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Yorodumi- PDB-6yal: Mammalian 48S late-stage initiation complex with beta-globin mRNA -
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-Basic information
Entry | Database: PDB / ID: 6yal | |||||||||
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Title | Mammalian 48S late-stage initiation complex with beta-globin mRNA | |||||||||
Components |
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Keywords | TRANSLATION / initiation complex / 48S / eIF1A / eIF3 / ABCE1 / rabbit | |||||||||
Function / homology | Function and homology information eukaryotic translation initiation factor 2 complex / ribosomal subunit / eukaryotic 48S preinitiation complex / laminin receptor activity / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / ribosomal small subunit binding ...eukaryotic translation initiation factor 2 complex / ribosomal subunit / eukaryotic 48S preinitiation complex / laminin receptor activity / mammalian oogenesis stage / activation-induced cell death of T cells / positive regulation of signal transduction by p53 class mediator / ubiquitin ligase inhibitor activity / phagocytic cup / ribosomal small subunit binding / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / TOR signaling / T cell proliferation involved in immune response / regulation of translational fidelity / ribosomal small subunit export from nucleus / erythrocyte development / translation regulator activity / ribosomal subunit export from nucleus / cytosolic ribosome / translational termination / laminin binding / rough endoplasmic reticulum / 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) / gastrulation / MDM2/MDM4 family protein binding / translational initiation / translation initiation factor activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / rescue of stalled ribosome / maturation of LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / 90S preribosome / maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / cellular response to leukemia inhibitory factor / maturation of SSU-rRNA / small-subunit processome / positive regulation of apoptotic signaling pathway / protein kinase C binding / positive regulation of protein-containing complex assembly / placenta development / cytoplasmic ribonucleoprotein granule / cytoplasmic stress granule / modification-dependent protein catabolic process / spindle / G1/S transition of mitotic cell cycle / rRNA processing / protein tag activity / rhythmic process / positive regulation of canonical Wnt signaling pathway / ribosome binding / glucose homeostasis / virus receptor activity / regulation of translation / ribosomal small subunit biogenesis / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / cell body / T cell differentiation in thymus / perikaryon / cytosolic small ribosomal subunit / cytosolic large ribosomal subunit / mitochondrial inner membrane / cytoplasmic translation / postsynaptic density / cell differentiation / rRNA binding / ribosome / protein ubiquitination / structural constituent of ribosome / ribonucleoprotein complex / iron ion binding / translation / positive regulation of protein phosphorylation / positive regulation of apoptotic process / cell cycle / cell division / DNA repair / centrosome / mRNA binding / apoptotic process / ubiquitin protein ligase binding / synapse / dendrite / positive regulation of cell population proliferation / nucleolus / negative regulation of apoptotic process / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / endoplasmic reticulum / ATP hydrolysis activity / DNA binding / RNA binding / zinc ion binding / ATP binding / membrane / nucleus / metal ion binding / plasma membrane Similarity search - Function | |||||||||
Biological species | Oryctolagus cuniculus (rabbit) Homo sapiens (human) | |||||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3 Å | |||||||||
Authors | Bochler, A. / Simonetti, A. / Guca, E. / Hashem, Y. | |||||||||
Funding support | European Union, France, 2items
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Citation | Journal: Cell Rep / Year: 2020 Title: Structural Insights into the Mammalian Late-Stage Initiation Complexes. Authors: Angelita Simonetti / Ewelina Guca / Anthony Bochler / Lauriane Kuhn / Yaser Hashem / Abstract: In higher eukaryotes, the mRNA sequence in the direct vicinity of the start codon, called the Kozak sequence (CRCCaugG, where R is a purine), is known to influence the rate of the initiation process. ...In higher eukaryotes, the mRNA sequence in the direct vicinity of the start codon, called the Kozak sequence (CRCCaugG, where R is a purine), is known to influence the rate of the initiation process. However, the molecular basis underlying its role remains poorly understood. Here, we present the cryoelectron microscopy (cryo-EM) structures of mammalian late-stage 48S initiation complexes (LS48S ICs) in the presence of two different native mRNA sequences, β-globin and histone 4, at overall resolution of 3 and 3.5 Å, respectively. Our high-resolution structures unravel key interactions from the mRNA to eukaryotic initiation factors (eIFs): 1A, 2, 3, 18S rRNA, and several 40S ribosomal proteins. In addition, we are able to study the structural role of ABCE1 in the formation of native 48S ICs. Our results reveal a comprehensive map of ribosome/eIF-mRNA and ribosome/eIF-tRNA interactions and suggest the impact of mRNA sequence on the structure of the LS48S IC. | |||||||||
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 | 6yal.cif.gz | 2 MB | Display | PDBx/mmCIF format |
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PDB format | pdb6yal.ent.gz | 1.5 MB | Display | PDB format |
PDBx/mmJSON format | 6yal.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6yal_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 6yal_full_validation.pdf.gz | 2 MB | Display | |
Data in XML | 6yal_validation.xml.gz | 214.8 KB | Display | |
Data in CIF | 6yal_validation.cif.gz | 351.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ya/6yal ftp://data.pdbj.org/pub/pdb/validation_reports/ya/6yal | HTTPS FTP |
-Related structure data
Related structure data | 10760MC 6yamC 6yanC C: citing same article (ref.) M: map data used to model this data |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 3 types, 3 molecules 123
#1: RNA chain | Mass: 24376.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: A at position 37 is modified (threonyl-carbamoyl-adenosine (t6A)) Source: (natural) Oryctolagus cuniculus (rabbit) |
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#34: RNA chain | Mass: 601015.688 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: U at position 1244 is modified / Source: (natural) Oryctolagus cuniculus (rabbit) |
#41: RNA chain | Mass: 13475.132 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) |
-Protein/peptide , 1 types, 1 molecules l
#2: Protein/peptide | Mass: 3473.451 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: A0A087WNH4 |
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+40S Ribosomal protein ... , 32 types, 32 molecules CDEFGHIJKLMNOPQSTVWXYZabcdefniUR
-Protein , 3 types, 3 molecules gjk
#31: Protein | Mass: 34669.113 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SJB4 |
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#37: Protein | Mass: 12788.764 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SYS4*PLUS |
#38: Protein | Mass: 66986.812 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1SG72*PLUS |
-Eukaryotic translation initiation factor 2 subunit ... , 2 types, 2 molecules AB
#35: Protein | Mass: 32792.867 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: G1T2G4 |
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#36: Protein | Mass: 45862.441 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) |
-Non-polymers , 3 types, 5 molecules
#42: Chemical | #43: Chemical | ChemComp-MG / | #44: Chemical | |
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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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Source (natural) |
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Source (recombinant) | Organism: synthetic construct (others) | ||||||||||||||||||||||||
Buffer solution | pH: 7.4 | ||||||||||||||||||||||||
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES | ||||||||||||||||||||||||
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
-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: 26 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
CTF correction | Type: NONE |
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3D reconstruction | Resolution: 3 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 252000 / Symmetry type: POINT |
Atomic model building | Protocol: FLEXIBLE FIT |