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- EMDB-29261: Human nucleolar pre-60S ribosomal subunit (State F) - Composite map -
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Open data
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Basic information
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Title | Human nucleolar pre-60S ribosomal subunit (State F) - Composite map | |||||||||
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![]() | Pre-60S ribosomal subunit / Assembly intermediate / ![]() ![]() | |||||||||
Function / homology | ![]() RNA 2'-O-methyltransferase activity / Noc1p-Noc2p complex / Noc2p-Noc3p complex / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / positive regulation of protein localization to chromosome, telomeric region / RNA metabolic process / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity ...RNA 2'-O-methyltransferase activity / Noc1p-Noc2p complex / Noc2p-Noc3p complex / TFAP2A acts as a transcriptional repressor during retinoic acid induced cell differentiation / positive regulation of protein localization to chromosome, telomeric region / RNA metabolic process / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / rRNA (cytosine-C5-)-methyltransferase activity / dendrite extension / preribosome binding / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Vanden Broeck A / Klinge S | |||||||||
Funding support | European Union, ![]()
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![]() | ![]() Title: Principles of human pre-60 biogenesis. Authors: Arnaud Vanden Broeck / Sebastian Klinge / ![]() Abstract: During the early stages of human large ribosomal subunit (60) biogenesis, an ensemble of assembly factors establishes and fine-tunes the essential RNA functional centers of pre-60 particles by an ...During the early stages of human large ribosomal subunit (60) biogenesis, an ensemble of assembly factors establishes and fine-tunes the essential RNA functional centers of pre-60 particles by an unknown mechanism. Here, we report a series of cryo-electron microscopy structures of human nucleolar and nuclear pre-60 assembly intermediates at resolutions of 2.5 to 3.2 angstroms. These structures show how protein interaction hubs tether assembly factor complexes to nucleolar particles and how guanosine triphosphatases and adenosine triphosphatase couple irreversible nucleotide hydrolysis steps to the installation of functional centers. Nuclear stages highlight how a conserved RNA-processing complex, the rixosome, couples large-scale RNA conformational changes with pre-ribosomal RNA processing by the RNA degradation machinery. Our ensemble of human pre-60 particles provides a rich foundation with which to elucidate the molecular principles of ribosome formation. | |||||||||
History |
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Structure visualization
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 59.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 95.2 KB 95.2 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 15.8 KB | Display | ![]() |
Images | ![]() | 173.4 KB | ||
Masks | ![]() | 421.9 MB | ![]() | |
Others | ![]() ![]() | 391.3 MB 391.3 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8fkyMC ![]() 8fkpC ![]() 8fkqC ![]() 8fkrC ![]() 8fksC ![]() 8fktC ![]() 8fkuC ![]() 8fkvC ![]() 8fkwC ![]() 8fkxC ![]() 8fkzC ![]() 8fl0C ![]() 8fl2C ![]() 8fl3C ![]() 8fl4C ![]() 8fl6C ![]() 8fl7C ![]() 8fl9C ![]() 8flaC ![]() 8flbC ![]() 8flcC ![]() 8fldC ![]() 8fleC ![]() 8flfC C: citing same article ( M: atomic model generated by this map |
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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
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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
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Projections & Slices |
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Density Histograms |
-Half map: #2
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Density Histograms |
-Half map: #1
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Density Histograms |
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Sample components
+Entire : Human nucleolar pre-60S ribosomal subunit (State F)
+Supramolecule #1: Human nucleolar pre-60S ribosomal subunit (State F)
+Macromolecule #1: 60S ribosomal protein L12
+Macromolecule #2: 60S ribosomal protein L10a
+Macromolecule #3: WD repeat-containing protein 55
+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 L23
+Macromolecule #17: 60S ribosomal protein L23a
+Macromolecule #18: 60S ribosomal protein L26
+Macromolecule #19: 60S ribosomal protein L27
+Macromolecule #20: 60S ribosomal protein L27a
+Macromolecule #21: 60S ribosomal protein L28
+Macromolecule #22: 60S ribosomal protein L3
+Macromolecule #23: 60S ribosomal protein L30
+Macromolecule #24: 60S ribosomal protein L31
+Macromolecule #25: 60S ribosomal protein L32
+Macromolecule #26: 60S ribosomal protein L34
+Macromolecule #27: 60S ribosomal protein L35
+Macromolecule #28: 60S ribosomal protein L35a
+Macromolecule #29: 60S ribosomal protein L36
+Macromolecule #30: 60S ribosomal protein L37
+Macromolecule #31: Nucleolar complex protein 2 homolog
+Macromolecule #32: Guanine nucleotide-binding protein-like 3
+Macromolecule #33: Ribosome biogenesis protein NSA2 homolog
+Macromolecule #34: 60S ribosome subunit biogenesis protein NIP7 homolog
+Macromolecule #35: ATP-dependent RNA helicase DDX54
+Macromolecule #36: Protein LLP homolog
+Macromolecule #37: 60S ribosomal protein L4
+Macromolecule #38: 60S ribosomal protein L6
+Macromolecule #39: 60S ribosomal protein L7
+Macromolecule #40: 60S ribosomal protein L7a
+Macromolecule #41: 60S ribosomal protein L9
+Macromolecule #42: MKI67 FHA domain-interacting nucleolar phosphoprotein
+Macromolecule #43: 60S ribosomal protein L7-like 1
+Macromolecule #44: pre-rRNA 2'-O-ribose RNA methyltransferase FTSJ3
+Macromolecule #45: Eukaryotic translation initiation factor 6
+Macromolecule #46: Ribosomal L1 domain-containing protein 1
+Macromolecule #47: Pescadillo homolog
+Macromolecule #48: Probable rRNA-processing protein EBP2
+Macromolecule #49: Ribosome biogenesis protein BRX1 homolog
+Macromolecule #50: Ribosome biogenesis protein WDR12
+Macromolecule #51: mRNA turnover protein 4 homolog
+Macromolecule #52: GTP-binding protein 4
+Macromolecule #53: Ribosome biogenesis protein BOP1
+Macromolecule #54: Ribosome biogenesis regulatory protein homolog
+Macromolecule #55: Nucleolar complex protein 3 homolog
+Macromolecule #56: Probable ribosome biogenesis protein RLP24
+Macromolecule #57: ATP-dependent RNA helicase DDX18
+Macromolecule #58: Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase
+Macromolecule #59: Nucleolar protein 16
+Macromolecule #4: 5.8S rRNA
+Macromolecule #5: ITS2 rRNA
+Macromolecule #6: 28S rRNA
+Macromolecule #60: MAGNESIUM ION
+Macromolecule #61: ZINC ION
+Macromolecule #62: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #63: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #64: POTASSIUM ION
-Experimental details
-Structure determination
Method | ![]() |
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Aggregation state | particle |
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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.. |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD![]() |
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 |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL |
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Output model | ![]() PDB-8fky: |