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- EMDB-29258: Human nucleolar pre-60S ribosomal subunit (State D1) - 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 D1) - Composite map | |||||||||
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![]() | Pre-60S ribosomal subunit / Assembly intermediate / Ribosome / Nucleoprotein complex | |||||||||
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 / dendrite extension / rRNA (uridine-2'-O-)-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 / dendrite extension / rRNA (uridine-2'-O-)-methyltransferase activity / rRNA (guanine) methyltransferase activity / rRNA (cytosine-C5-)-methyltransferase activity / preribosome binding / regulation of cellular senescence / lamin filament / regulation of fatty acid biosynthetic process / RNA methylation / regulation of megakaryocyte differentiation / positive regulation of protein sumoylation / miRNA-mediated post-transcriptional gene silencing / stem cell division / PeBoW complex / miRNA-mediated gene silencing by inhibition of translation / positive regulation of telomere maintenance / ribosomal protein import into nucleus / negative regulation of formation of translation preinitiation complex / rRNA base methylation / rRNA primary transcript binding / blastocyst formation / protein localization to nucleolus / TORC2 complex binding / negative regulation of B cell apoptotic process / maturation of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / GAIT complex / rRNA methylation / regulation of reactive oxygen species metabolic process / rRNA modification in the nucleus and cytosol / regulation of glycolytic process / A band / regulation of G1 to G0 transition / 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 DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator / cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / negative regulation of ubiquitin protein ligase activity / preribosome, small subunit precursor / mitotic metaphase chromosome alignment / stem cell population maintenance / regulation of cyclin-dependent protein serine/threonine kinase activity / rRNA metabolic process / G1 to G0 transition / negative regulation of cell-cell adhesion / homeostatic process / positive regulation of dendritic spine development / maturation of 5.8S rRNA / negative regulation of DNA replication / macrophage chemotaxis / lung morphogenesis / fat cell differentiation / Protein hydroxylation / ribosomal large subunit binding / Peptide chain elongation / Selenocysteine synthesis / rRNA transcription / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / nuclear-transcribed mRNA catabolic process / Eukaryotic Translation Termination / blastocyst development / preribosome, large subunit precursor / ubiquitin ligase inhibitor activity / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / DNA replication initiation / L13a-mediated translational silencing of Ceruloplasmin expression / Major pathway of rRNA processing in the nucleolus and cytosol / estrogen receptor signaling pathway / nucleosome binding / cellular response to interleukin-4 / hematopoietic progenitor cell differentiation / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of ubiquitin-dependent protein catabolic process / ribosomal subunit export from nucleus / cellular response to actinomycin D / RNA processing / ribonucleoprotein complex binding / negative regulation of intrinsic apoptotic signaling pathway / cytosolic ribosome / 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) / rough endoplasmic reticulum / MDM2/MDM4 family protein binding / negative regulation of protein ubiquitination / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / translation initiation factor activity / maturation of LSU-rRNA / transcription initiation-coupled chromatin remodeling Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.47 Å | |||||||||
![]() | 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 | ![]() | 207.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 91.5 KB 91.5 KB | Display Display | ![]() |
FSC (resolution estimation) | ![]() | 15.8 KB | Display | ![]() |
Images | ![]() | 149.5 KB | ||
Masks | ![]() | 421.9 MB | ![]() | |
Others | ![]() ![]() | 391.1 MB 391.1 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 8fkvMC ![]() 8fkpC ![]() 8fkqC ![]() 8fkrC ![]() 8fksC ![]() 8fktC ![]() 8fkuC ![]() 8fkwC ![]() 8fkxC ![]() 8fkyC ![]() 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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Projections & Slices |
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Density Histograms |
-Half map: #1
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Projections & Slices |
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Density Histograms |
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Sample components
+Entire : Human nucleolar pre-60S ribosomal subunit (State D1)
+Supramolecule #1: Human nucleolar pre-60S ribosomal subunit (State D1)
+Macromolecule #1: 60S ribosomal protein L12
+Macromolecule #2: 60S ribosomal protein L10a
+Macromolecule #6: 60S ribosomal protein L13
+Macromolecule #7: 60S ribosomal protein L13a
+Macromolecule #8: 60S ribosomal protein L14
+Macromolecule #9: 60S ribosomal protein L15
+Macromolecule #10: 60S ribosomal protein L17
+Macromolecule #11: 60S ribosomal protein L18
+Macromolecule #12: 60S ribosomal protein L18a
+Macromolecule #13: 60S ribosomal protein L21
+Macromolecule #14: 60S ribosomal protein L23
+Macromolecule #15: 60S ribosomal protein L23a
+Macromolecule #16: 60S ribosomal protein L26
+Macromolecule #17: 60S ribosomal protein L27a
+Macromolecule #18: 60S ribosomal protein L3
+Macromolecule #19: 60S ribosomal protein L31
+Macromolecule #20: 60S ribosomal protein L32
+Macromolecule #21: 60S ribosomal protein L35
+Macromolecule #22: 60S ribosomal protein L35a
+Macromolecule #23: 60S ribosomal protein L36
+Macromolecule #24: 60S ribosomal protein L37
+Macromolecule #25: Nucleolar complex protein 2 homolog
+Macromolecule #26: Guanine nucleotide-binding protein-like 3
+Macromolecule #27: Ribosome biogenesis protein NSA2 homolog
+Macromolecule #28: 60S ribosome subunit biogenesis protein NIP7 homolog
+Macromolecule #29: ATP-dependent RNA helicase DDX54
+Macromolecule #30: Protein LLP homolog
+Macromolecule #31: Protein MAK16 homolog
+Macromolecule #32: Ribosomal RNA processing protein 1 homolog A
+Macromolecule #33: WD repeat-containing protein 74
+Macromolecule #34: Ribosome production factor 1
+Macromolecule #35: 60S ribosomal protein L4
+Macromolecule #36: 60S ribosomal protein L6
+Macromolecule #37: 60S ribosomal protein L7
+Macromolecule #38: 60S ribosomal protein L7a
+Macromolecule #39: 60S ribosomal protein L9
+Macromolecule #40: MKI67 FHA domain-interacting nucleolar phosphoprotein
+Macromolecule #41: 60S ribosomal protein L7-like 1
+Macromolecule #42: pre-rRNA 2'-O-ribose RNA methyltransferase FTSJ3
+Macromolecule #43: Eukaryotic translation initiation factor 6
+Macromolecule #44: Ribosomal L1 domain-containing protein 1
+Macromolecule #45: Pescadillo homolog
+Macromolecule #46: Probable rRNA-processing protein EBP2
+Macromolecule #47: Ribosome biogenesis protein BRX1 homolog
+Macromolecule #48: mRNA turnover protein 4 homolog
+Macromolecule #49: GTP-binding protein 4
+Macromolecule #50: Ribosome biogenesis protein BOP1
+Macromolecule #51: Ribosome biogenesis regulatory protein homolog
+Macromolecule #52: Nucleolar complex protein 3 homolog
+Macromolecule #53: Probable ribosome biogenesis protein RLP24
+Macromolecule #54: ATP-dependent RNA helicase DDX18
+Macromolecule #55: Probable 28S rRNA (cytosine(4447)-C(5))-methyltransferase
+Macromolecule #56: Nucleolar protein 16
+Macromolecule #3: 5.8S rRNA
+Macromolecule #4: ITS2 rRNA
+Macromolecule #5: 28S rRNA
+Macromolecule #57: MAGNESIUM ION
+Macromolecule #58: ZINC ION
+Macromolecule #59: ADENOSINE-5'-DIPHOSPHATE
+Macromolecule #60: IRON/SULFUR CLUSTER
+Macromolecule #61: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #62: POTASSIUM ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
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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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 |
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: 0.5 µm / Nominal magnification: 64000 |
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-8fkv: |