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Yorodumi- EMDB-29275: Human nuclear pre-60S ribosomal subunit (State L1) - Composite map -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-29275 | |||||||||
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Title | Human nuclear pre-60S ribosomal subunit (State L1) - Composite map | |||||||||
Map data | ||||||||||
Sample |
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Keywords | Pre-60S ribosomal subunit / Assembly intermediate / Ribosome / Nucleoprotein complex | |||||||||
Function / homology | Function and homology information protein localization to nucleoplasm / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / regulation of RIG-I signaling pathway / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding / dendrite extension / preribosome binding / regulation of cellular senescence / lamin filament ...protein localization to nucleoplasm / negative regulation of transcription of nucleolar large rRNA by RNA polymerase I / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / regulation of RIG-I signaling pathway / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding / dendrite extension / preribosome binding / regulation of cellular senescence / lamin filament / regulation of fatty acid biosynthetic process / PeBoW complex / regulation of megakaryocyte differentiation / miRNA-mediated post-transcriptional gene silencing / negative regulation of signal transduction by p53 class mediator / embryonic brain development / eukaryotic 80S initiation complex / negative regulation of protein neddylation / miRNA-mediated gene silencing by inhibition of translation / translation at presynapse / axial mesoderm development / regulation of G1 to G0 transition / negative regulation of formation of translation preinitiation complex / ribosomal protein import into nucleus / 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 / blastocyst formation / protein-DNA complex disassembly / 90S preribosome assembly / positive regulation of DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / positive regulation of protein K63-linked deubiquitination / TORC2 complex binding / protein localization to nucleolus / GAIT complex / G1 to G0 transition / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / middle ear morphogenesis / nuclear-transcribed mRNA catabolic process / cytoplasmic side of rough endoplasmic reticulum membrane / A band / positive regulation of signal transduction by p53 class mediator / regulation of reactive oxygen species metabolic process / ubiquitin ligase inhibitor activity / alpha-beta T cell differentiation / positive regulation of dendritic spine development / negative regulation of ubiquitin protein ligase activity / regulation of glycolytic process / regulation of aerobic respiration / maturation of 5.8S rRNA / rRNA metabolic process / response to aldosterone / homeostatic process / lung morphogenesis / macrophage chemotaxis / negative regulation of DNA replication / negative regulation of cell-cell adhesion / ribosomal subunit export from nucleus / Protein hydroxylation / 90S preribosome / regulation of cyclin-dependent protein serine/threonine kinase activity / ribosomal large subunit binding / Peptide chain elongation / Selenocysteine synthesis / mitotic G2 DNA damage checkpoint signaling / protein-RNA complex assembly / Formation of a pool of free 40S subunits / rRNA transcription / Eukaryotic Translation Termination / preribosome, large subunit precursor / blastocyst development / Response of EIF2AK4 (GCN2) to amino acid deficiency / translation regulator activity / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / protein localization to nucleus / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / cellular response to actinomycin D / GTP hydrolysis and joining of the 60S ribosomal subunit / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / protein targeting / rough endoplasmic reticulum / MDM2/MDM4 family protein binding / negative regulation of protein-containing complex assembly / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / ribonucleoprotein complex binding / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / maturation of LSU-rRNA / negative regulation of ubiquitin-dependent protein catabolic process / ribosomal large subunit biogenesis / negative regulation of protein ubiquitination / embryo implantation / translation initiation factor activity / cellular response to interleukin-4 / ossification / assembly of large subunit precursor of preribosome / cytosolic ribosome Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.58 Å | |||||||||
Authors | Vanden Broeck A / Klinge S | |||||||||
Funding support | European Union, United States, 2 items
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Citation | Journal: Science / Year: 2023 Title: Principles of human pre-60S biogenesis Authors: Vanden Broeck A / Klinge S | |||||||||
History |
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-Structure visualization
Supplemental images |
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-Downloads & links
-EMDB archive
Map data | emd_29275.map.gz | 126.3 MB | EMDB map data format | |
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Header (meta data) | emd-29275-v30.xml emd-29275.xml | 79.5 KB 79.5 KB | Display Display | EMDB header |
FSC (resolution estimation) | emd_29275_fsc.xml | 15.8 KB | Display | FSC data file |
Images | emd_29275.png | 146.2 KB | ||
Masks | emd_29275_msk_1.map | 421.9 MB | Mask map | |
Others | emd_29275_half_map_1.map.gz emd_29275_half_map_2.map.gz | 391.1 MB 391.1 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-29275 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-29275 | HTTPS FTP |
-Related structure data
Related structure data | 8fldMC 8fkpC 8fleC 8flfC C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_29275.map.gz / Format: CCP4 / Size: 421.9 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||
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Voxel size | X=Y=Z: 1.072 Å | ||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||
Details | EMDB XML:
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-Supplemental data
-Mask #1
File | emd_29275_msk_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #2
File | emd_29275_half_map_1.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Half map: #1
File | emd_29275_half_map_2.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Human nuclear pre-60S ribosomal subunit (State L1)
+Supramolecule #1: Human nuclear pre-60S ribosomal subunit (State L1)
+Macromolecule #1: 60S ribosomal protein L10
+Macromolecule #6: 60S ribosomal protein L11
+Macromolecule #7: 60S ribosomal protein L13
+Macromolecule #8: 60S ribosomal protein L13a
+Macromolecule #9: 60S ribosomal protein L14
+Macromolecule #10: 60S ribosomal protein L15
+Macromolecule #11: 60S ribosomal protein L17
+Macromolecule #12: 60S ribosomal protein L18
+Macromolecule #13: 60S ribosomal protein L18a
+Macromolecule #14: 60S ribosomal protein L19
+Macromolecule #15: 60S ribosomal protein L21
+Macromolecule #16: 60S ribosomal protein L22
+Macromolecule #17: 60S ribosomal protein L23
+Macromolecule #18: 60S ribosomal protein L23a
+Macromolecule #19: 60S ribosomal protein L26
+Macromolecule #20: 60S ribosomal protein L27
+Macromolecule #21: 60S ribosomal protein L27a
+Macromolecule #22: 60S ribosomal protein L28
+Macromolecule #23: 60S ribosomal protein L29
+Macromolecule #24: 60S ribosomal protein L3
+Macromolecule #25: 60S ribosomal protein L30
+Macromolecule #26: 60S ribosomal protein L31
+Macromolecule #27: 60S ribosomal protein L32
+Macromolecule #28: 60S ribosomal protein L34
+Macromolecule #29: 60S ribosomal protein L35
+Macromolecule #30: 60S ribosomal protein L35a
+Macromolecule #31: 60S ribosomal protein L36
+Macromolecule #32: 60S ribosomal protein L36a
+Macromolecule #33: 60S ribosomal protein L37
+Macromolecule #34: 60S ribosomal protein L37a
+Macromolecule #35: 60S ribosomal protein L38
+Macromolecule #36: 60S ribosomal protein L39
+Macromolecule #37: Protein LLP homolog
+Macromolecule #38: Ribosome biogenesis protein NOP53
+Macromolecule #39: Zinc finger protein 593
+Macromolecule #40: 60S ribosomal protein L4
+Macromolecule #41: 60S ribosomal protein L5
+Macromolecule #42: 60S ribosomal protein L6
+Macromolecule #43: 60S ribosomal protein L7
+Macromolecule #44: 60S ribosomal protein L7a
+Macromolecule #45: 60S ribosomal protein L8
+Macromolecule #46: 60S ribosomal protein L9
+Macromolecule #47: MKI67 FHA domain-interacting nucleolar phosphoprotein
+Macromolecule #48: 60S ribosomal protein L7-like 1
+Macromolecule #49: Eukaryotic translation initiation factor 6
+Macromolecule #50: Ribosomal L1 domain-containing protein 1
+Macromolecule #51: Pescadillo homolog
+Macromolecule #52: mRNA turnover protein 4 homolog
+Macromolecule #53: GTP-binding protein 4
+Macromolecule #54: Probable ribosome biogenesis protein RLP24
+Macromolecule #2: 5.8S rRNA
+Macromolecule #3: ITS2 rRNA
+Macromolecule #4: 28S rRNA
+Macromolecule #5: 5S rRNA
+Macromolecule #55: MAGNESIUM ION
+Macromolecule #56: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.6 |
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Grid | Model: Quantifoil R3.5/1 / Material: GOLD / Mesh: 400 / Support film - Material: CARBON / Support film - topology: CONTINUOUS / Support film - Film thickness: 2 / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. |
Vitrification | Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 283 K / Instrument: FEI VITROBOT MARK IV Details: Four applications with manual blotting before last blotting with the Vitrobot.. |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy / Nominal defocus max: 2.5 µm / Nominal defocus min: 0.5 µm / Nominal magnification: 64000 |
Specialist optics | Energy filter - Slit width: 20 eV |
Image recording | Film or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 4 / Number real images: 172699 / Average exposure time: 2.0 sec. / Average electron dose: 60.0 e/Å2 |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | PDB-8fld: |