+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-37991 | |||||||||||||||
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Title | Dormant Ribosome with eIF5A,eEF2 and SERBP1 | |||||||||||||||
Map data | ||||||||||||||||
Sample |
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Keywords | Ribosome / eEF2 / eIF5A | |||||||||||||||
Function / homology | Function and homology information Synthesis of diphthamide-EEF2 / Hypusine synthesis from eIF5A-lysine / non-membrane-bounded organelle / positive regulation of translational termination / annulate lamellae / ribosome hibernation / translation elongation factor binding / PML body organization / positive regulation of translational elongation / SUMO binding ...Synthesis of diphthamide-EEF2 / Hypusine synthesis from eIF5A-lysine / non-membrane-bounded organelle / positive regulation of translational termination / annulate lamellae / ribosome hibernation / translation elongation factor binding / PML body organization / positive regulation of translational elongation / SUMO binding / 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 / eukaryotic 80S initiation complex / response to TNF agonist / positive regulation of base-excision repair / negative regulation of protein neddylation / protein tyrosine kinase inhibitor activity / positive regulation of respiratory burst involved in inflammatory response / translation at presynapse / 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 / axial mesoderm development / negative regulation of formation of translation preinitiation complex / nucleolus organization / ribosomal protein import into nucleus / IRE1-RACK1-PP2A complex / : / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / 90S preribosome assembly / TNFR1-mediated ceramide production / negative regulation of RNA splicing / negative regulation of DNA repair / TORC2 complex binding / GAIT complex / 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 / middle ear morphogenesis / aggresome / 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 / A band / laminin receptor activity / regulation of G1 to G0 transition / exit from mitosis / alpha-beta T cell differentiation / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / regulation of translation involved in cellular response to UV / protein kinase A binding / protein-DNA complex disassembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / Translation initiation complex formation / Ribosomal scanning and start codon recognition / negative regulation of ubiquitin protein ligase activity / optic nerve development / translational elongation / ion channel inhibitor activity / pigmentation / mammalian oogenesis stage / positive regulation of mitochondrial depolarization / response to aldosterone / retinal ganglion cell axon guidance / Uptake and function of diphtheria toxin / G1 to G0 transition / homeostatic process / activation-induced cell death of T cells / lung morphogenesis / 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 / male meiosis I / regulation of cell division / Protein hydroxylation / negative regulation of peptidyl-serine phosphorylation / BH3 domain binding / mTORC1-mediated signalling / macrophage chemotaxis / SARS-CoV-1 modulates host translation machinery / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Peptide chain elongation / 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 Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.4 Å | |||||||||||||||
Authors | Du M / Zeng F | |||||||||||||||
Funding support | China, 4 items
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Citation | Journal: To Be Published Title: dormant ribosome bound to Stm1, eEF2, eIF5A Authors: Du M / Li X / Zeng F | |||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_37991.map.gz | 61.6 MB | EMDB map data format | |
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Header (meta data) | emd-37991-v30.xml emd-37991.xml | 13.1 KB 13.1 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_37991_fsc.xml | 15.8 KB | Display | FSC data file |
Images | emd_37991.png | 73.3 KB | ||
Filedesc metadata | emd-37991.cif.gz | 3.9 KB | ||
Others | emd_37991_half_map_1.map.gz emd_37991_half_map_2.map.gz | 275.3 MB 275.3 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-37991 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-37991 | HTTPS FTP |
-Validation report
Summary document | emd_37991_validation.pdf.gz | 990.4 KB | Display | EMDB validaton report |
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Full document | emd_37991_full_validation.pdf.gz | 990 KB | Display | |
Data in XML | emd_37991_validation.xml.gz | 23.5 KB | Display | |
Data in CIF | emd_37991_validation.cif.gz | 31.2 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37991 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-37991 | HTTPS FTP |
-Related structure data
Related structure data | 8y0wM M: atomic model generated by this map |
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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_37991.map.gz / Format: CCP4 / Size: 343 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.08 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Half map: #2
File | emd_37991_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_37991_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Dormant Ribosome
Entire | Name: Dormant Ribosome |
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Components |
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-Supramolecule #1: Dormant Ribosome
Supramolecule | Name: Dormant Ribosome / type: complex / ID: 1 / Parent: 0 / Details: dormant ribosome with Stm1, eEF2, eIF5A |
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Source (natural) | Organism: Homo sapiens (human) |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.4 Details: 50mM HEPES, pH 7.4, 100 mM KOAc, 5 mM Mg(OAc)2, 1mM DTT |
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Pretreatment - Atmosphere: OTHER |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % / Chamber temperature: 277 K / Instrument: FEI VITROBOT MARK II |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 30.0 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: 1.5 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |