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Open data
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Basic information
| Entry | ![]() | |||||||||||||||
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| Title | human 48S PIC with mRNA (Kozak_2) | |||||||||||||||
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Keywords | translation initiation / 48S PIC / human / RIBOSOME | |||||||||||||||
| Function / homology | Function and homology informationmale germ cell proliferation / translation initiation ternary complex / regulation of translation in response to endoplasmic reticulum stress / glial limiting end-foot / HRI-mediated signaling / viral translational termination-reinitiation / response to manganese-induced endoplasmic reticulum stress / Cellular response to mitochondrial stress / positive regulation of type B pancreatic cell apoptotic process / Response of EIF2AK1 (HRI) to heme deficiency ...male germ cell proliferation / translation initiation ternary complex / regulation of translation in response to endoplasmic reticulum stress / glial limiting end-foot / HRI-mediated signaling / viral translational termination-reinitiation / response to manganese-induced endoplasmic reticulum stress / Cellular response to mitochondrial stress / positive regulation of type B pancreatic cell apoptotic process / Response of EIF2AK1 (HRI) to heme deficiency / eukaryotic translation initiation factor 3 complex, eIF3e / methionyl-initiator methionine tRNA binding / Recycling of eIF2:GDP / negative regulation of translational initiation in response to stress / cap-dependent translational initiation / PERK-mediated unfolded protein response / eukaryotic translation initiation factor 3 complex, eIF3m / PERK regulates gene expression / IRES-dependent viral translational initiation / response to kainic acid / translation reinitiation / eukaryotic translation initiation factor 2 complex / formation of cytoplasmic translation initiation complex / multi-eIF complex / regulation of translational initiation in response to stress / eukaryotic translation initiation factor 3 complex / eukaryotic 43S preinitiation complex / translation factor activity, RNA binding / formation of translation preinitiation complex / mRNA cap binding / eukaryotic 48S preinitiation complex / negative regulation of endoplasmic reticulum unfolded protein response / regulation of translational initiation / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / positive regulation of respiratory burst involved in inflammatory response / protein-synthesizing GTPase / positive regulation of gastrulation / nuclear-transcribed mRNA catabolic process, nonsense-mediated decay / positive regulation of ubiquitin-protein transferase activity / protein tyrosine kinase inhibitor activity / positive regulation of DNA-templated transcription initiation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / IRE1-RACK1-PP2A complex / positive regulation of Golgi to plasma membrane protein transport / nucleolus organization / TNFR1-mediated ceramide production / negative regulation of RNA splicing / metal-dependent deubiquitinase activity / neural crest cell differentiation / supercoiled DNA binding / cytoplasmic translational initiation / NF-kappaB complex / negative regulation of DNA repair / oxidized purine DNA binding / cysteine-type endopeptidase activator activity involved in apoptotic process / rRNA modification in the nucleus and cytosol / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of bicellular tight junction assembly / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / negative regulation of phagocytosis / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / Formation of the ternary complex, and subsequently, the 43S complex / ion channel inhibitor activity / protein kinase A binding / laminin receptor activity / pigmentation / Ribosomal scanning and start codon recognition / positive regulation of mitochondrial depolarization / Translation initiation complex formation / negative regulation of Wnt signaling pathway / fibroblast growth factor binding / Protein hydroxylation / monocyte chemotaxis / BH3 domain binding / negative regulation of translational frameshifting / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / positive regulation of GTPase activity / TOR signaling / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / iron-sulfur cluster binding / regulation of cell division / Peptide chain elongation / cellular response to ethanol / Selenocysteine synthesis / Formation of a pool of free 40S subunits / negative regulation of protein binding / protein serine/threonine kinase inhibitor activity / Eukaryotic Translation Termination / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / ubiquitin ligase inhibitor activity / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / negative regulation of respiratory burst involved in inflammatory response / Viral mRNA Translation / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) Similarity search - Function | |||||||||||||||
| Biological species | Homo sapiens (human) | |||||||||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.0 Å | |||||||||||||||
Authors | von Loeffelholz O / Barchet C / Klaholz B | |||||||||||||||
| Funding support | France, 4 items
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Citation | Journal: To Be PublishedTitle: human 48S PIC with Kozak_1 mRNA Authors: von Loeffelholz O / Barchet C / Holvec S / Abou Ramadan A / Maglott-Roth A / de Silva SNT / Hazemann I / Klaholz B | |||||||||||||||
| History |
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_57010.map.gz | 381.5 MB | EMDB map data format | |
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| Header (meta data) | emd-57010-v30.xml emd-57010.xml | 69.9 KB 69.9 KB | Display Display | EMDB header |
| Images | emd_57010.png | 65.9 KB | ||
| Filedesc metadata | emd-57010.cif.gz | 17.6 KB | ||
| Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-57010 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-57010 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 28zyMC ![]() 28zxC C: citing same article ( M: atomic model generated by this map |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_57010.map.gz / Format: CCP4 / Size: 536.4 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: 0.72 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : 48S PIC
+Supramolecule #1: 48S PIC
+Macromolecule #1: 18S ribosomal RNA
+Macromolecule #21: mRNA
+Macromolecule #40: initiator tRNA
+Macromolecule #2: 60S ribosomal protein L41
+Macromolecule #3: Small ribosomal subunit protein eS4, X isoform
+Macromolecule #4: 40S ribosomal protein SA
+Macromolecule #5: 40S ribosomal protein S3a
+Macromolecule #6: 40S ribosomal protein S7
+Macromolecule #7: 40S ribosomal protein S8
+Macromolecule #8: Small ribosomal subunit protein uS17
+Macromolecule #9: 40S ribosomal protein S21
+Macromolecule #10: 40S ribosomal protein S23
+Macromolecule #11: 40S ribosomal protein S26
+Macromolecule #12: 40S ribosomal protein S2
+Macromolecule #13: 40S ribosomal protein S6
+Macromolecule #14: 40S ribosomal protein S9
+Macromolecule #15: 40S ribosomal protein S13
+Macromolecule #16: 40S ribosomal protein S14
+Macromolecule #17: 40S ribosomal protein S15a
+Macromolecule #18: 40S ribosomal protein S24
+Macromolecule #19: 40S ribosomal protein S27
+Macromolecule #20: Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
+Macromolecule #22: 40S ribosomal protein S3
+Macromolecule #23: 40S ribosomal protein S5
+Macromolecule #24: Ubiquitin
+Macromolecule #25: 40S ribosomal protein S17
+Macromolecule #26: 40S ribosomal protein S29
+Macromolecule #27: Receptor of activated protein C kinase 1
+Macromolecule #28: 40S ribosomal protein S28
+Macromolecule #29: 40S ribosomal protein S10
+Macromolecule #30: 40S ribosomal protein S12
+Macromolecule #31: 40S ribosomal protein S20
+Macromolecule #32: 40S ribosomal protein S16
+Macromolecule #33: 40S ribosomal protein S18
+Macromolecule #34: Small ribosomal subunit protein eS19
+Macromolecule #35: 40S ribosomal protein S15
+Macromolecule #36: Small ribosomal subunit protein eS25
+Macromolecule #37: Eukaryotic translation initiation factor 2 subunit 1
+Macromolecule #38: Eukaryotic translation initiation factor 2 subunit 3
+Macromolecule #39: Eukaryotic translation initiation factor 2 subunit 2
+Macromolecule #41: Eukaryotic translation initiation factor 1A, X-chromosomal
+Macromolecule #42: Eukaryotic translation initiation factor 3 subunit E
+Macromolecule #43: Eukaryotic translation initiation factor 3 subunit D
+Macromolecule #44: Eukaryotic translation initiation factor 3 subunit C
+Macromolecule #45: Eukaryotic translation initiation factor 3 subunit A
+Macromolecule #46: Eukaryotic translation initiation factor 3 subunit F
+Macromolecule #47: Eukaryotic translation initiation factor 3 subunit M
+Macromolecule #48: Eukaryotic translation initiation factor 3 subunit H
+Macromolecule #49: Eukaryotic translation initiation factor 3 subunit K
+Macromolecule #50: Eukaryotic translation initiation factor 3 subunit L
+Macromolecule #51: POTASSIUM ION
+Macromolecule #52: MAGNESIUM ION
+Macromolecule #53: ZINC ION
+Macromolecule #54: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
+Macromolecule #55: METHIONINE
+Macromolecule #56: water
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.5 |
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| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: TFS FALCON 4i (4k x 4k) / Average electron dose: 40.0 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi




Keywords
Homo sapiens (human)
Authors
France, 4 items
Citation















































Z (Sec.)
Y (Row.)
X (Col.)
























Processing
FIELD EMISSION GUN
