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Yorodumi- PDB-5aj0: Cryo electron microscopy of actively translating human polysomes ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5aj0 | ||||||
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Title | Cryo electron microscopy of actively translating human polysomes (POST state). | ||||||
Components |
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Keywords | RIBOSOME / MAMMALIAN RIBOSOME / TRANSLATION / POLYSOME / CRYO ELECTRON MICROSCOPY / ELONGATION CYCLE | ||||||
Function / homology | Function and homology information eukaryotic 80S initiation complex / negative regulation of protein neddylation / embryonic brain development / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / translation at presynapse / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein tyrosine kinase inhibitor activity ...eukaryotic 80S initiation complex / negative regulation of protein neddylation / embryonic brain development / positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis / negative regulation of endoplasmic reticulum unfolded protein response / translation at presynapse / oxidized pyrimidine DNA binding / response to TNF agonist / positive regulation of base-excision repair / protein tyrosine kinase inhibitor activity / axial mesoderm development / positive regulation of respiratory burst involved in inflammatory response / ribosomal protein import into nucleus / regulation of adenylate cyclase-activating G protein-coupled receptor signaling pathway / negative regulation of formation of translation preinitiation complex / positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of gastrulation / nucleolus organization / IRE1-RACK1-PP2A complex / 90S preribosome assembly / positive regulation of endodeoxyribonuclease activity / positive regulation of Golgi to plasma membrane protein transport / TNFR1-mediated ceramide production / negative regulation of DNA repair / negative regulation of RNA splicing / TORC2 complex binding / GAIT complex / negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide / oxidized purine DNA binding / supercoiled DNA binding / neural crest cell differentiation / middle ear morphogenesis / NF-kappaB complex / ubiquitin-like protein conjugating enzyme binding / regulation of establishment of cell polarity / negative regulation of phagocytosis / positive regulation of ubiquitin-protein transferase activity / rRNA modification in the nucleus and cytosol / A band / Formation of the ternary complex, and subsequently, the 43S complex / erythrocyte homeostasis / cytoplasmic side of rough endoplasmic reticulum membrane / alpha-beta T cell differentiation / regulation of G1 to G0 transition / laminin receptor activity / 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 / protein kinase A binding / 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 / Ribosomal scanning and start codon recognition / ion channel inhibitor activity / response to aldosterone / Translation initiation complex formation / pigmentation / retinal ganglion cell axon guidance / positive regulation of mitochondrial depolarization / mammalian oogenesis stage / G1 to G0 transition / homeostatic process / activation-induced cell death of T cells / macrophage chemotaxis / negative regulation of Wnt signaling pathway / lung morphogenesis / positive regulation of T cell receptor signaling pathway / fibroblast growth factor binding / positive regulation of activated T cell proliferation / iron-sulfur cluster binding / regulation of cell division / Protein hydroxylation / monocyte chemotaxis / negative regulation of peptidyl-serine phosphorylation / BH3 domain binding / mTORC1-mediated signalling / SARS-CoV-1 modulates host translation machinery / Peptide chain elongation / positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator / cysteine-type endopeptidase activator activity involved in apoptotic process / Selenocysteine synthesis / positive regulation of signal transduction by p53 class mediator / Formation of a pool of free 40S subunits / Eukaryotic Translation Termination / phagocytic cup / blastocyst development / 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 / cyclin binding / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / Viral mRNA Translation / protein localization to nucleus / Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC) / GTP hydrolysis and joining of the 60S ribosomal subunit / TOR signaling / endonucleolytic cleavage to generate mature 3'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) / L13a-mediated translational silencing of Ceruloplasmin expression Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Yersinia pseudotuberculosis (bacteria) | ||||||
Method | ELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.5 Å | ||||||
Authors | Behrmann, E. / Loerke, J. / Budkevich, T.V. / Yamamoto, K. / Schmidt, A. / Penczek, P.A. / Vos, M.R. / Burger, J. / Mielke, T. / Scheerer, P. / Spahn, C.M.T. | ||||||
Citation | Journal: Cell / Year: 2015 Title: Structural snapshots of actively translating human ribosomes. Authors: Elmar Behrmann / Justus Loerke / Tatyana V Budkevich / Kaori Yamamoto / Andrea Schmidt / Pawel A Penczek / Matthijn R Vos / Jörg Bürger / Thorsten Mielke / Patrick Scheerer / Christian M T Spahn / Abstract: Macromolecular machines, such as the ribosome, undergo large-scale conformational changes during their functional cycles. Although their mode of action is often compared to that of mechanical ...Macromolecular machines, such as the ribosome, undergo large-scale conformational changes during their functional cycles. Although their mode of action is often compared to that of mechanical machines, a crucial difference is that, at the molecular dimension, thermodynamic effects dominate functional cycles, with proteins fluctuating stochastically between functional states defined by energetic minima on an energy landscape. Here, we have used cryo-electron microscopy to image ex-vivo-derived human polysomes as a source of actively translating ribosomes. Multiparticle refinement and 3D variability analysis allowed us to visualize a variety of native translation intermediates. Significantly populated states include not only elongation cycle intermediates in pre- and post-translocational states, but also eEF1A-containing decoding and termination/recycling complexes. Focusing on the post-translocational state, we extended this assessment to the single-residue level, uncovering striking details of ribosome-ligand interactions and identifying both static and functionally important dynamic elements. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW ...SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "VB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 5-STRANDED BARREL THIS IS REPRESENTED BY A 6-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "FA" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Movie |
Movie viewer |
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Structure viewer | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 5aj0.cif.gz | 4.8 MB | Display | PDBx/mmCIF format |
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PDB format | pdb5aj0.ent.gz | Display | PDB format | |
PDBx/mmJSON format | 5aj0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5aj0_validation.pdf.gz | 1.8 MB | Display | wwPDB validaton report |
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Full document | 5aj0_full_validation.pdf.gz | 2.2 MB | Display | |
Data in XML | 5aj0_validation.xml.gz | 303.9 KB | Display | |
Data in CIF | 5aj0_validation.cif.gz | 589.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aj/5aj0 ftp://data.pdbj.org/pub/pdb/validation_reports/aj/5aj0 | HTTPS FTP |
-Related structure data
Related structure data | 2875MUC 2902C 2903C 2904C 2905C 2906C 2907C 2908C 2909C 2910C 2911C M: map data used to model this data U: unfit; in different coordinate system*YM 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 , 6 types, 7 molecules A3A4A2B1BvBwBx
#1: RNA chain | Mass: 62616.344 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: GenBank: 51477016 | ||
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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: HEK 293T / References: GenBank: 23898 | ||
#48: RNA chain | Mass: 1627178.625 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: GenBank: 337381 | ||
#49: RNA chain | Mass: 602776.875 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: GenBank: 36162 | ||
#83: RNA chain | Mass: 24485.539 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: MIXTURE OF ALL ENDOGENOUS PRESENT / Source: (natural) Yersinia pseudotuberculosis (bacteria) / Cell line: HEK 293T / References: GenBank: 755367513 #84: RNA chain | | Mass: 8527.686 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: MIXTURE OF ALL ENDOGENOUS PRESENT / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T |
+60S ribosomal protein ... , 43 types, 43 molecules AAABACADAEAFAGAHAIAJALAMANAOAPAQARASATAUAVAWAXAYAZAaAbAcAdAe...
-Protein , 4 types, 4 molecules AKAmBfBg
#13: Protein | Mass: 34309.418 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P05388 |
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#41: Protein | Mass: 14758.394 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P62987 |
#81: Protein | Mass: 18004.041 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P62979 |
#82: Protein | Mass: 35115.652 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T / References: UniProt: P63244 |
+40S ribosomal protein ... , 31 types, 31 molecules BABBBCBDBEBFBGBHBIBJBKBLBMBNBOBPBQBRBSBTBUBVBWBXBYBZBaBbBcBdBe
-Protein/peptide , 1 types, 1 molecules By
#85: Protein/peptide | Mass: 2060.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: MIXTURE OF ALL ENDOGENOUS PRESENT / Source: (natural) Homo sapiens (human) / Cell line: HEK 293T |
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-Non-polymers , 2 types, 331 molecules
#86: Chemical | ChemComp-MG / #87: Chemical | ChemComp-ZN / |
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-Details
Sequence details | CGCGACCUCA |
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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: NATIVE RIBOSOMAL COMPLEX FROM POLYSOMES - POST STATE / Type: RIBOSOME |
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Buffer solution | Name: 20 MM HEPES-KOH, PH 7.5, 100 MM KCL, 1.5 MM MGCL2, 0.5 MM SPERMIDINE, 0.04 MM SPERMINE, 1 MM DTT pH: 7.5 Details: 20 MM HEPES-KOH, PH 7.5, 100 MM KCL, 1.5 MM MGCL2, 0.5 MM SPERMIDINE, 0.04 MM SPERMINE, 1 MM DTT |
Specimen | Conc.: 3.5 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Specimen support | Details: OTHER |
Vitrification | Instrument: FEI VITROBOT MARK II / Cryogen name: ETHANE Details: VITRIFICATION 1 -- CRYOGEN- ETHANE, HUMIDITY- 100, TEMPERATURE- 93, INSTRUMENT- FEI VITROBOT MARK II, METHOD- BLOT FOR 2-4 SECONDS BEFORE PLUNGING, |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS / Date: Aug 20, 2012 / Details: DATA WAS COLLECTED AUTOMATICALLY WITH LEGINON |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD / Nominal magnification: 115000 X / Calibrated magnification: 205000 X / Nominal defocus max: 4500 nm / Nominal defocus min: 2000 nm / Cs: 2 mm |
Image recording | Electron dose: 20 e/Å2 / Film or detector model: TVIPS TEMCAM-F416 (4k x 4k) |
-Processing
EM software |
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CTF correction | Details: DEFOCUS GROUPS | ||||||||||||||||||||
Symmetry | Point symmetry: C1 (asymmetric) | ||||||||||||||||||||
3D reconstruction | Method: MULTI-REFERENCE TEMPLATE MATCHING / Resolution: 3.5 Å / Num. of particles: 313321 / Actual pixel size: 0.945 Å Magnification calibration: CROSS- -CORRELATION DENSITIES WITHIN SPHERICAL SHELL Details: SUBMISSION BASED ON EXPERIMENTAL DATA FROM EMDB EMD-2875. (DEPOSITION ID: 13060). Symmetry type: POINT | ||||||||||||||||||||
Atomic model building | Space: REAL | ||||||||||||||||||||
Atomic model building | PDB-ID: 4UJE | ||||||||||||||||||||
Refinement | Highest resolution: 3.5 Å | ||||||||||||||||||||
Refinement step | Cycle: LAST / Highest resolution: 3.5 Å
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