+Open data
-Basic information
Entry | Database: PDB / ID: 6lu8 | ||||||
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Title | Cryo-EM structure of a human pre-60S ribosomal subunit - state A | ||||||
Components |
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Keywords | RIBOSOME / 60S / pre-60S / pre-ribosome / human 60S / human pre-ribosome / NMD3 / human NMD3 | ||||||
Function / homology | Function and homology information positive regulation of protein localization to nucleolus / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding / dendrite extension / preribosome binding / lamin filament / positive regulation of RNA biosynthetic process / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation ...positive regulation of protein localization to nucleolus / negative regulation of RNA polymerase II regulatory region sequence-specific DNA binding / basal RNA polymerase II transcription machinery binding / negative regulation of collagen binding / dendrite extension / preribosome binding / lamin filament / positive regulation of RNA biosynthetic process / regulation of fatty acid biosynthetic process / regulation of megakaryocyte differentiation / miRNA-mediated post-transcriptional gene silencing / eukaryotic 80S initiation complex / miRNA-mediated gene silencing by inhibition of translation / 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 / GAIT complex / middle ear morphogenesis / regulation of glycolytic process / regulation of reactive oxygen species metabolic process / A band / alpha-beta T cell differentiation / cytoplasmic side of rough endoplasmic reticulum membrane / 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 / maturation of 5.8S rRNA / 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 / response to aldosterone / regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of cell-cell adhesion / homeostatic process / positive regulation of dendritic spine development / G1 to G0 transition / negative regulation of DNA replication / macrophage chemotaxis / lung morphogenesis / Protein hydroxylation / ribosomal large subunit binding / Peptide chain elongation / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / preribosome, large subunit precursor / Formation of a pool of free 40S subunits / blastocyst development / ubiquitin ligase inhibitor activity / Eukaryotic Translation Termination / 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 / Major pathway of rRNA processing in the nucleolus and cytosol / protein targeting / cellular response to interleukin-4 / protein-RNA complex assembly / cellular response to actinomycin D / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of ubiquitin-dependent protein catabolic process / ribosomal subunit export from nucleus / rough endoplasmic reticulum / MDM2/MDM4 family protein binding / negative regulation of protein ubiquitination / negative regulation of proteasomal ubiquitin-dependent protein catabolic process / maturation of LSU-rRNA / cytosolic ribosome / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / embryo implantation / translation initiation factor activity / bone development / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / ossification / ribosomal large subunit biogenesis / assembly of large subunit precursor of preribosome / negative regulation of cell migration / regulation of signal transduction by p53 class mediator / cytosolic ribosome assembly / innate immune response in mucosa / skeletal system development / positive regulation of translation / mRNA 3'-UTR binding / sensory perception of sound / response to insulin / cellular response to type II interferon / cellular response to gamma radiation / mRNA 5'-UTR binding / transcription coactivator binding / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / osteoblast differentiation / rRNA processing / cellular response to UV Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / 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, 1items
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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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6lu8.cif.gz | 3.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6lu8.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 6lu8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6lu8_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 6lu8_full_validation.pdf.gz | 1.7 MB | Display | |
Data in XML | 6lu8_validation.xml.gz | 293 KB | Display | |
Data in CIF | 6lu8_validation.cif.gz | 471.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lu/6lu8 ftp://data.pdbj.org/pub/pdb/validation_reports/lu/6lu8 | HTTPS FTP |
-Related structure data
Related structure data | 0978MC 0948C 0963C 0964C 6lqmC 6lsrC 6lssC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-Nucleolar GTP-binding protein ... , 2 types, 2 molecules 14
#1: Protein | Mass: 83796.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q13823 |
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#4: Protein | Mass: 74107.820 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BZE4 |
-RNA chain , 3 types, 3 molecules 258
#2: RNA chain | Mass: 1641892.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) |
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#5: RNA chain | Mass: 38691.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: NR_023363 |
#8: RNA chain | Mass: 50157.676 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: KY962518 |
-Protein , 6 types, 6 molecules 3679Rz
#3: Protein | Mass: 57682.145 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: HEK293FT / Plasmid: pLVX-ACGFP1-N1 / Cell line (production host): HEK293FT / Production host: Homo sapiens (human) / References: UniProt: Q96D46 |
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#6: Protein | Mass: 26620.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P56537 |
#7: Protein | Mass: 19666.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9UHA3 |
#9: Protein | Mass: 15230.225 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: O00488 |
#26: Protein | Mass: 23912.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q96EY4 |
#50: Protein | Mass: 15268.361 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: Q9BRT6 |
+60S ribosomal protein ... , 39 types, 39 molecules ABCDEFGHIKLMNOPQSUVWXYZabcdegh...
-Non-polymers , 2 types, 263 molecules
#51: Chemical | ChemComp-MG / #52: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction |
-Sample preparation
Component |
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Molecular weight | Experimental value: NO | ||||||||||||||||||||||||
Source (natural) |
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Source (recombinant) | Organism: Homo sapiens (human) / Cell: HEK293FT / Plasmid: pLVX-ACGFP1-N1 | ||||||||||||||||||||||||
Buffer solution | pH: 7.8 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Alignment procedure: COMA FREE |
Specimen holder | Cryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER |
Image recording | Electron dose: 64 e/Å2 / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 3.13 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 21489 / Symmetry type: POINT |