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Yorodumi- EMDB-16052: Cryo-EM structure of stalled rabbit 80S ribosomes in complex with... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-16052 | ||||||||||||||||||
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Title | Cryo-EM structure of stalled rabbit 80S ribosomes in complex with human CCR4-NOT and CNOT4 | ||||||||||||||||||
Map data | Postprocessed map | ||||||||||||||||||
Sample |
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Keywords | translational control / mRNA decay / deadenylation / ribosome stalling / human CCR4-NOT / RIBOSOME | ||||||||||||||||||
Function / homology | Function and homology information CCR4-NOT core complex / nuclear-transcribed mRNA poly(A) tail shortening / ribosomal subunit / regulatory ncRNA-mediated gene silencing / 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 / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator ...CCR4-NOT core complex / nuclear-transcribed mRNA poly(A) tail shortening / ribosomal subunit / regulatory ncRNA-mediated gene silencing / 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 / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / 90S preribosome / TOR signaling / T cell proliferation involved in immune response / protein-RNA complex assembly / erythrocyte development / ribosomal small subunit export from nucleus / translation regulator activity / rough endoplasmic reticulum / gastrulation / MDM2/MDM4 family protein binding / maturation of LSU-rRNA / cytosolic ribosome / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / rescue of stalled ribosome / ribosomal large subunit biogenesis / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of SSU-rRNA / cellular response to leukemia inhibitory factor / positive regulation of translation / small-subunit processome / protein kinase C binding / positive regulation of apoptotic signaling pathway / P-body / positive regulation of protein-containing complex assembly / placenta development / cellular response to gamma radiation / mRNA 5'-UTR binding / spindle / cytoplasmic ribonucleoprotein granule / modification-dependent protein catabolic process / G1/S transition of mitotic cell cycle / rRNA processing / protein tag activity / antimicrobial humoral immune response mediated by antimicrobial peptide / ribosomal small subunit biogenesis / rhythmic process / positive regulation of canonical Wnt signaling pathway / small ribosomal subunit rRNA binding / ribosome binding / glucose homeostasis / regulation of translation / ribosomal small subunit assembly / ribosomal large subunit assembly / small ribosomal subunit / T cell differentiation in thymus / large ribosomal subunit rRNA binding / cell body / 5S rRNA binding / cytosolic small ribosomal subunit / perikaryon / cytoplasmic translation / defense response to Gram-negative bacterium / cytosolic large ribosomal subunit / killing of cells of another organism / tRNA binding / mitochondrial inner membrane / cell differentiation / postsynaptic density / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / positive regulation of apoptotic process / ribonucleoprotein complex / positive regulation of protein phosphorylation / translation / cell division / DNA repair / mRNA binding / ubiquitin protein ligase binding / dendrite / positive regulation of cell population proliferation / synapse / regulation of DNA-templated transcription / negative regulation of apoptotic process / nucleolus / apoptotic process / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / DNA binding / RNA binding / zinc ion binding / nucleoplasm Similarity search - Function | ||||||||||||||||||
Biological species | Oryctolagus cuniculus (rabbit) / Homo sapiens (human) | ||||||||||||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.1 Å | ||||||||||||||||||
Authors | Absmeier E / Chandrasekaran V / O'Reilly FJ / Stowell JAW / Rappsilber J / Passmore LA | ||||||||||||||||||
Funding support | United Kingdom, Germany, 5 items
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Citation | Journal: Nat Struct Mol Biol / Year: 2023 Title: Modulation of GluA2-γ5 synaptic complex desensitization, polyamine block and antiepileptic perampanel inhibition by auxiliary subunit cornichon-2. Authors: Shanti Pal Gangwar / Laura Y Yen / Maria V Yelshanskaya / Aryeh Korman / Drew R Jones / Alexander I Sobolevsky / Abstract: Synaptic complexes of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors (AMPARs) with auxiliary subunits mediate most excitatory neurotransmission and can be targeted to treat ...Synaptic complexes of α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors (AMPARs) with auxiliary subunits mediate most excitatory neurotransmission and can be targeted to treat neuropsychiatric and neurological disorders, including epilepsy. Here we present cryogenic-electron microscopy structures of rat GluA2 AMPAR complexes with inhibitory mouse γ5 and potentiating human cornichon-2 (CNIH2) auxiliary subunits. CNIH2 appears to destabilize the desensitized state of the complex by reducing the separation of the upper lobes in ligand-binding domain dimers. At the same time, CNIH2 stabilizes binding of polyamine spermidine to the selectivity filter of the closed ion channel. Nevertheless, CNIH2, and to a lesser extent γ5, attenuate polyamine block of the open channel and reduce the potency of the antiepileptic drug perampanel that inhibits the synaptic complex allosterically by binding to sites in the ion channel extracellular collar. These findings illustrate the fine-tuning of synaptic complex structure and function in an auxiliary subunit-dependent manner, which is critical for the study of brain region-specific neurotransmission and design of therapeutics for disease treatment. | ||||||||||||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_16052.map.gz | 99.1 MB | EMDB map data format | |
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Header (meta data) | emd-16052-v30.xml emd-16052.xml | 108 KB 108 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_16052_fsc.xml | 17.7 KB | Display | FSC data file |
Images | emd_16052.png | 202.6 KB | ||
Masks | emd_16052_msk_1.map | 476.8 MB | Mask map | |
Filedesc metadata | emd-16052.cif.gz | 20.2 KB | ||
Others | emd_16052_additional_1.map.gz emd_16052_additional_2.map.gz emd_16052_half_map_1.map.gz emd_16052_half_map_2.map.gz | 15.5 MB 382 MB 383.3 MB 383.4 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-16052 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-16052 | HTTPS FTP |
-Validation report
Summary document | emd_16052_validation.pdf.gz | 1.1 MB | Display | EMDB validaton report |
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Full document | emd_16052_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | emd_16052_validation.xml.gz | 25.5 KB | Display | |
Data in CIF | emd_16052_validation.cif.gz | 34 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16052 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-16052 | HTTPS FTP |
-Related structure data
Related structure data | 8bhfMC 8ss2C 8ss3C 8ss4C 8ss5C 8ss6C 8ss7C 8ss8C 8ss9C 8ssaC 8ssbC 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_16052.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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Annotation | Postprocessed map | ||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.829 Å | ||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_16052_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Additional map: 2-fold downscaled map used for interpretation
File | emd_16052_additional_1.map | ||||||||||||
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Annotation | 2-fold downscaled map used for interpretation | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Refined map before postprocessing
File | emd_16052_additional_2.map | ||||||||||||
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Annotation | Refined map before postprocessing | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half 1 map
File | emd_16052_half_map_1.map | ||||||||||||
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Annotation | Half 1 map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Half map: Half 2 map
File | emd_16052_half_map_2.map | ||||||||||||
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Annotation | Half 2 map | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Ribosome complex
+Supramolecule #1: Ribosome complex
+Macromolecule #1: Ribosomal protein L15
+Macromolecule #2: 60S ribosomal protein L13a
+Macromolecule #3: 60S ribosomal protein L17
+Macromolecule #4: Ribosomal protein L18
+Macromolecule #5: Ribosomal protein L19
+Macromolecule #6: 60S ribosomal protein L18a
+Macromolecule #7: 60S ribosomal protein L21
+Macromolecule #8: 60S ribosomal protein L22
+Macromolecule #9: 60S ribosomal protein L23
+Macromolecule #10: TRASH domain-containing protein
+Macromolecule #11: Ribosomal protein L23/L25 N-terminal domain-containing protein
+Macromolecule #12: Ribosomal protein L26
+Macromolecule #13: 60S ribosomal protein L27
+Macromolecule #14: 60S ribosomal protein L27a
+Macromolecule #15: 60S ribosomal protein L29
+Macromolecule #16: 60S ribosomal protein L30
+Macromolecule #17: 60S ribosomal protein L31
+Macromolecule #18: Ribosomal protein L32
+Macromolecule #19: 60S ribosomal protein L35a
+Macromolecule #20: 60S ribosomal protein L34
+Macromolecule #21: 60S ribosomal protein L35
+Macromolecule #22: 60S ribosomal protein L36
+Macromolecule #23: Ribosomal protein L37
+Macromolecule #24: 60S ribosomal protein L38
+Macromolecule #25: 60S ribosomal protein L39-like
+Macromolecule #26: Ubiquitin-60S ribosomal protein L40
+Macromolecule #27: 60S ribosomal protein L41
+Macromolecule #28: Ribosomal protein L36a like
+Macromolecule #29: 60S ribosomal protein L37a
+Macromolecule #30: 60S ribosomal protein L28
+Macromolecule #31: 60S acidic ribosomal protein P0
+Macromolecule #32: 60S ribosomal protein L12
+Macromolecule #33: 60S ribosomal protein L10a
+Macromolecule #35: CCR4-NOT transcription complex subunit 3
+Macromolecule #37: nascent chain
+Macromolecule #42: 40S_SA_C domain-containing protein
+Macromolecule #43: 40S ribosomal protein S3a
+Macromolecule #44: 40S ribosomal protein S2
+Macromolecule #45: Ribosomal protein S3
+Macromolecule #46: 40S ribosomal protein S4
+Macromolecule #47: Ribosomal protein S5
+Macromolecule #48: 40S ribosomal protein S6
+Macromolecule #49: 40S ribosomal protein S7
+Macromolecule #50: 40S ribosomal protein S8
+Macromolecule #51: Ribosomal protein S9 (Predicted)
+Macromolecule #52: Plectin/S10 N-terminal domain-containing protein
+Macromolecule #53: 40S ribosomal protein S11
+Macromolecule #54: 40S ribosomal protein S12
+Macromolecule #55: ribosomal protein uS15
+Macromolecule #56: Ribosomal protein S14
+Macromolecule #57: 40S ribosomal protein S15
+Macromolecule #58: Ribosomal protein S16
+Macromolecule #59: 40S ribosomal protein S17
+Macromolecule #60: 40S ribosomal protein S18
+Macromolecule #61: 40S ribosomal protein S19
+Macromolecule #62: Ribosomal protein S20
+Macromolecule #63: 40S ribosomal protein S21
+Macromolecule #64: Ribosomal protein S15a
+Macromolecule #65: Ribosomal protein S23
+Macromolecule #66: 40S ribosomal protein S24
+Macromolecule #67: 40S ribosomal protein S25
+Macromolecule #68: 40S ribosomal protein S26
+Macromolecule #69: 40S ribosomal protein S27
+Macromolecule #70: Ribosomal protein S28
+Macromolecule #71: 40S ribosomal protein S29
+Macromolecule #72: Ubiquitin-like domain-containing protein
+Macromolecule #73: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #74: Ribosomal protein RACK1
+Macromolecule #75: 60S ribosomal protein L8
+Macromolecule #76: Ribosomal protein L3
+Macromolecule #77: 60S ribosomal protein L4
+Macromolecule #78: 60S ribosomal protein L5
+Macromolecule #79: 60S ribosomal protein L6
+Macromolecule #80: 60S ribosomal protein L7
+Macromolecule #81: 60S ribosomal protein L7a
+Macromolecule #82: 60S ribosomal protein L9
+Macromolecule #83: Ribosomal protein L10
+Macromolecule #84: 60S ribosomal protein L11
+Macromolecule #85: 60S ribosomal protein L13
+Macromolecule #86: 60S ribosomal protein L14
+Macromolecule #34: mRNA
+Macromolecule #36: P-site tRNA
+Macromolecule #38: 28S ribosomal RNA
+Macromolecule #39: 5S ribosomal RNA
+Macromolecule #40: 5.8S ribosomal RNA
+Macromolecule #41: 18S ribosomal RNA
+Macromolecule #87: MAGNESIUM ION
+Macromolecule #88: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | TFS KRIOS |
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Image recording | Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 47.5 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: 3.0 µm / Nominal defocus min: 0.9 µm |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |