+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-38752 | |||||||||
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Title | Cryo-EM structure of the human 40S ribosome with PDCD4 | |||||||||
Map data | local resolution filtered map using Relion | |||||||||
Sample |
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Keywords | Ribosome / PDCD4 / eIF4A | |||||||||
Function / homology | Function and homology information epithelial to mesenchymal transition involved in cardiac fibroblast development / negative regulation of myofibroblast differentiation / negative regulation of vascular associated smooth muscle cell differentiation / negative regulation of JUN kinase activity / 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 ...epithelial to mesenchymal transition involved in cardiac fibroblast development / negative regulation of myofibroblast differentiation / negative regulation of vascular associated smooth muscle cell differentiation / negative regulation of JUN kinase activity / 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 respiratory burst involved in inflammatory response / 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 / positive regulation of endothelial cell apoptotic process / IRE1-RACK1-PP2A complex / : / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / response to alkaloid / negative regulation of RNA splicing / negative regulation of DNA repair / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / oxidized purine DNA binding / supercoiled DNA binding / 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 / rRNA modification in the nucleus and cytosol / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / 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 / positive regulation of vascular associated smooth muscle cell apoptotic process / 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 / regulation of cell division / Protein hydroxylation / negative regulation of peptidyl-serine phosphorylation / BH3 domain binding / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Peptide chain elongation / negative regulation of vascular associated smooth muscle cell proliferation / monocyte chemotaxis / Selenocysteine synthesis / cysteine-type endopeptidase activator activity involved in apoptotic process / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / Formation of a pool of free 40S subunits / phagocytic cup / Eukaryotic Translation Termination / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / negative regulation of respiratory burst involved in inflammatory response / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Viral mRNA Translation / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / TOR signaling / negative regulation of cytokine production involved in inflammatory response / T cell proliferation involved in immune response / Major pathway of rRNA processing in the nucleolus and cytosol / spindle assembly / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / regulation of translational fidelity / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribosomal small subunit export from nucleus / erythrocyte development / BMP signaling pathway / translation regulator activity / Protein methylation / Nuclear events stimulated by ALK signaling in cancer / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / cytosolic ribosome / positive regulation of cell cycle / signaling adaptor activity / negative regulation of smoothened signaling pathway / stress granule assembly / positive regulation of intrinsic apoptotic signaling pathway / Mitotic Prometaphase Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.9 Å | |||||||||
Authors | Ye X / Huang Z / Li Y / Wang M / Cheng J | |||||||||
Funding support | 1 items
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Citation | Journal: Cell Res / Year: 2024 Title: Human tumor suppressor PDCD4 directly interacts with ribosomes to repress translation. Authors: Xianwen Ye / Zixuan Huang / Yi Li / Mengjiao Wang / Wanyu Meng / Maojian Miao / Jingdong Cheng / | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_38752.map.gz | 161.7 MB | EMDB map data format | |
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Header (meta data) | emd-38752-v30.xml emd-38752.xml | 60.8 KB 60.8 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_38752_fsc.xml | 14.8 KB | Display | FSC data file |
Images | emd_38752.png | 107.5 KB | ||
Filedesc metadata | emd-38752.cif.gz | 11.9 KB | ||
Others | emd_38752_additional_1.map.gz emd_38752_additional_2.map.gz emd_38752_additional_3.map.gz emd_38752_additional_4.map.gz emd_38752_half_map_1.map.gz emd_38752_half_map_2.map.gz | 245.8 MB 224.6 MB 249.6 MB 249.7 MB 225.3 MB 225.2 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-38752 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-38752 | HTTPS FTP |
-Validation report
Summary document | emd_38752_validation.pdf.gz | 777.1 KB | Display | EMDB validaton report |
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Full document | emd_38752_full_validation.pdf.gz | 776.7 KB | Display | |
Data in XML | emd_38752_validation.xml.gz | 22.6 KB | Display | |
Data in CIF | emd_38752_validation.cif.gz | 30 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38752 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-38752 | HTTPS FTP |
-Related structure data
Related structure data | 8xxlMC 8xxmC 8xxnC M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_38752.map.gz / Format: CCP4 / Size: 282.6 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | local resolution filtered map using Relion | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.064 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Additional map: Multibody refined map focusing on 40S body and...
File | emd_38752_additional_1.map | ||||||||||||
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Annotation | Multibody refined map focusing on 40S body and filtered using DeepEMhancer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: consensus refined map without post process
File | emd_38752_additional_2.map | ||||||||||||
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Annotation | consensus refined map without post process | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Multibody refined map focusing on 40S head and...
File | emd_38752_additional_3.map | ||||||||||||
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Annotation | Multibody refined map focusing on 40S head and filtered using DeepEMhancer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: filtered map using DeepEMhancer
File | emd_38752_additional_4.map | ||||||||||||
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Annotation | filtered map using DeepEMhancer | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_38752_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_38752_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : 40S ribosome with PDCD4
+Supramolecule #1: 40S ribosome with PDCD4
+Macromolecule #1: 60S ribosomal protein L41
+Macromolecule #3: 40S ribosomal protein SA
+Macromolecule #4: 40S ribosomal protein S3a
+Macromolecule #5: 40S ribosomal protein S3
+Macromolecule #6: 40S ribosomal protein S4, X isoform
+Macromolecule #7: 40S ribosomal protein S5
+Macromolecule #8: 40S ribosomal protein S7
+Macromolecule #9: 40S ribosomal protein S8
+Macromolecule #10: 40S ribosomal protein S10
+Macromolecule #11: 40S ribosomal protein S11
+Macromolecule #12: 40S ribosomal protein S15
+Macromolecule #13: 40S ribosomal protein S16
+Macromolecule #14: 40S ribosomal protein S17
+Macromolecule #15: 40S ribosomal protein S18
+Macromolecule #16: 40S ribosomal protein S19
+Macromolecule #17: 40S ribosomal protein S20
+Macromolecule #18: 40S ribosomal protein S21
+Macromolecule #19: 40S ribosomal protein S23
+Macromolecule #20: 40S ribosomal protein S26
+Macromolecule #21: 40S ribosomal protein S28
+Macromolecule #22: 40S ribosomal protein S29
+Macromolecule #23: Receptor of activated protein C kinase 1
+Macromolecule #24: 40S ribosomal protein S2
+Macromolecule #25: 40S ribosomal protein S6
+Macromolecule #26: 40S ribosomal protein S9
+Macromolecule #27: 40S ribosomal protein S12
+Macromolecule #28: 40S ribosomal protein S13
+Macromolecule #29: 40S ribosomal protein S14
+Macromolecule #30: 40S ribosomal protein S15a
+Macromolecule #31: 40S ribosomal protein S24
+Macromolecule #32: 40S ribosomal protein S25
+Macromolecule #33: 40S ribosomal protein S27
+Macromolecule #34: 40S ribosomal protein S30
+Macromolecule #35: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #36: Programmed cell death protein 4
+Macromolecule #2: 18S rRNA
+Macromolecule #37: MAGNESIUM ION
+Macromolecule #38: ZINC 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 R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE |
Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 58.0 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: 1.0 µm |
Sample stage | Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |