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Yorodumi- PDB-6g4w: Cryo-EM structure of a late human pre-40S ribosomal subunit - State A -
+Open data
-Basic information
Entry | Database: PDB / ID: 6g4w | |||||||||||||||
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Title | Cryo-EM structure of a late human pre-40S ribosomal subunit - State A | |||||||||||||||
Components |
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Keywords | RIBOSOME / 40S / pre-40S / ribosome biogenesis | |||||||||||||||
Function / homology | Function and homology information peptidyl-glutamine methylation / regulation of protein localization to nucleolus / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / rRNA (guanine) methyltransferase activity / tRNA modification in the nucleus and cytosol / Methylation / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / trophectodermal cell differentiation / protein methyltransferase activity ...peptidyl-glutamine methylation / regulation of protein localization to nucleolus / rRNA (guanine-N7)-methylation / tRNA methyltransferase activator activity / rRNA (guanine) methyltransferase activity / tRNA modification in the nucleus and cytosol / Methylation / endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / trophectodermal cell differentiation / protein methyltransferase activity / tRNA methylation / positive regulation of rRNA processing / positive regulation of respiratory burst involved in inflammatory response / nucleolus organization / negative regulation of RNA splicing / rRNA methylation / neural crest cell differentiation / rRNA modification in the nucleus and cytosol / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / U3 snoRNA binding / negative regulation of ubiquitin protein ligase activity / Ribosomal scanning and start codon recognition / preribosome, small subunit precursor / Translation initiation complex formation / snoRNA binding / mammalian oogenesis stage / activation-induced cell death of T cells / fibroblast growth factor binding / Protein hydroxylation / monocyte chemotaxis / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / ubiquitin ligase inhibitor activity / Response of EIF2AK4 (GCN2) to amino acid deficiency / SRP-dependent cotranslational protein targeting to membrane / negative regulation of respiratory burst involved in inflammatory response / Viral mRNA Translation / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / TOR signaling / L13a-mediated translational silencing of Ceruloplasmin expression / T cell proliferation involved in immune response / Major pathway of rRNA processing in the nucleolus and cytosol / regulation of translational fidelity / erythrocyte development / Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC) / negative regulation of ubiquitin-dependent protein catabolic process / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / translation regulator activity / Nuclear events stimulated by ALK signaling in cancer / ribosomal small subunit export from nucleus / positive regulation of cell cycle / stress granule assembly / Mitotic Prometaphase / cytosolic ribosome / EML4 and NUDC in mitotic spindle formation / rough endoplasmic reticulum / gastrulation / MDM2/MDM4 family protein binding / translation initiation factor binding / Resolution of Sister Chromatid Cohesion / liver regeneration / transcription initiation-coupled chromatin remodeling / Transferases; Transferring one-carbon groups; Methyltransferases / erythrocyte differentiation / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / innate immune response in mucosa / stem cell proliferation / cellular response to leukemia inhibitory factor / methyltransferase activity / maturation of SSU-rRNA / neural tube closure / placenta development / small-subunit processome / mRNA 3'-UTR binding / positive regulation of translation / translational initiation / RHO GTPases Activate Formins / maintenance of translational fidelity / response to virus / G1/S transition of mitotic cell cycle / mRNA 5'-UTR binding / Regulation of expression of SLITs and ROBOs / cytoplasmic ribonucleoprotein granule / osteoblast differentiation / rRNA processing / Separation of Sister Chromatids / chromosome / antimicrobial humoral immune response mediated by antimicrobial peptide / glucose homeostasis / ribosome biogenesis / apical part of cell Similarity search - Function | |||||||||||||||
Biological species | Homo sapiens (human) | |||||||||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 4.5 Å | |||||||||||||||
Authors | Ameismeier, M. / Cheng, J. / Berninghausen, O. / Beckmann, R. | |||||||||||||||
Funding support | Germany, 4items
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Citation | Journal: Nature / Year: 2018 Title: Visualizing late states of human 40S ribosomal subunit maturation. Authors: Michael Ameismeier / Jingdong Cheng / Otto Berninghausen / Roland Beckmann / Abstract: The formation of eukaryotic ribosomal subunits extends from the nucleolus to the cytoplasm and entails hundreds of assembly factors. Despite differences in the pathways of ribosome formation, high- ...The formation of eukaryotic ribosomal subunits extends from the nucleolus to the cytoplasm and entails hundreds of assembly factors. Despite differences in the pathways of ribosome formation, high-resolution structural information has been available only from fungi. Here we present cryo-electron microscopy structures of late-stage human 40S assembly intermediates, representing one state reconstituted in vitro and five native states that range from nuclear to late cytoplasmic. The earliest particles reveal the position of the biogenesis factor RRP12 and distinct immature rRNA conformations that accompany the formation of the 40S subunit head. Molecular models of the late-acting assembly factors TSR1, RIOK1, RIOK2, ENP1, LTV1, PNO1 and NOB1 provide mechanistic details that underlie their contribution to a sequential 40S subunit assembly. The NOB1 architecture displays an inactive nuclease conformation that requires rearrangement of the PNO1-bound 3' rRNA, thereby coordinating the final rRNA folding steps with site 3 cleavage. | |||||||||||||||
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 | 6g4w.cif.gz | 1.2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6g4w.ent.gz | 848.9 KB | Display | PDB format |
PDBx/mmJSON format | 6g4w.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6g4w_validation.pdf.gz | 964.8 KB | Display | wwPDB validaton report |
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Full document | 6g4w_full_validation.pdf.gz | 1015.5 KB | Display | |
Data in XML | 6g4w_validation.xml.gz | 128.4 KB | Display | |
Data in CIF | 6g4w_validation.cif.gz | 232.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g4/6g4w ftp://data.pdbj.org/pub/pdb/validation_reports/g4/6g4w | HTTPS FTP |
-Related structure data
Related structure data | 4349MC 4337C 4348C 4350C 4351C 4352C 4353C 6g18C 6g4sC 6g51C 6g53C 6g5hC 6g5iC 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
-RNA chain , 1 types, 1 molecules 2
#1: RNA chain | Mass: 607057.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: GenBank: 151415227 |
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+40S ribosomal protein ... , 22 types, 22 molecules RbBcEeFHGZYXWTSQPONLJI
-Protein , 6 types, 6 molecules xwusrq
#13: Protein | Mass: 27970.355 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: Q9NRX1 |
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#15: Protein | Mass: 49673.258 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: Q13895 |
#17: Protein | Mass: 91951.188 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: Q2NL82 |
#28: Protein | Mass: 68101.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 |
#29: Protein | Mass: 14215.359 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: Q9UI30 |
#30: Protein | Mass: 31925.428 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 References: UniProt: O43709, Transferases; Transferring one-carbon groups; Methyltransferases |
-Protein/peptide , 2 types, 2 molecules tk
#18: Protein/peptide | Mass: 2054.328 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 / References: UniProt: Q96GA3*PLUS |
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#31: Protein/peptide | Mass: 1368.494 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK293 |
-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 | Name: Cryo-EM structure of a late human pre-40S ribosomal subunit - State A Type: RIBOSOME / Entity ID: all / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.6 |
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 |
Image recording | Electron dose: 2.5 e/Å2 / Film or detector model: FEI FALCON II (4k x 4k) |
-Processing
CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION |
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3D reconstruction | Resolution: 4.5 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 52414 / Symmetry type: POINT |