7nry

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (12:38, 1 February 2024) (edit) (undo)
 
Line 1: Line 1:
==Re-refinement of MAPKAP kinase-2/inhibitor complex 3fyj==
==Re-refinement of MAPKAP kinase-2/inhibitor complex 3fyj==
-
<StructureSection load='7nry' size='340' side='right'caption='[[7nry]]' scene=''>
+
<StructureSection load='7nry' size='340' side='right'caption='[[7nry]], [[Resolution|resolution]] 3.80&Aring;' scene=''>
== Structural highlights ==
== Structural highlights ==
-
<table><tr><td colspan='2'>Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NRY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NRY FirstGlance]. <br>
+
<table><tr><td colspan='2'>[[7nry]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=7NRY OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=7NRY FirstGlance]. <br>
-
</td></tr><tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7nry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nry OCA], [https://pdbe.org/7nry PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nry RCSB], [https://www.ebi.ac.uk/pdbsum/7nry PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nry ProSAT]</span></td></tr>
+
</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.8&#8491;</td></tr>
 +
<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=B97:(10R)-10-METHYL-3-(6-METHYLPYRIDIN-3-YL)-9,10,11,12-TETRAHYDRO-8H-[1,4]DIAZEPINO[5,6 4,5]THIENO[3,2-F]QUINOLIN-8-ONE'>B97</scene>, <scene name='pdbligand=CL:CHLORIDE+ION'>CL</scene>, <scene name='pdbligand=MLA:MALONIC+ACID'>MLA</scene></td></tr>
 +
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=7nry FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=7nry OCA], [https://pdbe.org/7nry PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=7nry RCSB], [https://www.ebi.ac.uk/pdbsum/7nry PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=7nry ProSAT]</span></td></tr>
</table>
</table>
 +
== Function ==
 +
[https://www.uniprot.org/uniprot/MAPK2_HUMAN MAPK2_HUMAN] Stress-activated serine/threonine-protein kinase involved in cytokines production, endocytosis, reorganization of the cytoskeleton, cell migration, cell cycle control, chromatin remodeling, DNA damage response and transcriptional regulation. Following stress, it is phosphorylated and activated by MAP kinase p38-alpha/MAPK14, leading to phosphorylation of substrates. Phosphorylates serine in the peptide sequence, Hyd-X-R-X(2)-S, where Hyd is a large hydrophobic residue. Phosphorylates ALOX5, CDC25B, CDC25C, ELAVL1, HNRNPA0, HSF1, HSP27/HSPB1, KRT18, KRT20, LIMK1, LSP1, PABPC1, PARN, PDE4A, RCSD1, RPS6KA3, TAB3 and TTP/ZFP36. Mediates phosphorylation of HSP27/HSPB1 in response to stress, leading to dissociate HSP27/HSPB1 from large small heat-shock protein (sHsps) oligomers and impair their chaperone activities and ability to protect against oxidative stress effectively. Involved in inflammatory response by regulating tumor necrosis factor (TNF) and IL6 production post-transcriptionally: acts by phosphorylating AU-rich elements (AREs)-binding proteins ELAVL1, HNRNPA0, PABPC1 and TTP/ZFP36, leading to regulate the stability and translation of TNF and IL6 mRNAs. Phosphorylation of TTP/ZFP36, a major post-transcriptional regulator of TNF, promotes its binding to 14-3-3 proteins and reduces its ARE mRNA affinity leading to inhibition of dependent degradation of ARE-containing transcript. Also involved in late G2/M checkpoint following DNA damage through a process of post-transcriptional mRNA stabilization: following DNA damage, relocalizes from nucleus to cytoplasm and phosphorylates HNRNPA0 and PARN, leading to stabilize GADD45A mRNA. Involved in toll-like receptor signaling pathway (TLR) in dendritic cells: required for acute TLR-induced macropinocytosis by phosphorylating and activating RPS6KA3.<ref>PMID:8280084</ref> <ref>PMID:8093612</ref> <ref>PMID:8774846</ref> <ref>PMID:10383393</ref> <ref>PMID:12456657</ref> <ref>PMID:11844797</ref> <ref>PMID:12565831</ref> <ref>PMID:14499342</ref> <ref>PMID:14517288</ref> <ref>PMID:15014438</ref> <ref>PMID:15629715</ref> <ref>PMID:16456544</ref> <ref>PMID:16278218</ref> <ref>PMID:17481585</ref> <ref>PMID:18021073</ref> <ref>PMID:20932473</ref>
 +
<div style="background-color:#fffaf0;">
 +
== Publication Abstract from PubMed ==
 +
When building atomic models into weak and/or low-resolution density, a common strategy is to restrain their conformation to that of a higher resolution model of the same or similar sequence. When doing so, it is important to avoid over-restraining to the reference model in the face of disagreement with the experimental data. The most common strategy for this is the use of `top-out' potentials. These act like simple harmonic restraints within a defined range, but gradually weaken when the deviation between the model and reference grows beyond that range. In each current implementation the rate at which the potential flattens at large deviations follows a fixed form, although the form chosen varies among implementations. A restraint potential with a tuneable rate of flattening would provide greater flexibility to encode the confidence in any given restraint. Here, two new such potentials are described: a Cartesian distance restraint derived from a recent generalization of common loss functions and a periodic torsion restraint based on a renormalization of the von Mises distribution. Further, their implementation as user-adjustable/switchable restraints in ISOLDE is described and their use in some real-world examples is demonstrated.
 +
 +
Adaptive Cartesian and torsional restraints for interactive model rebuilding.,Croll TI, Read RJ Acta Crystallogr D Struct Biol. 2021 Apr 1;77(Pt 4):438-446. doi:, 10.1107/S2059798321001145. Epub 2021 Mar 30. PMID:33825704<ref>PMID:33825704</ref>
 +
 +
From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
 +
</div>
 +
<div class="pdbe-citations 7nry" style="background-color:#fffaf0;"></div>
 +
== References ==
 +
<references/>
__TOC__
__TOC__
</StructureSection>
</StructureSection>
 +
[[Category: Homo sapiens]]
[[Category: Large Structures]]
[[Category: Large Structures]]
[[Category: Croll TI]]
[[Category: Croll TI]]
[[Category: Read RJ]]
[[Category: Read RJ]]

Current revision

Re-refinement of MAPKAP kinase-2/inhibitor complex 3fyj

PDB ID 7nry

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/7nry"
Personal tools