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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0948 | |||||||||
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Title | Cryo-EM structure of a pre-60S ribosomal subunit - state C | |||||||||
![]() | Cryo-EM structure of a human pre-60S ribosomal subunit - state C | |||||||||
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Function / homology | ![]() 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 / ribosomal protein import into nucleus / negative regulation of formation of translation preinitiation complex / 90S preribosome assembly / TORC2 complex binding / positive regulation of kinase activity / GAIT complex / middle ear morphogenesis / regulation of reactive oxygen species metabolic process / regulation of glycolytic process / A band / cytoplasmic side of rough endoplasmic reticulum membrane / alpha-beta T cell differentiation / regulation of G1 to G0 transition / exit from mitosis / 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 / optic nerve development / negative regulation of ubiquitin protein ligase activity / intrinsic apoptotic signaling pathway in response to oxidative stress / response to aldosterone / retinal ganglion cell axon guidance / G1 to G0 transition / homeostatic process / maturation of 5.8S rRNA / macrophage chemotaxis / lung morphogenesis / male meiosis I / Protein hydroxylation / ribosomal large subunit binding / Peptide chain elongation / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / 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 / protein localization to nucleus / ribosomal large subunit export from nucleus / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / L13a-mediated translational silencing of Ceruloplasmin expression / protein-RNA complex assembly / Major pathway of rRNA processing in the nucleolus and cytosol / protein targeting / cellular response to interleukin-4 / 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 / cytosolic ribosome / rough endoplasmic reticulum / Maturation of protein E / Maturation of protein E / ER Quality Control Compartment (ERQC) / MDM2/MDM4 family protein binding / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / Myoclonic epilepsy of Lafora / FLT3 signaling by CBL mutants / Prevention of phagosomal-lysosomal fusion / IRAK2 mediated activation of TAK1 complex / Alpha-protein kinase 1 signaling pathway / Glycogen synthesis / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / IRAK1 recruits IKK complex / IRAK1 recruits IKK complex upon TLR7/8 or 9 stimulation / Membrane binding and targetting of GAG proteins / Regulation of TBK1, IKKε-mediated activation of IRF3, IRF7 upon TLR3 ligation / Endosomal Sorting Complex Required For Transport (ESCRT) / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / PTK6 Regulates RTKs and Their Effectors AKT1 and DOK1 / Negative regulation of FLT3 / Constitutive Signaling by NOTCH1 HD Domain Mutants / Regulation of FZD by ubiquitination / TICAM1,TRAF6-dependent induction of TAK1 complex / TICAM1-dependent activation of IRF3/IRF7 / NOTCH2 Activation and Transmission of Signal to the Nucleus / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / APC/C:Cdc20 mediated degradation of Cyclin B / p75NTR recruits signalling complexes / Downregulation of ERBB4 signaling / translation initiation factor activity / embryo implantation Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.09 Å | |||||||||
![]() | Liang X / Zuo M / Zhang Y / Li N / Ma C / Dong M / Gao N | |||||||||
Funding support | ![]()
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![]() | ![]() 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 |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 39.5 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 65.9 KB 65.9 KB | Display Display | ![]() |
Images | ![]() | 84.9 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6lqmMC ![]() 0963C ![]() 0964C ![]() 0978C ![]() 6lsrC ![]() 6lssC ![]() 6lu8C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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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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Annotation | Cryo-EM structure of a human pre-60S ribosomal subunit - state C | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
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Sample components
+Entire : Cryo-EM structure of a human pre-60S ribosomal subunit state - C
+Supramolecule #1: Cryo-EM structure of a human pre-60S ribosomal subunit state - C
+Supramolecule #2: Cryo-EM structure of a human pre-60S ribosomal subunit state - C
+Supramolecule #3: 60S ribosomal export protein NMD3
+Macromolecule #1: Zinc finger protein 622
+Macromolecule #3: 60S ribosomal export protein NMD3
+Macromolecule #5: Eukaryotic translation initiation factor 6
+Macromolecule #7: 60S ribosomal protein L10a
+Macromolecule #8: 60S ribosomal protein L3
+Macromolecule #9: 60S ribosomal protein L29
+Macromolecule #10: 60S ribosomal protein L4
+Macromolecule #11: 60S ribosomal protein L30
+Macromolecule #12: 60S ribosomal protein L34
+Macromolecule #13: 60S ribosomal protein L7a
+Macromolecule #14: 60S ribosomal protein L35
+Macromolecule #15: 60S ribosomal protein L9
+Macromolecule #16: 60S ribosomal protein L10-like
+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: Ubiquitin-60S ribosomal protein L40
+Macromolecule #25: 60S ribosomal protein L14
+Macromolecule #26: 60S ribosomal protein L31
+Macromolecule #27: 60S ribosomal protein L15
+Macromolecule #28: 60S ribosomal protein L13a
+Macromolecule #29: 60S ribosomal protein L36a
+Macromolecule #30: 60S ribosomal protein L37a
+Macromolecule #31: 60S ribosomal protein L17
+Macromolecule #32: 60S ribosomal protein L18
+Macromolecule #33: 60S ribosomal protein L19
+Macromolecule #34: 60S ribosomal protein L18a
+Macromolecule #35: 60S ribosomal protein L21
+Macromolecule #36: 60S ribosomal protein L22
+Macromolecule #37: 60S ribosomal protein L23
+Macromolecule #38: 60S ribosomal protein L24
+Macromolecule #39: 60S ribosomal protein L23a
+Macromolecule #40: 60S ribosomal protein L26
+Macromolecule #41: 60S ribosomal protein L27
+Macromolecule #42: 60S ribosomal protein L28
+Macromolecule #43: 60S ribosomal protein L8
+Macromolecule #44: 60S ribosomal protein L5
+Macromolecule #45: 60S ribosomal protein L32
+Macromolecule #46: 60S ribosomal protein L35a
+Macromolecule #47: 60S ribosomal protein L6
+Macromolecule #48: 60S ribosomal protein L7
+Macromolecule #2: 28S rRNA
+Macromolecule #4: 5S rRNA
+Macromolecule #6: 5.8S rRNA
+Macromolecule #49: MAGNESIUM 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: 7.8 |
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Vitrification | Cryogen name: ETHANE |
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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: ![]() |
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 |
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Image processing
Final reconstruction | Applied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 3.09 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 21707 |
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Initial angle assignment | Type: NOT APPLICABLE |
Final angle assignment | Type: PROJECTION MATCHING |