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138270 results
  • Experimental Technique/Method:X-RAY DIFFRACTION Resolution:1.92 Classification:TRANSFERASE Release Date:2018-02-28 Deposition Date:2017-02-11 Revision Date: Molecular Weight:37442.14 Macromolecule Type:Protein Residue Count:327 Atom Site Count:2293 DOI:10.2210/pdb5n50/pdb
    Data Types:
    • Tabular Data
  • Experimental Technique/Method:X-RAY DIFFRACTION Resolution:3.3 Classification:TRANSFERASE/RNA Release Date:2018-02-28 Deposition Date:2017-02-23 Revision Date: Molecular Weight:367086.34 Macromolecule Type:Protein#RNA Residue Count:3228 Atom Site Count:24258 DOI:10.2210/pdb5x70/pdb
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    • Tabular Data
  • Experimental Technique/Method:ELECTRON MICROSCOPY Resolution:5.75 Classification:transcription/dna Release Date:2018-02-28 Deposition Date:2018-01-29 Revision Date: Molecular Weight:491425.19 Macromolecule Type:Protein#DNA Residue Count:4213 Atom Site Count:31098 DOI:10.2210/pdb6ca0/pdb
    Data Types:
    • Tabular Data
  • Experimental Technique/Method:X-RAY DIFFRACTION Resolution:2.5 Classification:TRANSCRIPTION Release Date:2018-02-28 Deposition Date:2018-02-05 Revision Date: Molecular Weight:55137.11 Macromolecule Type:Protein Residue Count:474 Atom Site Count:3899 DOI:10.2210/pdb6cc0/pdb Abstract: Pseudomonas aeruginosa is an opportunistic pathogen that uses the process of quorum sensing (QS) to coordinate the expression of many virulence genes. During quorum sensing, N-acyl-homoserine lactone (AHL) signaling molecules regulate the activity of three LuxR-type transcription factors, LasR, RhlR, and QscR. To better understand P. aeruginosa QS signal reception, we examined the mechanism underlying the response of QscR to synthetic agonists and antagonists using biophysical and structural approaches. The structure of QscR bound to a synthetic agonist reveals a novel mode of ligand binding supporting a general mechanism for agonist activity. In turn, antagonists of QscR with partial agonist activity were found to destabilize and greatly impair QscR dimerization and DNA binding. These results highlight the diversity of LuxR-type receptor responses to small molecule agonists and antagonists and demonstrate the potential for chemical strategies for the selective targeting of individual quorum-sensing systems. This article is protected by copyright. All rights reserved.
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  • Experimental Technique/Method:X-RAY DIFFRACTION Resolution:1.99 Classification:HYDROLASE Release Date:2018-02-28 Deposition Date:2017-07-26 Revision Date: Molecular Weight:75156.16 Macromolecule Type:Protein Residue Count:684 Atom Site Count:4387 DOI:10.2210/pdb5ol0/pdb
    Data Types:
    • Tabular Data
  • Experimental Technique/Method:X-RAY DIFFRACTION Resolution:2.6 Classification:HYDROLASE, LYASE/DNA Release Date:2018-02-28 Deposition Date:2017-07-31 Revision Date: Molecular Weight:75157.3 Macromolecule Type:Protein#DNA Residue Count:594 Atom Site Count:5147 DOI:10.2210/pdb5wn0/pdb Abstract: Human apurinic/apyrimidinic (AP) endonuclease 1 (APE1) is an essential DNA repair enzyme which uses a single active site to process DNA damage via two distinct activities: (1) AP-endonuclease and (2) 3' to 5' exonuclease. The AP-endonuclease activity cleaves at AP-sites, while the exonuclease activity excises bulkier 3' mismatches and DNA damage to generate clean DNA ends suitable for downstream repair. Molecular details of the exonuclease reaction and how one active site can accommodate various toxic DNA repair intermediates remains elusive despite being biologically important. Here, we report multiple high-resolution APE1-DNA structural snapshots revealing how APE1 removes 3' mismatches and DNA damage by placing the 3' group within the intra-helical DNA cavity via a non-base flipping mechanism. This process is facilitated by a DNA nick, instability of a mismatched/damaged base, and bending of the DNA. These results illustrate how APE1 cleanses DNA dirty-ends to generate suitable substrates for downstream repair enzymes.
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    • Tabular Data
  • Experimental Technique/Method:ELECTRON MICROSCOPY Resolution:4.1 Classification:MEMBRANE PROTEIN Release Date:2018-02-28 Deposition Date:2018-02-05 Revision Date: Molecular Weight:507986.25 Macromolecule Type:Protein Residue Count:4552 Atom Site Count:30994 DOI:10.2210/pdb6fo0/pdb
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    • Tabular Data
  • Experimental Technique/Method:NEUTRON DIFFRACTION Resolution:1.5 Classification:HYDROLASE Release Date:2018-02-28 Deposition Date:2016-12-13 Revision Date: Molecular Weight:23485.53 Macromolecule Type:Protein Residue Count:223 Atom Site Count:1630 DOI:10.2210/pdb5mo0/pdb
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    • Tabular Data
  • Experimental Technique/Method:X-RAY DIFFRACTION Resolution:2.6 Classification:SIGNALING PROTEIN Release Date:2018-02-28 Deposition Date:2017-12-04 Revision Date: Molecular Weight:83392.51 Macromolecule Type:Protein Residue Count:712 Atom Site Count:5499 DOI:10.2210/pdb6bt0/pdb Abstract: The small G-protein Rheb activates the mechanistic target of rapamycin complex 1 (mTORC1) in response to growth factor signals. mTORC1 is a master regulator of cellular growth and metabolism; aberrant mTORC1 signaling is associated with fibrotic, metabolic, and neurodegenerative diseases, cancers, and rare disorders. Point mutations in the Rheb switch II domain impair its ability to activate mTORC1. Here, we report the discovery of a small molecule (NR1) that binds Rheb in the switch II domain and selectively blocks mTORC1 signaling. NR1 potently inhibits mTORC1 driven phosphorylation of ribosomal protein S6 kinase beta-1 (S6K1) but does not inhibit phosphorylation of AKT or ERK. In contrast to rapamycin, NR1 does not cause inhibition of mTORC2 upon prolonged treatment. Furthermore, NR1 potently and selectively inhibits mTORC1 in mouse kidney and muscle in vivo. The data presented herein suggest that pharmacological inhibition of Rheb is an effective approach for selective inhibition of mTORC1 with therapeutic potential.
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  • Experimental Technique/Method:X-RAY DIFFRACTION Resolution:2.73 Classification:TRANSFERASE Release Date:2018-02-28 Deposition Date:2017-02-20 Revision Date: Molecular Weight:330095.78 Macromolecule Type:Protein Residue Count:2880 Atom Site Count:20496 DOI:10.2210/pdb5uw0/pdb
    Data Types:
    • Tabular Data