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Open data
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Basic information
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Title | Human pre-60S - State 3 | |||||||||
![]() | Human pre-60S - State 3 - Composite map | |||||||||
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![]() | Human / ribosome biogenesis / NLE1 / RIX1 complex / 5S RNP / RIBOSOME | |||||||||
Function / homology | ![]() positive regulation of protein localization to chromosome, telomeric region / basal RNA polymerase II transcription machinery binding / : / hematopoietic stem cell homeostasis / inner cell mass cell differentiation / dendrite extension / preribosome binding / regulation of Notch signaling pathway / lamin filament / regulation of fatty acid biosynthetic process ...positive regulation of protein localization to chromosome, telomeric region / basal RNA polymerase II transcription machinery binding / : / hematopoietic stem cell homeostasis / inner cell mass cell differentiation / dendrite extension / preribosome binding / regulation of Notch signaling pathway / lamin filament / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / positive regulation of protein sumoylation / miRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation / stem cell division / eukaryotic 80S initiation complex / negative regulation of protein neddylation / negative regulation of formation of translation preinitiation complex / regulation of G1 to G0 transition / axial mesoderm development / protein localization to nucleolus / 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 / protein-DNA complex disassembly / 90S preribosome assembly / positive regulation of DNA damage response, signal transduction by p53 class mediator / GAIT complex / A band / TORC2 complex binding / alpha-beta T cell differentiation / G1 to G0 transition / regulation of cyclin-dependent protein serine/threonine kinase activity / skeletal system morphogenesis / middle ear morphogenesis / regulation of glycolytic process / regulation of reactive oxygen species metabolic process / translation at presynapse / negative regulation of cell-cell adhesion / positive regulation of dendritic spine development / cytoplasmic side of rough endoplasmic reticulum membrane / mitotic metaphase chromosome alignment / maturation of 5.8S rRNA / negative regulation of ubiquitin protein ligase activity / stem cell population maintenance / homeostatic process / response to aldosterone / negative regulation of DNA replication / macrophage chemotaxis / positive regulation of telomere maintenance / lung morphogenesis / ribosomal large subunit binding / Protein hydroxylation / preribosome, large subunit precursor / Peptide chain elongation / nuclear-transcribed mRNA catabolic process / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / negative regulation of mitotic cell cycle / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / blastocyst development / cellular response to actinomycin D / negative regulation of ubiquitin-dependent protein catabolic process / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / protein localization to nucleus / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / somitogenesis / Major pathway of rRNA processing in the nucleolus and cytosol / ribosomal subunit export from nucleus / protein targeting / hematopoietic progenitor cell differentiation / 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) / protein-RNA complex assembly / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / maturation of LSU-rRNA / rough endoplasmic reticulum / Notch signaling pathway / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / MDM2/MDM4 family protein binding / cytosolic ribosome / translation initiation factor activity / negative regulation of protein ubiquitination / cellular response to interleukin-4 / ossification / innate immune response in mucosa / assembly of large subunit precursor of preribosome / DNA damage response, signal transduction by p53 class mediator / negative regulation of cell migration / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cytosolic ribosome assembly / ribosomal large subunit biogenesis / condensed nuclear chromosome / regulation of signal transduction by p53 class mediator / positive regulation of translation Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.04 Å | |||||||||
![]() | Thoms M / Denk T / Beckmann R | |||||||||
Funding support | European Union, 1 items
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![]() | ![]() Title: Highly conserved ribosome biogenesis pathways between human and yeast revealed by the MDN1-NLE1 interaction and NLE1 containing pre-60S subunits. Authors: Federica Fiorentino / Matthias Thoms / Klemens Wild / Timo Denk / Jingdong Cheng / Jakub Zeman / Irmgard Sinning / Ed Hurt / Roland Beckmann / ![]() ![]() Abstract: The assembly of ribosomal subunits, primarily occurring in the nucleolar and nuclear compartments, is a highly complex process crucial for cellular function. This study reveals the conservation of ...The assembly of ribosomal subunits, primarily occurring in the nucleolar and nuclear compartments, is a highly complex process crucial for cellular function. This study reveals the conservation of ribosome biogenesis between yeast and humans, illustrated by the structural similarities of ribosomal subunit intermediates. By using X-ray crystallography and cryo-EM, the interaction between the human AAA+ ATPase MDN1 and the 60S assembly factor NLE1 is compared with the yeast homologs Rea1 and Rsa4. The MDN1-MIDAS and NLE1-Ubl complex structure at 2.3 Å resolution mirrors the highly conserved interaction patterns observed in yeast. Moreover, human pre-60S intermediates bound to the dominant negative NLE1-E85A mutant revealed at 2.8 Å resolution an architecture that largely matched the equivalent yeast structures. Conformation of rRNA, assembly factors and their interaction networks are highly conserved. Additionally, novel human pre-60S intermediates with a non-rotated 5S RNP and processed ITS2/foot structure but incomplete intersubunit surface were identified to be similar to counterparts observed in yeast. These findings confirm that the MDN1-NLE1-driven transition phase of the 60S assembly is essentially identical, supporting the idea that ribosome biogenesis is a highly conserved process across eukaryotic cells, employing an evolutionary preservation of ribosomal assembly mechanisms. #1: ![]() Title: 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 | ![]() | 18.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 68.6 KB 68.6 KB | Display Display | ![]() |
Images | ![]() | 86.2 KB | ||
Filedesc metadata | ![]() | 17 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Validation report
Summary document | ![]() | 400.6 KB | Display | ![]() |
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Full document | ![]() | 400.2 KB | Display | |
Data in XML | ![]() | 7.7 KB | Display | |
Data in CIF | ![]() | 9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 9qiwMC ![]() 8ql1C ![]() 8rl2C 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
File | ![]() | ||||||||||||||||||||||||||||||||||||
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Annotation | Human pre-60S - State 3 - 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 #13: 60S ribosomal protein L8
+Macromolecule #14: 60S ribosomal protein L3
+Macromolecule #15: 60S ribosomal protein L4
+Macromolecule #16: 60S ribosomal protein L5
+Macromolecule #17: Large ribosomal subunit protein eL6
+Macromolecule #18: Large ribosomal subunit protein uL30
+Macromolecule #19: 60S ribosomal protein L7a
+Macromolecule #20: 60S ribosomal protein L9
+Macromolecule #21: 60S ribosomal protein L11
+Macromolecule #22: 60S ribosomal protein L13
+Macromolecule #23: 60S ribosomal protein L14
+Macromolecule #24: 60S ribosomal protein L15
+Macromolecule #25: 60S ribosomal protein L13a
+Macromolecule #26: 60S ribosomal protein L17
+Macromolecule #27: 60S ribosomal protein L18
+Macromolecule #28: 60S ribosomal protein L19
+Macromolecule #29: 60S ribosomal protein L18a
+Macromolecule #30: 60S ribosomal protein L21
+Macromolecule #31: 60S ribosomal protein L22
+Macromolecule #32: 60S ribosomal protein L23
+Macromolecule #33: 60S ribosomal protein L23a
+Macromolecule #34: 60S ribosomal protein L26
+Macromolecule #35: 60S ribosomal protein L27
+Macromolecule #36: 60S ribosomal protein L27a
+Macromolecule #37: 60S ribosomal protein L30
+Macromolecule #38: 60S ribosomal protein L31
+Macromolecule #39: 60S ribosomal protein L32
+Macromolecule #40: 60S ribosomal protein L35a
+Macromolecule #41: 60S ribosomal protein L34
+Macromolecule #42: 60S ribosomal protein L35
+Macromolecule #43: 60S ribosomal protein L36
+Macromolecule #44: Large ribosomal subunit protein eL37
+Macromolecule #45: 60S ribosomal protein L38
+Macromolecule #46: 60S ribosomal protein L39
+Macromolecule #47: 60S ribosomal protein L37a
+Macromolecule #48: 60S ribosomal protein L28
+Macromolecule #49: Large ribosomal subunit protein uL11
+Macromolecule #12: 5S rRNA
+Macromolecule #50: 28S rRNA
+Macromolecule #51: 5.8S rRNA
+Macromolecule #52: GUANOSINE-5'-TRIPHOSPHATE
+Macromolecule #53: GUANOSINE-5'-DIPHOSPHATE
+Macromolecule #54: MAGNESIUM ION
+Macromolecule #55: ZINC 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: 7.5 |
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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: ![]() |
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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Image processing
Startup model | Type of model: NONE |
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Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.04 Å / Resolution method: FSC 0.143 CUT-OFF Details: Resolution given for Consensus refinement - this is a composite map Number images used: 33891 |
Initial angle assignment | Type: MAXIMUM LIKELIHOOD |
Final angle assignment | Type: MAXIMUM LIKELIHOOD |