initiation factor 3 subunit C
+Macromolecule #3: Eukaryotic translation initiation factor 3 subunit E
+Macromolecule #4: Eukaryotic translation initiation factor 3 subunit F
+Macromolecule #5: Eukaryotic translation initiation factor 3 subunit H
+Macromolecule #6: Eukaryotic translation initiation factor 3 subunit K
+Macromolecule #7: Eukaryotic translation initiation factor 3 subunit L
+Macromolecule #8: Eukaryotic translation initiation factor 3 subunit M
+Macromolecule #9: EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT D
+Macromolecule #12: 40S ribosomal protein S11
+Macromolecule #13: 40S ribosomal protein S16
+Macromolecule #14: 40S ribosomal protein S4, X isoform
+Macromolecule #15: 40S ribosomal protein S29
+Macromolecule #16: 40S ribosomal protein S9
+Macromolecule #17: 40S ribosomal protein S18
+Macromolecule #19: Eukaryotic translation initiation factor 2 subunit 1
+Macromolecule #20: 40S ribosomal protein S23
+Macromolecule #21: 40S ribosomal protein S19
+Macromolecule #22: Eukaryotic translation initiation factor 2 subunit 3
+Macromolecule #23: 40S ribosomal protein S5
+Macromolecule #24: 40S ribosomal protein S30
+Macromolecule #25: 40S ribosomal protein S25
+Macromolecule #26: 40S ribosomal protein S7
+Macromolecule #27: 40S ribosomal protein S27
+Macromolecule #28: 40S ribosomal protein S13
+Macromolecule #29: 40S ribosomal protein S15a
+Macromolecule #30: 40S ribosomal protein S21
+Macromolecule #31: 40S ribosomal protein S2
+Macromolecule #32: EUKARYOTIC TRANSLATION INITIATION FACTOR 2 BETA SUBUNIT (eIF2-Beta)
+Macromolecule #33: 40S ribosomal protein S17
+Macromolecule #34: 40S ribosomal protein SA
+Macromolecule #35: 40S ribosomal protein S3
+Macromolecule #36: 40S ribosomal protein S20
+Macromolecule #37: 40S ribosomal protein S3a
+Macromolecule #38: 40S ribosomal protein S14
+Macromolecule #39: 40S ribosomal protein S26
+Macromolecule #40: 40S ribosomal protein S28
+Macromolecule #41: Receptor of activated protein C kinase 1
+Macromolecule #42: 40S ribosomal protein S15
+Macromolecule #43: 40S ribosomal protein S8
+Macromolecule #44: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #45: 40S ribosomal protein S6
+Macromolecule #46: 40S ribosomal protein S12
+Macromolecule #47: 40S ribosomal protein S24
+Macromolecule #48: 40S ribosomal protein S10
+Macromolecule #49: Eukaryotic translation initiation factor 4B
+Macromolecule #50: Eukaryotic translation initiation factor 3 subunit B
+Macromolecule #10: 18S ribosomal RNA
+Macromolecule #11: Messenger RNA (26-MER)
+Macromolecule #18: Transfer RNA (75-MER)
+Macromolecule #51: 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 Details: 20 mM Tris HCl, 50 mM KOAc, 2.5 mM MgCl2, 2 mM DTT, 0.25 mM spermidine 0.25 mM GMPPNP |
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Grid | Model: Quantifoil R2/2 |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
-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 / Nominal defocus max: 4.0 µm / Nominal defocus min: 1.5 µm / Nominal magnification: 112000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Image recording | Film or detector model: FEI FALCON II (4k x 4k) / Detector mode: INTEGRATING / Average electron dose: 30.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
CTF correction | Software - Name: CTFFIND (ver. 4) |
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Startup model | Type of model: EMDB MAP EMDB ID: |
Initial angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4) |
Final 3D classification | Software - Name: RELION (ver. 1.4) |
Final angle assignment | Type: PROJECTION MATCHING / Software - Name: RELION (ver. 1.4) |
Final reconstruction | Number classes used: 1 / Applied symmetry - Point group: C1 (asymmetric) / Algorithm: BACK PROJECTION / Resolution.type: BY AUTHOR / Resolution: 6.3 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 1.4) / Number images used: 50604 |
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: RIGID BODY FIT / Target criteria: Cross-correlation coefficient |
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Output model | PDB-6fec: |