8xe8: Difference between revisions

Line 1:

~~'''Unreleased structure'''~~

~~The entry~~ 8xe8 is ~~ON HOLD until Paper~~ Publication

==Solution structure of ubiquitin-like domain (UBL) of human ZFAND1==

== Structural highlights ==

<table><tr><td colspan='2'>[[8xe8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8XE8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8XE8 FirstGlance]. <br>

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 20 models</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=8xe8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8xe8 OCA], [https://pdbe.org/8xe8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8xe8 RCSB], [https://www.ebi.ac.uk/pdbsum/8xe8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8xe8 ProSAT]</span></td></tr>

</table>

== Publication Abstract from PubMed ==

Arsenite-induced stress granule (SG) formation can be cleared by the ubiquitin-proteasome system aided by the ATP-dependent unfoldase p97. ZFAND1 participates in this pathway by recruiting p97 to trigger SG clearance. ZFAND1 contains two An1-type zinc finger domains (ZF1 and ZF2), followed by a ubiquitin-like domain (UBL); but their structures are not experimentally determined. To shed light on the structural basis of the ZFAND1-p97 interaction, we determined the atomic structures of the individual domains of ZFAND1 by solution-state NMR spectroscopy and X-ray crystallography. We further characterized the interaction between ZFAND1 and p97 by methyl NMR spectroscopy and cryo-EM. (15)N spin relaxation dynamics analysis indicated independent domain motions for ZF1, ZF2, and UBL. The crystal structure and NMR structure of UBL showed a conserved beta-grasp fold homologous to ubiquitin and other UBLs. Nevertheless, the UBL of ZFAND1 contains an additional N-terminal helix that adopts different conformations in the crystalline and solution states. ZFAND1 uses the C-terminal UBL to bind to p97, evidenced by the pronounced line-broadening of the UBL domain during the p97 titration monitored by methyl NMR spectroscopy. ZFAND1 binding induces pronounced conformational heterogeneity in the N-terminal domain of p97, leading to a partial loss of the cryo-EM density of the N-terminal domain of p97. In conclusion, this work paved the way for a better understanding of the interplay between p97 and ZFAND1 in the context of SG clearance.

~~Authors:~~ Lai, ~~C.H.~~, Ko, ~~K.T.~~, ~~Fan~~, P.J.~~, Yu, T~~.A.~~, Chang, C~~.F.~~, Hsu, S~~.T.D.

Structural insight into the ZFAND1-p97 interaction involved in stress granule clearance.,Lai CH, Ko KT, Fan PJ, Yu TA, Chang CF, Draczkowski P, Hsu SD J Biol Chem. 2024 May;300(5):107230. doi: 10.1016/j.jbc.2024.107230. Epub 2024 , Mar 25. PMID:38537699<ref>PMID:38537699</ref>

~~Description: Solution structure~~ of ~~ubiquitin~~-~~like domain (UBL) of human ZFAND1~~

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

[[Category: ~~Unreleased~~ Structures]]

</div>

[[Category: ~~Ko, K.T~~]]

[[Category: Fan~~, P.J~~]]

== References ==

[[Category: ~~Chang, C.F~~]]

[[Category: ~~Yu, T.A~~]]

__TOC__

[[Category: ~~Hsu, S.T.D~~]]

</StructureSection>

[[Category: ~~Lai, C.H~~]]

[[Category: Homo sapiens]]

[[Category: Large Structures]]

[[Category: Chang CF]]

[[Category: Fan PJ]]

[[Category: Hsu STD]]

[[Category: Ko KT]]

[[Category: Lai CH]]

[[Category: Yu TA]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 8xe8 is ON HOLD  until Paper Publication
+==Solution structure of ubiquitin-like domain (UBL) of human ZFAND1==
+<StructureSection load='8xe8' size='340' side='right'caption='[[8xe8]]' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[8xe8]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Homo_sapiens Homo sapiens]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=8XE8 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=8XE8 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 20 models</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=8xe8 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=8xe8 OCA], [https://pdbe.org/8xe8 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=8xe8 RCSB], [https://www.ebi.ac.uk/pdbsum/8xe8 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=8xe8 ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Arsenite-induced stress granule (SG) formation can be cleared by the ubiquitin-proteasome system aided by the ATP-dependent unfoldase p97. ZFAND1 participates in this pathway by recruiting p97 to trigger SG clearance. ZFAND1 contains two An1-type zinc finger domains (ZF1 and ZF2), followed by a ubiquitin-like domain (UBL); but their structures are not experimentally determined. To shed light on the structural basis of the ZFAND1-p97 interaction, we determined the atomic structures of the individual domains of ZFAND1 by solution-state NMR spectroscopy and X-ray crystallography. We further characterized the interaction between ZFAND1 and p97 by methyl NMR spectroscopy and cryo-EM. (15)N spin relaxation dynamics analysis indicated independent domain motions for ZF1, ZF2, and UBL. The crystal structure and NMR structure of UBL showed a conserved beta-grasp fold homologous to ubiquitin and other UBLs. Nevertheless, the UBL of ZFAND1 contains an additional N-terminal helix that adopts different conformations in the crystalline and solution states. ZFAND1 uses the C-terminal UBL to bind to p97, evidenced by the pronounced line-broadening of the UBL domain during the p97 titration monitored by methyl NMR spectroscopy. ZFAND1 binding induces pronounced conformational heterogeneity in the N-terminal domain of p97, leading to a partial loss of the cryo-EM density of the N-terminal domain of p97. In conclusion, this work paved the way for a better understanding of the interplay between p97 and ZFAND1 in the context of SG clearance.
-Authors: Lai, C.H., Ko, K.T., Fan, P.J., Yu, T.A., Chang, C.F., Hsu, S.T.D.
+Structural insight into the ZFAND1-p97 interaction involved in stress granule clearance.,Lai CH, Ko KT, Fan PJ, Yu TA, Chang CF, Draczkowski P, Hsu SD J Biol Chem. 2024 May;300(5):107230. doi: 10.1016/j.jbc.2024.107230. Epub 2024 , Mar 25. PMID:38537699<ref>PMID:38537699</ref>
-Description: Solution structure of ubiquitin-like domain (UBL) of human ZFAND1
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Ko, K.T]]
+<div class="pdbe-citations 8xe8" style="background-color:#fffaf0;"></div>
-[[Category: Fan, P.J]]
+== References ==
-[[Category: Chang, C.F]]
+<references/>
-[[Category: Yu, T.A]]
+__TOC__
-[[Category: Hsu, S.T.D]]
+</StructureSection>
-[[Category: Lai, C.H]]
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Chang CF]]
+[[Category: Fan PJ]]
+[[Category: Hsu STD]]
+[[Category: Ko KT]]
+[[Category: Lai CH]]
+[[Category: Yu TA]]