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Open data
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Basic information
Entry | ![]() | |||||||||
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Title | In situ human P-E state 80S ribosome | |||||||||
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![]() | In situ / Ribosome | |||||||||
Function / homology | ![]() male meiosis I / eukaryotic 80S initiation complex / negative regulation of protein neddylation / response to insecticide / regulation of translation involved in cellular response to UV / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / axial mesoderm development ...male meiosis I / eukaryotic 80S initiation complex / negative regulation of protein neddylation / response to insecticide / regulation of translation involved in cellular response to UV / negative regulation of endoplasmic reticulum unfolded protein response / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / axial mesoderm development / negative regulation of formation of translation preinitiation complex / regulation of G1 to G0 transition / 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 gastrulation / 90S preribosome assembly / protein tyrosine kinase inhibitor activity / protein-DNA complex disassembly / IRE1-RACK1-PP2A complex / positive regulation of endodeoxyribonuclease activity / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / nucleolus organization / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of DNA repair / negative regulation of RNA splicing / GAIT complex / positive regulation of DNA damage response, signal transduction by p53 class mediator / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / supercoiled DNA binding / TORC2 complex binding / neural crest cell differentiation / G1 to G0 transition / NF-kappaB complex / positive regulation of ubiquitin-protein transferase activity / 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 / ubiquitin-like protein conjugating enzyme binding / negative regulation of bicellular tight junction assembly / regulation of establishment of cell polarity / 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 / protein kinase A binding / ion channel inhibitor activity / pigmentation / Ribosomal scanning and start codon recognition / homeostatic process / Translation initiation complex formation / 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 / monocyte chemotaxis / positive regulation of natural killer cell proliferation / positive regulation of activated T cell proliferation / negative regulation of translational frameshifting / Protein hydroxylation / TOR signaling / BH3 domain binding / SARS-CoV-1 modulates host translation machinery / regulation of cell division / cellular response to ethanol / mTORC1-mediated signalling / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / iron-sulfur cluster binding / Peptide chain elongation / Selenocysteine synthesis / Formation of a pool of free 40S subunits / 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 / positive regulation of GTPase activity / cellular response to actinomycin D / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / negative regulation of ubiquitin-dependent protein catabolic process / positive regulation of signal transduction by p53 class mediator / protein serine/threonine kinase inhibitor activity / Viral mRNA Translation / negative regulation of respiratory burst involved in inflammatory response / Maturation of protein E / Maturation of protein E / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / protein localization to nucleus / GTP hydrolysis and joining of the 60S ribosomal subunit / ER Quality Control Compartment (ERQC) / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.43 Å | |||||||||
![]() | Wei Z / Yong X | |||||||||
Funding support | 1 items
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![]() | ![]() Title: In situ human P-E state 80S ribosome Authors: Wei Z / Yong X | |||||||||
History |
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Structure visualization
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Downloads & links
-EMDB archive
Map data | ![]() | 483.7 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 101.7 KB 101.7 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 16.8 KB | Display | ![]() |
Images | ![]() | 12.9 KB | ||
Filedesc metadata | ![]() | 19.3 KB | ||
Others | ![]() ![]() | 475.1 MB 475.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 26.5 KB | Display | |
Data in CIF | ![]() | 35.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8uizMC M: atomic model generated by this map C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
File | ![]() | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.068 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
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Sample components
+Entire : In situ human P-E state 80S ribosome
+Supramolecule #1: In situ human P-E state 80S ribosome
+Macromolecule #1: 60S ribosomal protein L19
+Macromolecule #2: Small ribosomal subunit protein eS4, X isoform
+Macromolecule #3: 40S ribosomal protein S8
+Macromolecule #4: 40S ribosomal protein S11
+Macromolecule #5: 40S ribosomal protein S23
+Macromolecule #6: 40S ribosomal protein S6
+Macromolecule #7: 40S ribosomal protein S9
+Macromolecule #8: 40S ribosomal protein S24
+Macromolecule #9: Small ribosomal subunit protein eS30
+Macromolecule #10: 40S ribosomal protein SA
+Macromolecule #11: 40S ribosomal protein S3a
+Macromolecule #12: Small ribosomal subunit protein eS7
+Macromolecule #13: 40S ribosomal protein S21
+Macromolecule #14: 40S ribosomal protein S26
+Macromolecule #15: 40S ribosomal protein S2
+Macromolecule #16: 40S ribosomal protein S13
+Macromolecule #17: Small ribosomal subunit protein uS11
+Macromolecule #18: 40S ribosomal protein S15a
+Macromolecule #19: Small ribosomal subunit protein eS27
+Macromolecule #23: 60S ribosomal protein L8
+Macromolecule #24: Large ribosomal subunit protein uL3
+Macromolecule #25: 60S ribosomal protein L4
+Macromolecule #26: Large ribosomal subunit protein uL18
+Macromolecule #27: Large ribosomal subunit protein eL6
+Macromolecule #28: 60S ribosomal protein L7
+Macromolecule #29: 60S ribosomal protein L7a
+Macromolecule #30: 60S ribosomal protein L9
+Macromolecule #31: Ribosomal protein uL16-like
+Macromolecule #32: 60S ribosomal protein L11
+Macromolecule #33: Large ribosomal subunit protein eL13
+Macromolecule #34: 60S ribosomal protein L14
+Macromolecule #35: 60S ribosomal protein L15
+Macromolecule #36: 60S ribosomal protein L13a
+Macromolecule #37: 60S ribosomal protein L17
+Macromolecule #38: 60S ribosomal protein L18
+Macromolecule #39: 60S ribosomal protein L18a
+Macromolecule #40: 60S ribosomal protein L21
+Macromolecule #41: Heparin-binding protein HBp15
+Macromolecule #42: 60S ribosomal protein L23
+Macromolecule #43: 60S ribosomal protein L23a
+Macromolecule #44: 60S ribosomal protein L26
+Macromolecule #45: 60S ribosomal protein L27
+Macromolecule #46: 60S ribosomal protein L27a
+Macromolecule #47: Large ribosomal subunit protein eL29
+Macromolecule #48: 60S ribosomal protein L30
+Macromolecule #49: 60S ribosomal protein L31
+Macromolecule #50: 60S ribosomal protein L32
+Macromolecule #51: 60S ribosomal protein L35a
+Macromolecule #52: 60S ribosomal protein L34
+Macromolecule #53: 60S ribosomal protein L35
+Macromolecule #54: 60S ribosomal protein L36
+Macromolecule #55: 60S ribosomal protein L37
+Macromolecule #56: 60S ribosomal protein L38
+Macromolecule #57: 60S ribosomal protein L39
+Macromolecule #58: Large ribosomal subunit protein eL40
+Macromolecule #59: 60S ribosomal protein L41
+Macromolecule #60: 60S ribosomal protein L36a
+Macromolecule #61: 60S ribosomal protein L37a
+Macromolecule #62: 60S ribosomal protein L28
+Macromolecule #63: 40S ribosomal protein S17
+Macromolecule #64: Small ribosomal subunit protein uS3
+Macromolecule #65: 40S ribosomal protein S5
+Macromolecule #66: 40S ribosomal protein S10
+Macromolecule #67: Small ribosomal subunit protein uS19
+Macromolecule #68: Small ribosomal subunit protein uS9
+Macromolecule #69: 40S ribosomal protein S18
+Macromolecule #70: 40S ribosomal protein S19
+Macromolecule #71: 40S ribosomal protein S20
+Macromolecule #72: 40S ribosomal protein S28
+Macromolecule #73: 40S ribosomal protein S29
+Macromolecule #74: Receptor of activated protein C kinase 1
+Macromolecule #75: Small ribosomal subunit protein eS12
+Macromolecule #76: Small ribosomal subunit protein eS25
+Macromolecule #77: Ubiquitin-40S ribosomal protein S27a
+Macromolecule #81: Large ribosomal subunit protein uL11
+Macromolecule #82: 60S ribosomal protein L10a
+Macromolecule #83: 60S acidic ribosomal protein P0
+Macromolecule #84: Ribosomal protein L24
+Macromolecule #20: 28S rRNA
+Macromolecule #21: 5S rRNA [Homo sapiens]
+Macromolecule #22: 5.8S rRNA [Homo sapiens]
+Macromolecule #78: 18S rRNA [Homo sapiens]
+Macromolecule #79: E site tRNA
+Macromolecule #80: P site tRNA
+Macromolecule #85: ZINC ION
+Macromolecule #86: MAGNESIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | cell |
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Sample preparation
Buffer | pH: 7.4 |
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Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K3 (6k x 4k) / Average electron dose: 50.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.5 µm / Nominal defocus min: 1.2 µm |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
Startup model | Type of model: EMDB MAP EMDB ID: |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.43 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 12376 |
Initial angle assignment | Type: ANGULAR RECONSTITUTION |
Final angle assignment | Type: ANGULAR RECONSTITUTION |