+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-11302 | ||||||||||||
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Title | Structure of a human 48S translational initiation complex | ||||||||||||
Map data | |||||||||||||
Sample |
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Function / homology | Function and homology information positive regulation of eukaryotic translation initiation factor 4F complex assembly / positive regulation of mRNA cap binding / male germ cell proliferation / positive regulation of mRNA binding / regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / viral translational termination-reinitiation / glial limiting end-foot / response to kainic acid / positive regulation of mRNA cis splicing, via spliceosome ...positive regulation of eukaryotic translation initiation factor 4F complex assembly / positive regulation of mRNA cap binding / male germ cell proliferation / positive regulation of mRNA binding / regulation of translation in response to endoplasmic reticulum stress / translation initiation ternary complex / viral translational termination-reinitiation / glial limiting end-foot / response to kainic acid / positive regulation of mRNA cis splicing, via spliceosome / positive regulation of translation in response to endoplasmic reticulum stress / eukaryotic translation initiation factor 3 complex, eIF3e / response to manganese-induced endoplasmic reticulum stress / positive regulation of type B pancreatic cell apoptotic process / cap-dependent translational initiation / methionyl-initiator methionine tRNA binding / eukaryotic translation initiation factor 3 complex, eIF3m / translation reinitiation / Response of EIF2AK1 (HRI) to heme deficiency / negative regulation of translational initiation in response to stress / macromolecule biosynthetic process / Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S / Recycling of eIF2:GDP / PERK-mediated unfolded protein response / eukaryotic translation initiation factor 2 complex / eukaryotic initiation factor 4E binding / IRES-dependent viral translational initiation / PERK regulates gene expression / regulation of cellular response to stress / regulation of translational initiation in response to stress / multi-eIF complex / eukaryotic translation initiation factor 3 complex / RNA cap binding / eukaryotic translation initiation factor 4F complex / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / eukaryotic 43S preinitiation complex / cytoplasmic translational initiation / translation factor activity, RNA binding / protein-synthesizing GTPase / mRNA cap binding / formation of cytoplasmic translation initiation complex / formation of translation preinitiation 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 / miRNA-mediated gene silencing by inhibition of translation / 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 / metal-dependent deubiquitinase activity / response to extracellular stimulus / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of DNA repair / negative regulation of RNA splicing / M-decay: degradation of maternal mRNAs by maternally stored factors / laminin receptor activity / : / oxidized purine DNA binding / positive regulation of protein localization to cell periphery / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / supercoiled DNA binding / neural crest cell differentiation / NF-kappaB complex / rRNA modification in the nucleus and cytosol / negative regulation of phagocytosis / 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 / regulation of translational initiation / 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 / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / 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 / fibroblast growth factor binding / regulation of cell division / SARS-CoV-1 modulates host translation machinery / iron-sulfur cluster binding / Protein hydroxylation Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) / Human (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||
Authors | Brito Querido J / Sokabe M / Kraatz S / Gordiyenko Y / Skehel M / Fraser C / Ramakrishnan V | ||||||||||||
Funding support | United Kingdom, United States, 3 items
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Citation | Journal: Science / Year: 2020 Title: Structure of a human 48 translational initiation complex. Authors: Jailson Brito Querido / Masaaki Sokabe / Sebastian Kraatz / Yuliya Gordiyenko / J Mark Skehel / Christopher S Fraser / V Ramakrishnan / Abstract: A key step in translational initiation is the recruitment of the 43 preinitiation complex by the cap-binding complex [eukaryotic initiation factor 4F (eIF4F)] at the 5' end of messenger RNA (mRNA) to ...A key step in translational initiation is the recruitment of the 43 preinitiation complex by the cap-binding complex [eukaryotic initiation factor 4F (eIF4F)] at the 5' end of messenger RNA (mRNA) to form the 48 initiation complex (i.e., the 48). The 48 then scans along the mRNA to locate a start codon. To understand the mechanisms involved, we used cryo-electron microscopy to determine the structure of a reconstituted human 48 The structure reveals insights into early events of translation initiation complex assembly, as well as how eIF4F interacts with subunits of eIF3 near the mRNA exit channel in the 43 The location of eIF4F is consistent with a slotting model of mRNA recruitment and suggests that downstream mRNA is unwound at least in part by being "pulled" through the 40 subunit during scanning. | ||||||||||||
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_11302.map.gz | 416.6 MB | EMDB map data format | |
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Header (meta data) | emd-11302-v30.xml emd-11302.xml | 95.7 KB 95.7 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_11302_fsc.xml | 17.7 KB | Display | FSC data file |
Images | emd_11302.png | 156.1 KB | ||
Masks | emd_11302_msk_1.map | 476.8 MB | Mask map | |
Others | emd_11302_additional_1.map.gz emd_11302_additional_2.map.gz emd_11302_additional_3.map.gz emd_11302_additional_4.map.gz emd_11302_additional_5.map.gz emd_11302_additional_6.map.gz emd_11302_half_map_1.map.gz emd_11302_half_map_2.map.gz | 13.2 MB 382 MB 26.5 MB 34.1 MB 25.8 MB 382.5 MB 384.2 MB 384.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-11302 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-11302 | HTTPS FTP |
-Related structure data
Related structure data | 6zmwMC 6ybdC 6ybsC 6ybtC 6ybvC 6ybwC 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_11302.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Voxel size | X=Y=Z: 1.074 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Mask #1
File | emd_11302_msk_1.map | ||||||||||||
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-Additional map: #1
File | emd_11302_additional_1.map | ||||||||||||
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-Additional map: #5
File | emd_11302_additional_2.map | ||||||||||||
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-Additional map: #4
File | emd_11302_additional_3.map | ||||||||||||
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-Additional map: #3
File | emd_11302_additional_4.map | ||||||||||||
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-Additional map: #2
File | emd_11302_additional_5.map | ||||||||||||
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-Additional map: Additional map 3j
File | emd_11302_additional_6.map | ||||||||||||
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Annotation | Additional map 3j | ||||||||||||
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-Half map: #2
File | emd_11302_half_map_1.map | ||||||||||||
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Density Histograms |
-Half map: #1
File | emd_11302_half_map_2.map | ||||||||||||
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Density Histograms |
-Sample components
+Entire : 48S initiation complex
+Supramolecule #1: 48S initiation complex
+Supramolecule #2: 48S initiation complex
+Supramolecule #3: 48S initiation complex
+Macromolecule #1: Eukaryotic translation initiation factor 3 subunit I
+Macromolecule #2: Eukaryotic translation initiation factor 3 subunit B
+Macromolecule #3: Eukaryotic translation initiation factor 3 subunit M
+Macromolecule #4: Eukaryotic translation initiation factor 3 subunit F
+Macromolecule #5: Eukaryotic translation initiation factor 3 subunit A
+Macromolecule #6: Eukaryotic translation initiation factor 3 subunit E
+Macromolecule #7: 40S ribosomal protein S6
+Macromolecule #8: Eukaryotic translation initiation factor 3 subunit C
+Macromolecule #9: Eukaryotic translation initiation factor 3 subunit H
+Macromolecule #10: 40S ribosomal protein S7
+Macromolecule #11: 40S ribosomal protein S27
+Macromolecule #12: 40S ribosomal protein S21
+Macromolecule #13: 40S ribosomal protein S2
+Macromolecule #14: 40S ribosomal protein S3a
+Macromolecule #15: 40S ribosomal protein SA
+Macromolecule #16: 40S ribosomal protein S26
+Macromolecule #17: 40S ribosomal protein S14
+Macromolecule #18: 40S ribosomal protein S13
+Macromolecule #19: Eukaryotic translation initiation factor 3 subunit D
+Macromolecule #20: Eukaryotic translation initiation factor 3 subunit K
+Macromolecule #21: Eukaryotic translation initiation factor 3 subunit L
+Macromolecule #23: 60S ribosomal protein L41
+Macromolecule #25: 40S ribosomal protein S11
+Macromolecule #26: 40S ribosomal protein S4, X isoform
+Macromolecule #27: 40S ribosomal protein S9
+Macromolecule #28: 40S ribosomal protein S23
+Macromolecule #29: 40S ribosomal protein S30
+Macromolecule #30: Eukaryotic translation initiation factor 2 subunit 1
+Macromolecule #31: 40S ribosomal protein S15a
+Macromolecule #32: 40S ribosomal protein S8
+Macromolecule #33: 40S ribosomal protein S24
+Macromolecule #34: 40S ribosomal protein S5
+Macromolecule #35: 40S ribosomal protein S16
+Macromolecule #36: 40S ribosomal protein S3
+Macromolecule #37: 40S ribosomal protein S10
+Macromolecule #38: 40S ribosomal protein S15
+Macromolecule #39: Receptor of activated protein C kinase 1
+Macromolecule #40: 40S ribosomal protein S19
+Macromolecule #41: 40S ribosomal protein S25
+Macromolecule #42: 40S ribosomal protein S18
+Macromolecule #43: 40S ribosomal protein S29
+Macromolecule #44: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #45: 40S ribosomal protein S12
+Macromolecule #46: 40S ribosomal protein S28
+Macromolecule #47: Eukaryotic translation initiation factor 3 subunit G
+Macromolecule #48: Eukaryotic translation initiation factor 1
+Macromolecule #49: Eukaryotic translation initiation factor 1A, X-chromosomal
+Macromolecule #50: Eukaryotic translation initiation factor 3 subunit J
+Macromolecule #51: 40S ribosomal protein S17
+Macromolecule #52: 40S ribosomal protein S20
+Macromolecule #53: Eukaryotic translation initiation factor 2 subunit 2
+Macromolecule #55: Eukaryotic translation initiation factor 2 subunit 3
+Macromolecule #56: Eukaryotic initiation factor 4A-I
+Macromolecule #57: Eukaryotic translation initiation factor 4 gamma 1
+Macromolecule #22: mRNA
+Macromolecule #24: 18S rRNA
+Macromolecule #54: Initiator Met-tRNA-i
+Macromolecule #58: ZINC ION
+Macromolecule #59: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 |
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Grid | Model: Quantifoil / Material: COPPER / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / 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 |
Image recording | Film or detector model: FEI FALCON III (4k x 4k) / Detector mode: INTEGRATING / Average exposure time: 1.0 sec. / Average electron dose: 107.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |