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Open data
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Basic information
Entry | Database: PDB / ID: 9azs | ||||||||||||||||||||||||
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Title | In situ human Post-eEF1A-AT-P-E state 80S ribosome | ||||||||||||||||||||||||
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![]() | RIBOSOME / In situ | ||||||||||||||||||||||||
Function / homology | ![]() cytoplasmic side of lysosomal membrane / Eukaryotic Translation Elongation / eukaryotic translation elongation factor 1 complex / regulation of chaperone-mediated autophagy / positive regulation by host of viral genome replication / eukaryotic 80S initiation complex / negative regulation of protein neddylation / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist ...cytoplasmic side of lysosomal membrane / Eukaryotic Translation Elongation / eukaryotic translation elongation factor 1 complex / regulation of chaperone-mediated autophagy / positive regulation by host of viral genome replication / eukaryotic 80S initiation complex / negative regulation of protein neddylation / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / kinase activator activity / negative regulation of formation of translation preinitiation complex / regulation of G1 to G0 transition / axial mesoderm development / 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 / 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-DNA complex disassembly / positive regulation of gastrulation / nucleolus organization / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / protein tyrosine kinase inhibitor activity / 90S preribosome assembly / : / IRE1-RACK1-PP2A complex / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / translation at postsynapse / TNFR1-mediated ceramide production / negative regulation of DNA repair / negative regulation of RNA splicing / TORC2 complex binding / mammalian oogenesis stage / GAIT complex / A band / supercoiled DNA binding / activation-induced cell death of T cells / G1 to G0 transition / oxidized purine DNA binding / NF-kappaB complex / middle ear morphogenesis / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / ubiquitin-like protein conjugating enzyme binding / translation at presynapse / regulation of establishment of cell polarity / positive regulation of ubiquitin-protein transferase activity / rRNA modification in the nucleus and cytosol / negative regulation of phagocytosis / 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 peptidyl-serine phosphorylation / protein kinase A binding / cortical actin cytoskeleton / negative regulation of ubiquitin protein ligase activity / pigmentation / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / response to aldosterone / Translation initiation complex formation / homeostatic process / positive regulation of mitochondrial depolarization / positive regulation of T cell receptor signaling pathway / macrophage chemotaxis / fibroblast growth factor binding / negative regulation of Wnt signaling pathway / lung morphogenesis / positive regulation of activated T cell proliferation / negative regulation of translational frameshifting / monocyte chemotaxis / Protein hydroxylation / BH3 domain binding / TOR signaling / cysteine-type endopeptidase activator activity involved in apoptotic process / SARS-CoV-1 modulates host translation machinery / regulation of cell division / mTORC1-mediated signalling / T cell proliferation involved in immune response / iron-sulfur cluster binding / Peptide chain elongation / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / Formation of a pool of free 40S subunits / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / phagocytic cup / blastocyst development / translational elongation / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / cellular response to actinomycin D / negative regulation of ubiquitin-dependent protein catabolic process / Viral mRNA Translation / negative regulation of respiratory burst involved in inflammatory response / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) Similarity search - Function | ||||||||||||||||||||||||
Biological species | ![]() | ||||||||||||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.8 Å | ||||||||||||||||||||||||
![]() | Wei, Z. / Yong, X. | ||||||||||||||||||||||||
Funding support | 1items
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![]() | ![]() Title: In situ human Post-eEF1A-AT-P-E state 80S ribosome Authors: Wei, Z. / Yong, X. | ||||||||||||||||||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 5.5 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 | ![]() | 367.6 KB | Display | |
Data in CIF | ![]() | 649.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 44021MC 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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Components
+60S ribosomal protein ... , 39 types, 39 molecules LRLALCLELFLGLHLILJLMLNLOLPLQLSLTLVLXLYLZLaLbLcLdLeLfLgLhLiLj...
-Small ribosomal subunit protein ... , 9 types, 9 molecules SESeSOSbSDSPSQSMSZ
#2: Protein | Mass: 29523.674 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#9: Protein | Mass: 6539.758 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#17: Protein | Mass: 15014.187 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#19: Protein | Mass: 9348.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#64: Protein | Mass: 25172.561 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#67: Protein | Mass: 14092.600 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#68: Protein | Mass: 16249.062 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#75: Protein | Mass: 13652.019 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#76: Protein | Mass: 8526.119 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
+40S ribosomal protein ... , 22 types, 22 molecules SISLSXSGSJSYSASBSHSVSaSCSNSWSRSFSKSSSTSUScSd
-RNA chain , 7 types, 7 molecules L5L7L8S2EtPtAT
#20: RNA chain | Mass: 1211748.500 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#21: RNA chain | Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#22: RNA chain | Mass: 50143.648 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#78: RNA chain | Mass: 561332.438 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#79: RNA chain | Mass: 24102.275 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#80: RNA chain | Mass: 23825.205 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#85: RNA chain | Mass: 24436.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Large ribosomal subunit protein ... , 4 types, 4 molecules LBLDLLLm
#24: Protein | Mass: 46079.918 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#26: Protein | Mass: 34008.324 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#33: Protein | Mass: 24190.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#58: Protein | Mass: 6199.574 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Protein , 5 types, 5 molecules LUSgSfLsCF
#41: Protein | Mass: 11722.535 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#74: Protein | Mass: 34669.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#77: Protein | Mass: 7884.286 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#83: Protein | Mass: 21507.035 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
#86: Protein | Mass: 48247.309 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
-Non-polymers , 2 types, 261 molecules 


#87: Chemical | ChemComp-ZN / #88: Chemical | ChemComp-MG / |
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-Details
Has ligand of interest | Y |
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Has protein modification | Y |
-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: CELL / 3D reconstruction method: single particle reconstruction |
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Sample preparation
Component | Name: In situ human Post-eEF1A-AT-P-E state 80S ribosome / Type: COMPLEX / Entity ID: #1-#86 / Source: NATURAL |
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Source (natural) | Organism: ![]() |
Buffer solution | pH: 7.4 |
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: 2500 nm / Nominal defocus min: 1200 nm |
Image recording | Electron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) |
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Processing
EM software | Name: PHENIX / Version: 1.20.1_4487: / Category: model refinement | ||||||||||||||||||||||||
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CTF correction | Type: NONE | ||||||||||||||||||||||||
3D reconstruction | Resolution: 2.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 48914 / Symmetry type: POINT | ||||||||||||||||||||||||
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