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Yorodumi- PDB-7qgg: Neuronal RNA granules are ribosome complexes stalled at the pre-t... -
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-Basic information
Entry | Database: PDB / ID: 7qgg | ||||||||||||
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Title | Neuronal RNA granules are ribosome complexes stalled at the pre-translocation state | ||||||||||||
Components |
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Keywords | RIBOSOME / RNA granule / rat | ||||||||||||
Function / homology | Function and homology information regulation of myeloid dendritic cell activation / : / positive regulation of selenocysteine incorporation / : / : / : / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Regulation of NF-kappa B signaling / mTORC1-mediated signalling ...regulation of myeloid dendritic cell activation / : / positive regulation of selenocysteine incorporation / : / : / : / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Regulation of NF-kappa B signaling / mTORC1-mediated signalling / Translesion synthesis by REV1 / Recognition of DNA damage by PCNA-containing replication complex / APC/C:Cdc20 mediated degradation of Cyclin B / APC-Cdc20 mediated degradation of Nek2A / Activated NOTCH1 Transmits Signal to the Nucleus / Downregulation of TGF-beta receptor signaling / Regulation of FZD by ubiquitination / Regulation of TNFR1 signaling / TNFR1-induced NF-kappa-B signaling pathway / CLEC7A (Dectin-1) signaling / Translesion synthesis by POLK / Translesion synthesis by POLI / Termination of translesion DNA synthesis / Gap-filling DNA repair synthesis and ligation in GG-NER / Formation of TC-NER Pre-Incision Complex / Dual incision in TC-NER / Gap-filling DNA repair synthesis and ligation in TC-NER / Fanconi Anemia Pathway / Regulation of TP53 Degradation / Regulation of TP53 Activity through Methylation / Cyclin D associated events in G1 / Stabilization of p53 / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Synthesis of active ubiquitin: roles of E1 and E2 enzymes / ER Quality Control Compartment (ERQC) / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Alpha-protein kinase 1 signaling pathway / Inactivation of CSF3 (G-CSF) signaling / : / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / NOD1/2 Signaling Pathway / activated TAK1 mediates p38 MAPK activation / JNK (c-Jun kinases) phosphorylation and activation mediated by activated human TAK1 / DNA Damage Recognition in GG-NER / Formation of Incision Complex in GG-NER / Dual Incision in GG-NER / E3 ubiquitin ligases ubiquitinate target proteins / : / Translesion Synthesis by POLH / Downregulation of ERBB2:ERBB3 signaling / TCF dependent signaling in response to WNT / Regulation of innate immune responses to cytosolic DNA / HDR through Homologous Recombination (HRR) / Downregulation of ERBB2 signaling / Regulation of signaling by CBL / Downstream TCR signaling / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / NOTCH3 Activation and Transmission of Signal to the Nucleus / Downregulation of ERBB4 signaling / Stimuli-sensing channels / Deactivation of the beta-catenin transactivating complex / Josephin domain DUBs / Ovarian tumor domain proteases / Negative regulation of MET activity / Translation initiation complex formation / Formation of the ternary complex, and subsequently, the 43S complex / Ribosomal scanning and start codon recognition / Interleukin-1 signaling / L13a-mediated translational silencing of Ceruloplasmin expression / SRP-dependent cotranslational protein targeting to membrane / Formation of a pool of free 40S subunits / GTP hydrolysis and joining of the 60S ribosomal subunit / Regulation of PTEN localization / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / FCERI mediated NF-kB activation / Major pathway of rRNA processing in the nucleolus and cytosol / Pexophagy / cellular response to Thyroid stimulating hormone / N-glycan trimming in the ER and Calnexin/Calreticulin cycle / 5.8S rRNA binding / SCF-beta-TrCP mediated degradation of Emi1 / Metalloprotease DUBs / Assembly of the pre-replicative complex / GSK3B and BTRC:CUL1-mediated-degradation of NFE2L2 / Regulation of necroptotic cell death / Aggrephagy / Oxygen-dependent proline hydroxylation of Hypoxia-inducible Factor Alpha / Autodegradation of Cdh1 by Cdh1:APC/C / APC/C:Cdc20 mediated degradation of Securin / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / SCF(Skp2)-mediated degradation of p27/p21 / NRIF signals cell death from the nucleus / NF-kB is activated and signals survival / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / Autodegradation of the E3 ubiquitin ligase COP1 / Asymmetric localization of PCP proteins Similarity search - Function | ||||||||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.86 Å | ||||||||||||
Authors | Pulk, A. / Kipper, K. / Mansour, A. | ||||||||||||
Funding support | Estonia, 3items
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Citation | Journal: J Mol Biol / Year: 2022 Title: Neuronal RNA granules are ribosome complexes stalled at the pre-translocation state. Authors: Kalle Kipper / Abbas Mansour / Arto Pulk / Abstract: The polarized cell morphology of neurons dictates many neuronal processes, including the axodendridic transport of specific mRNAs and subsequent translation. mRNAs together with ribosomes and RNA- ...The polarized cell morphology of neurons dictates many neuronal processes, including the axodendridic transport of specific mRNAs and subsequent translation. mRNAs together with ribosomes and RNA-binding proteins form RNA granules that are targeted to axodendrites for localized translation in neurons. It has been established that localized protein synthesis in neurons is essential for long-term memory formation, synaptic plasticity, and neurodegeneration. We have used proteomics and electron microscopy to characterize neuronal RNA granules (nRNAg) isolated from rat brain tissues or human neuroblastoma. We show that ribosome-containing RNA granules are morula-like structures when visualized by electron microscopy. Crosslinking-coupled mass-spectrometry identified a potential G3BP2 binding site on the ribosome near the eIF3d-binding site on the 40S ribosomal subunit. We used cryo-EM to resolve the structure of the ribosome-component of nRNAg. The cryo-EM reveals that predominant particles in nRNAg are 80S ribosomes, resembling the pre-translocation state where tRNA's are in the hybrid A/P and P/E site. We also describe a new kind of principal motion of the ribosome, which we call the rocking motion. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qgg.cif.gz | 5.4 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7qgg.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7qgg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qg/7qgg ftp://data.pdbj.org/pub/pdb/validation_reports/qg/7qgg | HTTPS FTP |
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-Related structure data
Related structure data | 13954MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 7 types, 7 molecules S2DEtuvw
#1: RNA chain | Mass: 604241.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) |
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#38: RNA chain | Mass: 50449.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: GenBank: 57148 |
#39: RNA chain | Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: GenBank: 793860 |
#79: RNA chain | Mass: 1553954.250 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) |
#80: RNA chain | Mass: 24414.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: A/P and P/E tRNAs. For some reason it has united the two tRNAs into one molecule, although these are different molecules with different sequences. As the structure contains heterogeneous ...Details: A/P and P/E tRNAs. For some reason it has united the two tRNAs into one molecule, although these are different molecules with different sequences. As the structure contains heterogeneous population of tRNAs then the identity of tRNA is unknown. Source: (natural) Rattus norvegicus (Norway rat) / References: GenBank: 1851728667 |
#81: RNA chain | Mass: 24436.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: A/P and P/E tRNAs. For some reason it has united the two tRNAs into one molecule, although these are different molecules with different sequences.As the structure contains heterogeneous ...Details: A/P and P/E tRNAs. For some reason it has united the two tRNAs into one molecule, although these are different molecules with different sequences.As the structure contains heterogeneous population of tRNAs then the identity of tRNA is unknown. Source: (natural) Rattus norvegicus (Norway rat) / References: GenBank: 1879656365 |
#82: RNA chain | Mass: 6360.800 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) |
+40S ribosomal protein ... , 29 types, 29 molecules SASBSDSESFSHSISKSLSPSRSSSTSUSVSXSaScSdSCSGSJSMSNSOSWSYSZSb
-Protein , 5 types, 5 molecules SQSgSeSfn
#12: Protein | Mass: 16477.377 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q5XFV9 |
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#22: Protein | Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A2K6K8B0 |
#33: Protein | Mass: 6668.938 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A2K6U587 |
#34: Protein | Mass: 17990.014 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: P62982 |
#74: Protein | Mass: 14758.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: Q6P7R7 |
+60S ribosomal protein ... , 38 types, 38 molecules ABCFGHIJKLMNPQRTUVWXYZabcdefgh...
-Ribosomal protein ... , 4 types, 4 molecules OSkp
#49: Protein | Mass: 24207.285 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: L8Y0W1 |
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#53: Protein | Mass: 23535.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A2J8KH59 |
#71: Protein | Mass: 11111.032 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A2Y9RW09 |
#76: Protein | Mass: 12476.973 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) / References: UniProt: A0A7J7V6K8 |
-Protein/peptide , 1 types, 1 molecules y
#84: Protein/peptide | Mass: 360.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Rattus norvegicus (Norway rat) |
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-Non-polymers , 3 types, 47 molecules
#85: Chemical | ChemComp-MG / #86: Chemical | ChemComp-ZN / #87: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component | Name: Ribosome structure in the rat cortex-hippocampus derived neuronal RNA granules. Type: COMPLEX / Entity ID: #1-#79, #82-#84 / Source: NATURAL | |||||||||||||||||||||||||
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Molecular weight | Experimental value: NO | |||||||||||||||||||||||||
Source (natural) | Organism: Rattus norvegicus (Norway rat) / Organ: Brain / Organelle: RNA granule / Tissue: Cortex and hippocampus | |||||||||||||||||||||||||
Buffer solution | pH: 7.5 | |||||||||||||||||||||||||
Buffer component |
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Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | |||||||||||||||||||||||||
Specimen support | Grid material: COPPER / Grid mesh size: 300 divisions/in. / Grid type: C-flat-1.2/1.3 | |||||||||||||||||||||||||
Vitrification | Instrument: FEI VITROBOT MARK IV / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 10 K |
-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: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 59000 X / Nominal defocus max: 3000 nm / Nominal defocus min: 500 nm / Cs: 2.7 mm / C2 aperture diameter: 70 µm / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 30 e/Å2 / Detector mode: INTEGRATING / Film or detector model: FEI FALCON III (4k x 4k) / Num. of grids imaged: 1 / Num. of real images: 3644 |
-Processing
Software |
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EM software |
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CTF correction | Type: NONE | ||||||||||||||||||||||||||||||||||||||||
Particle selection | Num. of particles selected: 499054 | ||||||||||||||||||||||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.86 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 62369 / Symmetry type: POINT | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | Protocol: RIGID BODY FIT / Space: REAL | ||||||||||||||||||||||||||||||||||||||||
Atomic model building | PDB-ID: 6OLE Accession code: 6OLE / Source name: PDB / Type: experimental model | ||||||||||||||||||||||||||||||||||||||||
Refinement | Cross valid method: NONE Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2 | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 69.49 Å2 | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
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