+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-0963 | |||||||||
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Title | Cryo-EM structure of a pre-60S ribosomal subunit - state B | |||||||||
Map data | ||||||||||
Sample |
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Function / homology | Function and homology information positive regulation of protein localization to nucleolus / preribosome binding / lamin filament / regulation of fatty acid biosynthetic process / positive regulation of RNA biosynthetic process / regulation of megakaryocyte differentiation / miRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation / eukaryotic 80S initiation complex / negative regulation of protein neddylation ...positive regulation of protein localization to nucleolus / preribosome binding / lamin filament / regulation of fatty acid biosynthetic process / positive regulation of RNA biosynthetic process / regulation of megakaryocyte differentiation / miRNA-mediated post-transcriptional gene silencing / miRNA-mediated gene silencing by inhibition of translation / eukaryotic 80S initiation complex / negative regulation of protein neddylation / translation at presynapse / axial mesoderm development / negative regulation of formation of translation preinitiation complex / ribosomal protein import into nucleus / 90S preribosome assembly / TORC2 complex binding / positive regulation of kinase activity / nuclear export / GAIT complex / middle ear morphogenesis / cytoplasmic side of rough endoplasmic reticulum membrane / regulation of reactive oxygen species metabolic process / regulation of glycolytic process / A band / regulation of G1 to G0 transition / exit from mitosis / alpha-beta T cell differentiation / 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 / negative regulation of ubiquitin protein ligase activity / optic nerve development / intrinsic apoptotic signaling pathway in response to oxidative stress / response to aldosterone / retinal ganglion cell axon guidance / G1 to G0 transition / homeostatic process / lung morphogenesis / maturation of 5.8S rRNA / Protein hydroxylation / macrophage chemotaxis / Peptide chain elongation / ribosomal large subunit binding / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / Formation of a pool of free 40S subunits / Hydrolases; Acting on acid anhydrides; In phosphorus-containing anhydrides / Eukaryotic Translation Termination / blastocyst development / preribosome, large subunit precursor / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / Viral mRNA Translation / protein localization to nucleus / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / L13a-mediated translational silencing of Ceruloplasmin expression / GTP hydrolysis and joining of the 60S ribosomal subunit / ribosomal large subunit export from nucleus / Major pathway of rRNA processing in the nucleolus and cytosol / protein-RNA complex assembly / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / protein targeting / cellular response to interleukin-4 / cellular response to actinomycin D / ribosomal subunit export from nucleus / cytosolic ribosome / Cajal body / rough endoplasmic reticulum / MDM2/MDM4 family protein binding / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / translation initiation factor activity / embryo implantation / negative regulation of ubiquitin-dependent protein catabolic process / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ossification / assembly of large subunit precursor of preribosome / maturation of LSU-rRNA / innate immune response in mucosa / regulation of signal transduction by p53 class mediator / cytosolic ribosome assembly / ribosomal large subunit biogenesis / skeletal system development / mRNA 3'-UTR binding / positive regulation of translation / positive regulation of cell differentiation / positive regulation of JNK cascade / sensory perception of sound / response to insulin / bone development / ribosomal large subunit assembly / cellular response to gamma radiation / mRNA 5'-UTR binding / Regulation of expression of SLITs and ROBOs / transcription coactivator binding / cytoplasmic ribonucleoprotein granule / cellular response to type II interferon / rRNA processing Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) / Human (human) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.13 Å | |||||||||
Authors | Liang X / Zuo M / Zhang Y / Li N / Ma C / Dong M / Gao N | |||||||||
Funding support | China, 1 items
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Citation | Journal: Nat Commun / Year: 2020 Title: Structural snapshots of human pre-60S ribosomal particles before and after nuclear export. Authors: Xiaomeng Liang / Mei-Qing Zuo / Yunyang Zhang / Ningning Li / Chengying Ma / Meng-Qiu Dong / Ning Gao / Abstract: Ribosome biogenesis is an elaborate and energetically expensive program that involve two hundred protein factors in eukaryotes. Nuclear export of pre-ribosomal particles is one central step which ...Ribosome biogenesis is an elaborate and energetically expensive program that involve two hundred protein factors in eukaryotes. Nuclear export of pre-ribosomal particles is one central step which also serves as an internal structural checkpoint to ensure the proper completion of nuclear assembly events. Here we present four structures of human pre-60S particles isolated through a nuclear export factor NMD3, representing assembly stages immediately before and after nuclear export. These structures reveal locations of a dozen of human factors, including an uncharacterized factor TMA16 localized between the 5S RNA and the P0 stalk. Comparison of these structures shows a progressive maturation for the functional regions, such as peptidyl transferase centre and peptide exit tunnel, and illustrate a sequence of factor-assisted rRNA maturation events. These data facilitate our understanding of the global conservation of ribosome assembly in eukaryotes and species-specific features of human assembly factors. | |||||||||
History |
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-Structure visualization
Movie |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_0963.map.gz | 37.6 MB | EMDB map data format | |
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Header (meta data) | emd-0963-v30.xml emd-0963.xml | 68.8 KB 68.8 KB | Display Display | EMDB header |
Images | emd_0963.png | 88.2 KB | ||
Others | emd_0963_additional.map.gz | 33 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-0963 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-0963 | HTTPS FTP |
-Validation report
Summary document | emd_0963_validation.pdf.gz | 375.2 KB | Display | EMDB validaton report |
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Full document | emd_0963_full_validation.pdf.gz | 374.7 KB | Display | |
Data in XML | emd_0963_validation.xml.gz | 7.7 KB | Display | |
Data in CIF | emd_0963_validation.cif.gz | 8.8 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0963 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-0963 | HTTPS FTP |
-Related structure data
Related structure data | 6lsrMC 0948C 0964C 0978C 6lqmC 6lssC 6lu8C M: atomic model generated by this map C: citing same article (ref.) |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_0963.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: 1.058 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: #1
File | emd_0963_additional.map | ||||||||||||
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Projections & Slices |
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Density Histograms |
-Sample components
+Entire : Cryo-EM structure of a human pre-60S ribosomal subunit state - B
+Supramolecule #1: Cryo-EM structure of a human pre-60S ribosomal subunit state - B
+Supramolecule #2: Cryo-EM structure of a human pre-60S ribosomal subunit state - B
+Supramolecule #3: 60S ribosomal export protein NMD3
+Macromolecule #1: Zinc finger protein 622
+Macromolecule #2: Large subunit GTPase 1 homolog
+Macromolecule #4: 60S ribosomal export protein NMD3
+Macromolecule #6: Eukaryotic translation initiation factor 6
+Macromolecule #8: 60S ribosomal protein L10a
+Macromolecule #9: 60S ribosomal protein L3
+Macromolecule #10: 60S ribosomal protein L29
+Macromolecule #11: 60S ribosomal protein L4
+Macromolecule #12: 60S ribosomal protein L30
+Macromolecule #13: 60S ribosomal protein L34
+Macromolecule #14: 60S ribosomal protein L7a
+Macromolecule #15: 60S ribosomal protein L35
+Macromolecule #16: 60S ribosomal protein L9
+Macromolecule #17: 60S ribosomal protein L36
+Macromolecule #18: 60S ribosomal protein L27a
+Macromolecule #19: 60S ribosomal protein L37
+Macromolecule #20: 60S ribosomal protein L11
+Macromolecule #21: 60S ribosomal protein L38
+Macromolecule #22: 60S ribosomal protein L39
+Macromolecule #23: 60S ribosomal protein L13
+Macromolecule #24: 60S ribosomal protein L14
+Macromolecule #25: 60S ribosomal protein L31
+Macromolecule #26: 60S ribosomal protein L15
+Macromolecule #27: 60S ribosomal protein L13a
+Macromolecule #28: 60S ribosomal protein L36a
+Macromolecule #29: 60S ribosomal protein L37a
+Macromolecule #30: 60S ribosomal protein L17
+Macromolecule #31: 60S ribosomal protein L18
+Macromolecule #32: 60S ribosomal protein L19
+Macromolecule #33: 60S ribosomal protein L18a
+Macromolecule #34: 60S ribosomal protein L21
+Macromolecule #35: 60S ribosomal protein L22
+Macromolecule #36: 60S ribosomal protein L23
+Macromolecule #37: 60S ribosomal protein L24
+Macromolecule #38: 60S ribosomal protein L23a
+Macromolecule #39: 60S ribosomal protein L26
+Macromolecule #40: 60S ribosomal protein L27
+Macromolecule #41: 60S ribosomal protein L28
+Macromolecule #42: 60S ribosomal protein L8
+Macromolecule #43: 60S ribosomal protein L5
+Macromolecule #44: 60S ribosomal protein L32
+Macromolecule #45: 60S ribosomal protein L35a
+Macromolecule #46: 60S ribosomal protein L6
+Macromolecule #47: 60S ribosomal protein L7
+Macromolecule #48: Proliferation-associated protein 2G4
+Macromolecule #3: 28S rRNA
+Macromolecule #5: 5S rRNA
+Macromolecule #7: 5.8S rRNA
+Macromolecule #49: MAGNESIUM ION
+Macromolecule #50: water
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Buffer | pH: 7.8 |
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Vitrification | Cryogen name: ETHANE |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 64.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Resolution.type: BY AUTHOR / Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 18819 |
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Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: PROJECTION MATCHING |