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Yorodumi- EMDB-57204: Dormant 80S:eEF2:SERBP1:tRNA complex from human cells treated wit... -
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Open data
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Basic information
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| Title | Dormant 80S:eEF2:SERBP1:tRNA complex from human cells treated with toxin NT-2 | |||||||||
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Keywords | Toxin NT-2 / translation inhibitor / mycotoxin / trichothecene / RIBOSOME | |||||||||
| Function / homology | Function and homology informationSynthesis of diphthamide-EEF2 / translation at postsynapse / PML body organization / glial cell proliferation / skeletal muscle cell differentiation / translation elongation factor binding / ribosome hibernation / response to folic acid / SUMO binding / positive regulation of cytoplasmic translation ...Synthesis of diphthamide-EEF2 / translation at postsynapse / PML body organization / glial cell proliferation / skeletal muscle cell differentiation / translation elongation factor binding / ribosome hibernation / response to folic acid / SUMO binding / positive regulation of cytoplasmic translation / male meiosis I / translation at presynapse / response to insecticide / negative regulation of endoplasmic reticulum unfolded protein response / eukaryotic 80S initiation complex / ribosomal protein import into nucleus / regulation of G1 to G0 transition / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / 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 / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / protein tyrosine kinase inhibitor activity / IRE1-RACK1-PP2A complex / TNFR1-mediated ceramide production / positive regulation of Golgi to plasma membrane protein transport / G1 to G0 transition / negative regulation of formation of translation preinitiation complex / nucleolus organization / positive regulation of ubiquitin-protein transferase activity / positive regulation of DNA-templated transcription initiation / negative regulation of RNA splicing / GAIT complex / negative regulation of DNA repair / TORC2 complex binding / erythrocyte homeostasis / supercoiled DNA binding / regulation of establishment of cell polarity / rRNA modification in the nucleus and cytosol / oxidized purine DNA binding / NF-kappaB complex / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of phagocytosis / Uptake and function of diphtheria toxin / ubiquitin-like protein conjugating enzyme binding / cytoplasmic translational initiation / cytoplasmic side of rough endoplasmic reticulum membrane / regulation of translation involved in cellular response to UV / A band / Formation of the ternary complex, and subsequently, the 43S complex / laminin receptor activity / ion channel inhibitor activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / response to aldosterone / negative regulation of myoblast fusion / protein-DNA complex disassembly / lncRNA binding / Ribosomal scanning and start codon recognition / protein kinase A binding / Translation initiation complex formation / negative regulation of Wnt signaling pathway / positive regulation of DNA damage response, signal transduction by p53 class mediator / fibroblast growth factor binding / BH3 domain binding / Protein hydroxylation / TOR signaling / mTORC1-mediated signalling / negative regulation of translational frameshifting / monocyte chemotaxis / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / SRC activates STAT3 in a quantitative manner, through Cadherin-11 (CDH11), RAC1 and gp130 (IL6ST) / SARS-CoV-1 modulates host translation machinery / regulation of cell division / positive regulation of GTPase activity / protein localization to nucleus / translational elongation / Peptide chain elongation / Selenocysteine synthesis / negative regulation of protein binding / Formation of a pool of free 40S subunits / translation elongation factor activity / negative regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / protein targeting / protein serine/threonine kinase inhibitor activity / Eukaryotic Translation Termination / Dengue Virus Attachment and Entry / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / response to ischemia / ubiquitin ligase inhibitor activity / Viral mRNA Translation / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / positive regulation of signal transduction by p53 class mediator / GTP hydrolysis and joining of the 60S ribosomal subunit / embryo implantation / L13a-mediated translational silencing of Ceruloplasmin expression Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 2.08 Å | |||||||||
Authors | Rabl J / Karousis ED | |||||||||
| Funding support | Switzerland, 1 items
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Citation | Journal: To Be PublishedTitle: Toxin NT-2 bound to human ribosome Authors: Rabl J / Karousis ED | |||||||||
| History |
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_57204.map.gz | 945.6 MB | EMDB map data format | |
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| Header (meta data) | emd-57204-v30.xml emd-57204.xml | 95.3 KB 95.3 KB | Display Display | EMDB header |
| FSC (resolution estimation) | emd_57204_fsc.xml | 21.1 KB | Display | FSC data file |
| Images | emd_57204.png | 197.3 KB | ||
| Filedesc metadata | emd-57204.cif.gz | 22 KB | ||
| Others | emd_57204_half_map_1.map.gz emd_57204_half_map_2.map.gz | 926.7 MB 926.7 MB | ||
| Archive directory | https://data.pdbj.org/pub/emdb/structures/EMD-57204 ftp://data.pdbj.org/pub/emdb/structures/EMD-57204 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 29izMC ![]() 29iwC ![]() 29ixC ![]() 29iyC M: atomic model generated by this map C: citing same article ( |
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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_57204.map.gz / Format: CCP4 / Size: 1000 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: 0.648 Å | ||||||||||||||||||||||||||||||||||||
| Density |
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| Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
| Details | EMDB XML:
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-Supplemental data
-Half map: #2
| File | emd_57204_half_map_1.map | ||||||||||||
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| Density Histograms |
-Half map: #1
| File | emd_57204_half_map_2.map | ||||||||||||
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| Density Histograms |
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Sample components
+Entire : PTC site of human cytoplasmic ribosome with bound NT-2 toxin
+Supramolecule #1: PTC site of human cytoplasmic ribosome with bound NT-2 toxin
+Macromolecule #1: Large ribosomal subunit protein uL30
+Macromolecule #2: 60S ribosomal protein L7a
+Macromolecule #3: 60S ribosomal protein L9
+Macromolecule #4: Ribosomal protein uL16-like
+Macromolecule #5: 60S ribosomal protein L11
+Macromolecule #6: 60S ribosomal protein L13
+Macromolecule #7: 60S ribosomal protein L14
+Macromolecule #8: 60S ribosomal protein L15
+Macromolecule #9: 60S ribosomal protein L13a
+Macromolecule #10: 60S ribosomal protein L17
+Macromolecule #11: 60S ribosomal protein L18
+Macromolecule #12: 60S ribosomal protein L19
+Macromolecule #13: 60S ribosomal protein L18a
+Macromolecule #14: 60S ribosomal protein L21
+Macromolecule #15: 60S ribosomal protein L22
+Macromolecule #16: 60S ribosomal protein L23
+Macromolecule #17: 60S ribosomal protein L24
+Macromolecule #18: 60S ribosomal protein L23a
+Macromolecule #19: 60S ribosomal protein L26
+Macromolecule #20: 60S ribosomal protein L27
+Macromolecule #21: Large ribosomal subunit protein uL15
+Macromolecule #22: 60S ribosomal protein L29
+Macromolecule #23: 60S ribosomal protein L30
+Macromolecule #24: 60S ribosomal protein L31
+Macromolecule #25: 60S ribosomal protein L32
+Macromolecule #26: Large ribosomal subunit protein eL33
+Macromolecule #27: 60S ribosomal protein L34
+Macromolecule #28: 60S ribosomal protein L35
+Macromolecule #29: 60S ribosomal protein L36
+Macromolecule #30: Large ribosomal subunit protein eL37
+Macromolecule #31: 60S ribosomal protein L38
+Macromolecule #32: 60S ribosomal protein L39
+Macromolecule #33: Large ribosomal subunit protein eL40
+Macromolecule #34: 60S ribosomal protein L36a
+Macromolecule #35: 60S ribosomal protein L37a
+Macromolecule #36: 60S ribosomal protein L28
+Macromolecule #40: Large ribosomal subunit protein uL2
+Macromolecule #41: Large ribosomal subunit protein uL3
+Macromolecule #42: 60S ribosomal protein L4
+Macromolecule #43: 60S ribosomal protein L5
+Macromolecule #44: Large ribosomal subunit protein eL6
+Macromolecule #46: Elongation factor 2
+Macromolecule #47: Plasminogen activator inhibitor 1 RNA-binding protein
+Macromolecule #48: 60S ribosomal protein L41
+Macromolecule #50: 40S ribosomal protein S3a
+Macromolecule #51: Small ribosomal subunit protein eS4, X isoform
+Macromolecule #52: 40S ribosomal protein S7
+Macromolecule #53: 40S ribosomal protein S8
+Macromolecule #54: Small ribosomal subunit protein uS17
+Macromolecule #55: 40S ribosomal protein S17
+Macromolecule #56: Small ribosomal subunit protein eS21
+Macromolecule #57: Small ribosomal subunit protein uS12
+Macromolecule #58: 40S ribosomal protein S26
+Macromolecule #59: 40S ribosomal protein S2
+Macromolecule #60: 40S ribosomal protein S6
+Macromolecule #61: 40S ribosomal protein S9
+Macromolecule #62: 40S ribosomal protein S13
+Macromolecule #63: 40S ribosomal protein S14
+Macromolecule #64: 40S ribosomal protein S15a
+Macromolecule #65: 40S ribosomal protein S24
+Macromolecule #66: 40S ribosomal protein S27
+Macromolecule #67: Ubiquitin-like FUBI-ribosomal protein eS30 fusion protein
+Macromolecule #68: Small ribosomal subunit protein uS2
+Macromolecule #69: 40S ribosomal protein S3
+Macromolecule #70: 40S ribosomal protein S5
+Macromolecule #71: 40S ribosomal protein S10
+Macromolecule #72: 40S ribosomal protein S15
+Macromolecule #73: 40S ribosomal protein S16
+Macromolecule #74: 40S ribosomal protein S18
+Macromolecule #75: 40S ribosomal protein S19
+Macromolecule #76: 40S ribosomal protein S20
+Macromolecule #77: 40S ribosomal protein S28
+Macromolecule #78: 40S ribosomal protein S29
+Macromolecule #79: 40S ribosomal protein S12
+Macromolecule #80: Small ribosomal subunit protein eS25
+Macromolecule #81: Ubiquitin
+Macromolecule #82: Receptor of activated protein C kinase 1
+Macromolecule #37: 28S rRNA
+Macromolecule #38: 5S rRNA
+Macromolecule #39: 5.8S rRNA
+Macromolecule #45: tRNA
+Macromolecule #49: 18S rRNA
+Macromolecule #83: MAGNESIUM ION
+Macromolecule #84: 1,4-DIAMINOBUTANE
+Macromolecule #85: POTASSIUM ION
+Macromolecule #86: ZINC ION
+Macromolecule #87: SPERMIDINE
+Macromolecule #88: SPERMINE
+Macromolecule #89: Toxin NT-2
+Macromolecule #90: 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: 7.4 |
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| Grid | Model: Quantifoil R2/2 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 0.16 |
| Vitrification | Cryogen name: ETHANE-PROPANE / Chamber humidity: 95 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK IV |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 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: 2.8000000000000003 µm / Nominal defocus min: 0.8 µm |
| Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi



Keywords
Homo sapiens (human)
Authors
Switzerland, 1 items
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Processing
FIELD EMISSION GUN

