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- PDB-9c3h: Structure of the CNOT3-bound human 80S ribosome with tRNA-ARG in ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 9c3h | ||||||||||||||||||||||||
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Title | Structure of the CNOT3-bound human 80S ribosome with tRNA-ARG in the P-site. | ||||||||||||||||||||||||
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![]() | RIBOSOME / mRNA degradation / CCR4-NOT complex / tRNA | ||||||||||||||||||||||||
Function / homology | ![]() CCR4-NOT core complex / CCR4-NOT complex / regulation of stem cell population maintenance / nuclear-transcribed mRNA poly(A) tail shortening / trophectodermal cell differentiation / Deadenylation of mRNA / translation at presynapse / embryonic brain development / exit from mitosis / eukaryotic 80S initiation complex ...CCR4-NOT core complex / CCR4-NOT complex / regulation of stem cell population maintenance / nuclear-transcribed mRNA poly(A) tail shortening / trophectodermal cell differentiation / Deadenylation of mRNA / translation at presynapse / embryonic brain development / exit from mitosis / eukaryotic 80S initiation complex / negative regulation of protein neddylation / response to insecticide / optic nerve development / M-decay: degradation of maternal mRNAs by maternally stored factors / negative regulation of endoplasmic reticulum unfolded protein response / regulation of G1 to G0 transition / axial mesoderm development / oxidized pyrimidine DNA binding / response to TNF agonist / negative regulation of formation of translation preinitiation complex / positive regulation of base-excision repair / regulation of translation involved in cellular response to UV / ribosomal protein import into nucleus / positive regulation of respiratory burst involved in inflammatory response / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / protein-DNA complex disassembly / positive regulation of gastrulation / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / 90S preribosome assembly / protein tyrosine kinase inhibitor activity / IRE1-RACK1-PP2A complex / positive regulation of endodeoxyribonuclease activity / nucleolus organization / regulatory ncRNA-mediated gene silencing / positive regulation of Golgi to plasma membrane protein transport / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / retinal ganglion cell axon guidance / TNFR1-mediated ceramide production / negative regulation of RNA splicing / negative regulation of DNA repair / GAIT complex / positive regulation of DNA damage response, signal transduction by p53 class mediator / TORC2 complex binding / alpha-beta T cell differentiation / G1 to G0 transition / supercoiled DNA binding / neural crest cell differentiation / TP53 regulates transcription of additional cell cycle genes whose exact role in the p53 pathway remain uncertain / positive regulation of ubiquitin-protein transferase activity / NF-kappaB complex / cysteine-type endopeptidase activator activity involved in apoptotic process / oxidized purine DNA binding / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / negative regulation of bicellular tight junction assembly / regulation of establishment of cell polarity / ubiquitin-like protein conjugating enzyme binding / middle ear morphogenesis / negative regulation of phagocytosis / rRNA modification in the nucleus and cytosol / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / laminin receptor activity / negative regulation of ubiquitin protein ligase activity / ion channel inhibitor activity / protein kinase A binding / pigmentation / Ribosomal scanning and start codon recognition / homeostatic process / Translation initiation complex formation / positive regulation of mitochondrial depolarization / macrophage chemotaxis / positive regulation of T cell receptor signaling pathway / fibroblast growth factor binding / negative regulation of Wnt signaling pathway / lung morphogenesis / monocyte chemotaxis / positive regulation of activated T cell proliferation / positive regulation of natural killer cell proliferation / negative regulation of translational frameshifting / Protein hydroxylation / TOR signaling / BH3 domain binding / regulation of cell division / SARS-CoV-1 modulates host translation machinery / mTORC1-mediated signalling / cellular response to ethanol / iron-sulfur cluster binding / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / blastocyst development / cellular response to actinomycin D / Response of EIF2AK4 (GCN2) to amino acid deficiency / positive regulation of signal transduction by p53 class mediator / negative regulation of ubiquitin-dependent protein catabolic process Similarity search - Function | ||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2 Å | ||||||||||||||||||||||||
![]() | Erzberger, J.P. / Cruz, V.E. | ||||||||||||||||||||||||
Funding support | ![]()
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![]() | ![]() Title: Specific tRNAs promote mRNA decay by recruiting the CCR4-NOT complex to translating ribosomes. Authors: Xiaoqiang Zhu / Victor Emmanuel Cruz / He Zhang / Jan P Erzberger / Joshua T Mendell / ![]() Abstract: The CCR4-NOT complex is a major regulator of eukaryotic messenger RNA (mRNA) stability. Slow decoding during translation promotes association of CCR4-NOT with ribosomes, accelerating mRNA degradation. ...The CCR4-NOT complex is a major regulator of eukaryotic messenger RNA (mRNA) stability. Slow decoding during translation promotes association of CCR4-NOT with ribosomes, accelerating mRNA degradation. We applied selective ribosome profiling to further investigate the determinants of CCR4-NOT recruitment to ribosomes in mammalian cells. This revealed that specific arginine codons in the P-site are strong signals for ribosomal recruitment of human CNOT3, a CCR4-NOT subunit. Cryo-electron microscopy and transfer RNA (tRNA) mutagenesis demonstrated that the D-arms of select arginine tRNAs interact with CNOT3 and promote its recruitment whereas other tRNA D-arms sterically clash with CNOT3. These effects link codon content to mRNA stability. Thus, in addition to their canonical decoding function, tRNAs directly engage regulatory complexes during translation, a mechanism we term P-site tRNA-mediated mRNA decay. | ||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 5.6 MB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2.1 MB | Display | ![]() |
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Full document | ![]() | 2.3 MB | Display | |
Data in XML | ![]() | 360.2 KB | Display | |
Data in CIF | ![]() | 657.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 45170MC ![]() 9c3iC M: map data used to model this data C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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1 |
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Components
-RNA chain , 6 types, 6 molecules L1L5L9S4S2S5
#1: RNA chain | Mass: 50463.840 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: RNA chain | Mass: 1640938.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#4: RNA chain | Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#6: RNA chain | Mass: 24661.789 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#48: RNA chain | Mass: 603582.125 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#49: RNA chain | Mass: 2847.742 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
+Large ribosomal subunit protein ... , 41 types, 41 molecules L8LBLCLDLELFLGLHLILJLKLMLNLOLPLQLRLSLTLULVLWLYLZLaLbLcLdLeLf...
-Protein/peptide , 1 types, 1 molecules NC
#46: Protein/peptide | Mass: 3258.725 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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+Small ribosomal subunit protein ... , 30 types, 30 molecules S1SASCSDSESGSHSISJSKSLSMSNSOSPSQSSSTSUSVSWSXSZSaSbScSdSfSoSy
-Protein , 5 types, 5 molecules SBSYSeSgSz
#51: Protein | Mass: 64125.828 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#72: Protein | Mass: 15366.284 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#78: Protein | Mass: 14415.724 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#80: Protein | Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#83: Protein | Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 5 types, 9914 molecules 








#84: Chemical | ChemComp-MG / #85: Chemical | ChemComp-K / #86: Chemical | ChemComp-B3P / | #87: Chemical | ChemComp-ZN / #88: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: 80S ribosome in complex with CNOT3 and P-site tRNA ARG CCG-1 Type: RIBOSOME / Entity ID: #1-#54, #56-#83 / Source: NATURAL |
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Molecular weight | Value: 4.3 MDa / Experimental value: NO |
Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy imaging
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: ![]() |
Electron lens | Mode: BRIGHT FIELD / Nominal defocus max: 1900 nm / Nominal defocus min: 600 nm |
Image recording | Electron dose: 17 e/Å2 / Film or detector model: FEI FALCON IV (4k x 4k) |
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Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 2 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 276000 / Symmetry type: POINT |