+Open data
-Basic information
Entry | Database: PDB / ID: 7ow7 | ||||||
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Title | EIF6-bound large subunit of the human ribosome | ||||||
Components |
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Keywords | TRANSLATION / Ribosome / EIF6 / human / SDS | ||||||
Function / homology | Function and homology information lamin filament / regulation of fatty acid 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 / axial mesoderm development / negative regulation of formation of translation preinitiation complex / ribosomal protein import into nucleus ...lamin filament / regulation of fatty acid 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 / axial mesoderm development / negative regulation of formation of translation preinitiation complex / ribosomal protein import into nucleus / 90S preribosome assembly / TORC2 complex binding / 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 / 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 / response to aldosterone / retinal ganglion cell axon guidance / G1 to G0 transition / homeostatic process / lung morphogenesis / maturation of 5.8S rRNA / male meiosis I / 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 / 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 / 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 actinomycin D / ribosomal subunit export from nucleus / cytosolic ribosome / 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 / 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 / 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 / large ribosomal subunit / antimicrobial humoral immune response mediated by antimicrobial peptide / cellular response to UV / positive regulation of protein binding / ribosome binding / retina development in camera-type eye / regulation of translation / heparin binding / cell body / 5S rRNA binding / large ribosomal subunit rRNA binding / postsynapse / spermatogenesis / response to ethanol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.4 Å | ||||||
Authors | Faille, A. / Warren, A.J. | ||||||
Funding support | United Kingdom, 1items
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Citation | Journal: To Be Published Title: Structure of human EIF6-bound large ribosomal subunit Authors: Faille, A. / Warren, A.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7ow7.cif.gz | 3.6 MB | Display | PDBx/mmCIF format |
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PDB format | pdb7ow7.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 7ow7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7ow7_validation.pdf.gz | 1.3 MB | Display | wwPDB validaton report |
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Full document | 7ow7_full_validation.pdf.gz | 1.8 MB | Display | |
Data in XML | 7ow7_validation.xml.gz | 263 KB | Display | |
Data in CIF | 7ow7_validation.cif.gz | 468.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/7ow7 ftp://data.pdbj.org/pub/pdb/validation_reports/ow/7ow7 | HTTPS FTP |
-Related structure data
Related structure data | 13094MC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
-RNA chain , 3 types, 3 molecules ABC
#1: RNA chain | Mass: 1641134.750 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Expi293 |
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#2: RNA chain | Mass: 38998.078 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Expi293 / References: GenBank: 23898 |
#3: RNA chain | Mass: 50462.855 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: Expi293 |
+60S ribosomal protein ... , 39 types, 39 molecules DEFGHmnopqrstIJKLMNRSTUVWXYZab...
-Protein , 1 types, 1 molecules P
#41: Protein | Mass: 26620.010 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P56537 |
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-Non-polymers , 6 types, 9430 molecules
#44: Chemical | ChemComp-MG / #45: Chemical | ChemComp-ZN / #46: Chemical | ChemComp-K / #47: Chemical | ChemComp-NA / #48: Chemical | ChemComp-BR / | #49: 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 | Name: Human large ribosomal subunit / Type: COMPLEX / Entity ID: #1-#43 / Source: NATURAL |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Homo sapiens (human) |
Buffer solution | pH: 7.4 |
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: 40 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k) |
-Processing
Software | Name: REFMAC / Version: 5.8.0258 / Classification: refinement / Contact author: Garib N. Murshudov / Contact author email: garib[at]mrc-lmb.cam.ac.uk / Date: Sep 10, 2019 Description: (un)restrained refinement or idealisation of macromolecular structures | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
3D reconstruction | Resolution: 2.4 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 30000 / Symmetry type: POINT | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | Resolution: 2.4→2.4 Å / Cor.coef. Fo:Fc: 0.802 / WRfactor Rwork: 0.333 / SU B: 4.002 / SU ML: 0.079 / Average fsc overall: 0.7418 / Average fsc work: 0.7418 / ESU R: 0.071 Details: Hydrogens have been added in their riding positions
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Solvent computation | Solvent model: BABINET MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 63.368 Å2
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Refine LS restraints |
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LS refinement shell | Refine-ID: ELECTRON MICROSCOPY / Num. reflection Rfree: _ / Total num. of bins used: 20 / % reflection obs: 100 %
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