+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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Keywords | ribosome / translation / initiation complex | ||||||||||||
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 / glial limiting end-foot / response to kainic acid / viral translational termination-reinitiation / Cellular response to mitochondrial stress ...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 / glial limiting end-foot / response to kainic acid / viral translational termination-reinitiation / Cellular response to mitochondrial stress / positive regulation of mRNA cis splicing, via spliceosome / positive regulation of translation in response to endoplasmic reticulum stress / response to manganese-induced endoplasmic reticulum stress / eukaryotic translation initiation factor 3 complex, eIF3e / positive regulation of type B pancreatic cell apoptotic process / methionyl-initiator methionine tRNA binding / cap-dependent translational initiation / eukaryotic translation initiation factor 3 complex, eIF3m / negative regulation of translational initiation in response to stress / Response of EIF2AK1 (HRI) to heme deficiency / 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 / translation reinitiation / PERK-mediated unfolded protein response / regulation of cellular response to stress / eukaryotic initiation factor 4E binding / IRES-dependent viral translational initiation / PERK regulates gene expression / eukaryotic translation initiation factor 2 complex / regulation of translational initiation in response to stress / Z-decay: degradation of maternal mRNAs by zygotically expressed factors / multi-eIF complex / eukaryotic translation initiation factor 3 complex / selenocysteine metabolic process / RNA cap binding / eukaryotic translation initiation factor 4F complex / selenocysteine incorporation / eukaryotic 43S preinitiation complex / Deadenylation of mRNA / protein-synthesizing GTPase / cytoplasmic translational initiation / translation factor activity, RNA binding / mRNA cap binding / formation of cytoplasmic translation initiation complex / selenocysteine insertion sequence binding / 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 / miRNA-mediated gene silencing by inhibition of translation / response to TNF agonist / positive regulation of base-excision repair / protein tyrosine kinase inhibitor activity / positive regulation of respiratory burst involved in inflammatory response / eukaryotic 48S preinitiation complex / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / nucleolus organization / M-decay: degradation of maternal mRNAs by maternally stored factors / IRE1-RACK1-PP2A complex / : / 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 / metal-dependent deubiquitinase activity / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / oxidized purine DNA binding / supercoiled DNA binding / positive regulation of protein localization to cell periphery / neural crest cell differentiation / NF-kappaB complex / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / negative regulation of phagocytosis / positive regulation of ubiquitin-protein transferase activity / Formation of the ternary complex, and subsequently, the 43S complex / regulation of translational initiation / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / laminin receptor activity / protein kinase A binding / Translation initiation complex formation / Ribosomal scanning and start codon recognition / negative regulation of ubiquitin protein ligase activity / ion channel inhibitor activity / pigmentation / mammalian oogenesis stage / positive regulation of mitochondrial depolarization / activation-induced cell death of T cells / negative regulation of Wnt signaling pathway / fibroblast growth factor binding / positive regulation of T cell receptor signaling pathway / positive regulation of activated T cell proliferation / iron-sulfur cluster binding Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.7 Å | ||||||||||||
Authors | Brito Querido J / Sokabe M | ||||||||||||
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 | 100.5 KB 100.5 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 | |
Filedesc metadata | emd-11302.cif.gz | 19.7 KB | ||
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 |
-Validation report
Summary document | emd_11302_validation.pdf.gz | 189.9 KB | Display | EMDB validaton report |
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Full document | emd_11302_full_validation.pdf.gz | 189.4 KB | Display | |
Data in XML | emd_11302_validation.xml.gz | 501 B | Display | |
Data in CIF | emd_11302_validation.cif.gz | 373 B | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-11302 ftp://ftp.pdbj.org/pub/emdb/validation_reports/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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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 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |