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Open data
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Basic information
| Entry | ![]() | |||||||||
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| Title | Human pre-60S - State 1B | |||||||||
Map data | Human pre-60S - State 1B - Composite map | |||||||||
Sample |
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Keywords | Human / ribosome biogenesis / NLE1 / RIX1 complex / 5S RNP / RIBOSOME | |||||||||
| Function / homology | Function and homology informationpositive regulation of protein localization to chromosome, telomeric region / dendrite extension / lamin filament / regulation of Notch signaling pathway / regulation of fatty acid biosynthetic process / preribosome binding / regulation of megakaryocyte differentiation / miRNA-mediated post-transcriptional gene silencing / positive regulation of protein sumoylation / negative regulation of G2/M transition of mitotic cell cycle ...positive regulation of protein localization to chromosome, telomeric region / dendrite extension / lamin filament / regulation of Notch signaling pathway / regulation of fatty acid biosynthetic process / preribosome binding / regulation of megakaryocyte differentiation / miRNA-mediated post-transcriptional gene silencing / positive regulation of protein sumoylation / negative regulation of G2/M transition of mitotic cell cycle / miRNA-mediated gene silencing by inhibition of translation / stem cell division / negative regulation of DNA replication / protein localization to nucleolus / negative regulation of cell-cell adhesion / ribosomal protein import into nucleus / regulation of G1 to G0 transition / regulation of reactive oxygen species metabolic process / regulation of glycolytic process / G1 to G0 transition / stem cell population maintenance / negative regulation of formation of translation preinitiation complex / maturation of 5.8S rRNA / GAIT complex / positive regulation of dendritic spine development / regulation of translation involved in cellular response to UV / A band / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator / ribosomal large subunit binding / negative regulation of myoblast fusion / protein-DNA complex disassembly / preribosome, large subunit precursor / positive regulation of telomere maintenance / positive regulation of DNA damage response, signal transduction by p53 class mediator / Protein hydroxylation / PELO:HBS1L and ABCE1 dissociate a ribosome on a non-stop mRNA / protein localization to nucleus / Peptide chain elongation / nuclear-transcribed mRNA catabolic process / Selenocysteine synthesis / mitotic metaphase chromosome alignment / Formation of a pool of free 40S subunits / protein targeting / Eukaryotic Translation Termination / SRP-dependent cotranslational protein targeting to membrane / Response of EIF2AK4 (GCN2) to amino acid deficiency / ubiquitin ligase inhibitor activity / Viral mRNA Translation / ribosomal subunit export from nucleus / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / positive regulation of signal transduction by p53 class mediator / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / maturation of LSU-rRNA / negative regulation of ubiquitin-dependent protein catabolic process / endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of protein ubiquitination / rough endoplasmic reticulum / translation initiation factor activity / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of cell migration / regulation of signal transduction by p53 class mediator / response to insulin / condensed nuclear chromosome / cytosolic ribosome assembly / ZNF598 and the Ribosome-associated Quality Trigger (RQT) complex dissociate a ribosome stalled on a no-go mRNA / ribosomal large subunit biogenesis / assembly of large subunit precursor of preribosome / DNA damage response, signal transduction by p53 class mediator / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / striated muscle contraction / mRNA 3'-UTR binding / positive regulation of translation / cellular response to type II interferon / bone development / cellular response to gamma radiation / positive regulation of miRNA transcription / fibrillar center / osteoblast differentiation / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / mRNA 5'-UTR binding / transcription coactivator binding / Ribosome Quality Control (RQC) complex extracts and degrades nascent peptide / cellular response to UV / rRNA processing / cytosolic ribosome / regulation of cell population proliferation / large ribosomal subunit / ribosome binding / Dengue Virus-Host Interactions / 5S rRNA binding / cell body / ribosomal large subunit assembly / spermatogenesis / large ribosomal subunit rRNA binding / cytosolic large ribosomal subunit / response to ethanol Similarity search - Function | |||||||||
| Biological species | Homo sapiens (human) | |||||||||
| Method | single particle reconstruction / cryo EM / Resolution: 3.13 Å | |||||||||
Authors | Thoms M / Denk T / Beckmann R | |||||||||
| Funding support | European Union, 1 items
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Citation | #1: Journal: Acta Crystallogr., Sect. D: Biol. Crystallogr. / Year: 2018Title: Real-space refinement in PHENIX for cryo-EM and crystallography Authors: Adams PD | |||||||||
| History |
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Structure visualization
| Supplemental images |
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Downloads & links
-EMDB archive
| Map data | emd_53092.map.gz | 16.9 MB | EMDB map data format | |
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| Header (meta data) | emd-53092-v30.xml emd-53092.xml | 61.4 KB 61.4 KB | Display Display | EMDB header |
| Images | emd_53092.png | 76.7 KB | ||
| Filedesc metadata | emd-53092.cif.gz | 15.7 KB | ||
| Archive directory | https://data.pdbj.org/pub/emdb/structures/EMD-53092 ftp://data.pdbj.org/pub/emdb/structures/EMD-53092 | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 9qetMC M: atomic model generated by this map C: citing same article ( |
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| Similar structure data | Similarity search - Function & homology F&H Search |
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Links
| EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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| Related items in Molecule of the Month |
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Map
| File | Download / File: emd_53092.map.gz / Format: CCP4 / Size: 476.8 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||
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| Annotation | Human pre-60S - State 1B - Composite map | ||||||||||||||||||||||||||||||||||||
| Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||
| Voxel size | X=Y=Z: 1.045 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 : Human pre-60S - State 1A
+Supramolecule #1: Human pre-60S - State 1A
+Macromolecule #1: Eukaryotic translation initiation factor 6
+Macromolecule #2: Nucleolar GTP-binding protein 2
+Macromolecule #3: Guanine nucleotide-binding protein-like 3
+Macromolecule #4: GTP-binding protein 4
+Macromolecule #5: Protein LLP homolog
+Macromolecule #6: mRNA turnover protein 4 homolog
+Macromolecule #7: Notchless protein homolog 1
+Macromolecule #8: Ribosome biogenesis protein NSA2 homolog
+Macromolecule #9: Probable ribosome biogenesis protein RLP24
+Macromolecule #10: Ribosome production factor 2 homolog
+Macromolecule #11: Ribosome biogenesis regulatory protein homolog
+Macromolecule #15: 60S ribosomal protein L3
+Macromolecule #16: 60S ribosomal protein L4
+Macromolecule #17: 60S ribosomal protein L5
+Macromolecule #18: Large ribosomal subunit protein eL6
+Macromolecule #19: Large ribosomal subunit protein uL30
+Macromolecule #20: 60S ribosomal protein L7a
+Macromolecule #21: 60S ribosomal protein L9
+Macromolecule #22: 60S ribosomal protein L11
+Macromolecule #23: 60S ribosomal protein L13
+Macromolecule #24: 60S ribosomal protein L14
+Macromolecule #25: 60S ribosomal protein L15
+Macromolecule #26: 60S ribosomal protein L13a
+Macromolecule #27: 60S ribosomal protein L17
+Macromolecule #28: 60S ribosomal protein L18
+Macromolecule #29: 60S ribosomal protein L18a
+Macromolecule #30: 60S ribosomal protein L21
+Macromolecule #31: 60S ribosomal protein L23
+Macromolecule #32: 60S ribosomal protein L26
+Macromolecule #33: 60S ribosomal protein L27a
+Macromolecule #34: 60S ribosomal protein L31
+Macromolecule #35: 60S ribosomal protein L32
+Macromolecule #36: 60S ribosomal protein L35a
+Macromolecule #37: 60S ribosomal protein L35
+Macromolecule #38: 60S ribosomal protein L36
+Macromolecule #39: 60S ribosomal protein L28
+Macromolecule #40: Large ribosomal subunit protein uL11
+Macromolecule #41: 60S ribosomal protein L10a
+Macromolecule #12: 28S rRNA
+Macromolecule #13: 5S rRNA
+Macromolecule #14: 5.8S rRNA
+Macromolecule #42: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #43: MAGNESIUM ION
+Macromolecule #44: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #45: ZINC ION
-Experimental details
-Structure determination
| Method | cryo EM |
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Processing | single particle reconstruction |
| Aggregation state | particle |
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Sample preparation
| Buffer | pH: 7.5 |
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| Vitrification | Cryogen name: ETHANE |
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Electron microscopy
| Microscope | TFS KRIOS |
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| Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 43.6 e/Å2 |
| Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
| Electron optics | Illumination mode: SPOT SCAN / Imaging mode: BRIGHT FIELD / Nominal defocus max: 3.5 µm / Nominal defocus min: 0.5 µm |
| Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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About Yorodumi




Keywords
Homo sapiens (human)
Authors
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Processing
FIELD EMISSION GUN
