9zr7: Difference between revisions

Line 1:

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

~~The entry~~ 9zr7 is ~~ON HOLD~~

==Cryo-EM structure of NRAS(Q61K)-BRIL fusion in complex with Fab(BAG2) and Monobody(Mb24)==

== Structural highlights ==

<table><tr><td colspan='2'>[[9zr7]] is a 3 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=9ZR7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9ZR7 FirstGlance]. <br>

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.28Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</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=9zr7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9zr7 OCA], [https://pdbe.org/9zr7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9zr7 RCSB], [https://www.ebi.ac.uk/pdbsum/9zr7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9zr7 ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/RASN_CAVPO RASN_CAVPO] Signal transducer in the Ras-MAPK signaling pathway that regulates cell proliferation and survival (By similarity). Ras proteins bind GDP/GTP and possess intrinsic GTPase activity (By similarity). Recognized by LZTR1 that mediates its ubiquitination by a BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex (By similarity).[UniProtKB:P01111][https://www.uniprot.org/uniprot/C562_ECOLX C562_ECOLX] Electron-transport protein of unknown function.

== Publication Abstract from PubMed ==

Small GTPases play important roles in cellular signaling. Due to their small sizes ( approximately 21 kDa), structural studies of small GTPases have been predominantly performed using x-ray crystallography in which crystal lattice contacts made it challenging to define unperturbed conformations of the key switch regions. Here, we developed a protein-engineering strategy that enables cryo-EM analysis of small soluble proteins and applied to RAS. We fused the C-terminal alpha5 helix of the RAS globular domain to a small protein BRIL by forming a continuous helix, which leaves most RAS surfaces exposed to the solvent and unperturbed, followed by the complex formation with an anti-BRIL Fab. This engineered complex with an increased molecular weight, termed "RAS-lollipop", enabled single-particle cryo-EM of RAS. Using this approach, we determined the cryo-EM structure of NRAS, whose structural studies using crystallography have been the least successful among the RAS isoforms. We revealed the conformations of the switch region and alpha 5 helix that differ from those observed in published crystal structures, and also defined the binding site of an NRAS-specific monobody. We uncovered an unexpected surfactant-like property of this monobody, which reduces orientation biases of particles on cryo-EM grids. Together, this work establishes a platform for visualizing small GTPases and potentially other small proteins with minimal perturbation of their surfaces.

~~Authors~~:

Protein Engineering-Enabled Cryo-EM Investigation of Small GTPases.,Hu Z, Patel UR, Glasser E, Koide A, Koide S J Mol Biol. 2026 Sep 1;438(17):169860. doi: 10.1016/j.jmb.2026.169860. Epub 2026 , May 13. PMID:42134495<ref>PMID:42134495</ref>

~~Description~~:

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

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

</div>

== References ==

__TOC__

</StructureSection>

[[Category: Homo sapiens]]

[[Category: Large Structures]]

[[Category: Hu Z]]

[[Category: Koide S]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9zr7 is ON HOLD
+==Cryo-EM structure of NRAS(Q61K)-BRIL fusion in complex with Fab(BAG2) and Monobody(Mb24)==
+<StructureSection load='9zr7' size='340' side='right'caption='[[9zr7]], [[Resolution|resolution]] 3.28&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9zr7]] is a 3 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=9ZR7 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9ZR7 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution|Resolution]] 3.28&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=GDP:GUANOSINE-5-DIPHOSPHATE'>GDP</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=9zr7 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9zr7 OCA], [https://pdbe.org/9zr7 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9zr7 RCSB], [https://www.ebi.ac.uk/pdbsum/9zr7 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9zr7 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/RASN_CAVPO RASN_CAVPO] Signal transducer in the Ras-MAPK signaling pathway that regulates cell proliferation and survival (By similarity). Ras proteins bind GDP/GTP and possess intrinsic GTPase activity (By similarity). Recognized by LZTR1 that mediates its ubiquitination by a BCR (BTB-CUL3-RBX1) E3 ubiquitin-protein ligase complex (By similarity).[UniProtKB:P01111][https://www.uniprot.org/uniprot/C562_ECOLX C562_ECOLX] Electron-transport protein of unknown function.
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Small GTPases play important roles in cellular signaling. Due to their small sizes ( approximately 21 kDa), structural studies of small GTPases have been predominantly performed using x-ray crystallography in which crystal lattice contacts made it challenging to define unperturbed conformations of the key switch regions. Here, we developed a protein-engineering strategy that enables cryo-EM analysis of small soluble proteins and applied to RAS. We fused the C-terminal alpha5 helix of the RAS globular domain to a small protein BRIL by forming a continuous helix, which leaves most RAS surfaces exposed to the solvent and unperturbed, followed by the complex formation with an anti-BRIL Fab. This engineered complex with an increased molecular weight, termed "RAS-lollipop", enabled single-particle cryo-EM of RAS. Using this approach, we determined the cryo-EM structure of NRAS, whose structural studies using crystallography have been the least successful among the RAS isoforms. We revealed the conformations of the switch region and alpha 5 helix that differ from those observed in published crystal structures, and also defined the binding site of an NRAS-specific monobody. We uncovered an unexpected surfactant-like property of this monobody, which reduces orientation biases of particles on cryo-EM grids. Together, this work establishes a platform for visualizing small GTPases and potentially other small proteins with minimal perturbation of their surfaces.
-Authors:
+Protein Engineering-Enabled Cryo-EM Investigation of Small GTPases.,Hu Z, Patel UR, Glasser E, Koide A, Koide S J Mol Biol. 2026 Sep 1;438(17):169860. doi: 10.1016/j.jmb.2026.169860. Epub 2026 , May 13. PMID:42134495<ref>PMID:42134495</ref>
-Description:
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
+<div class="pdbe-citations 9zr7" style="background-color:#fffaf0;"></div>
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Homo sapiens]]
+[[Category: Large Structures]]
+[[Category: Hu Z]]
+[[Category: Koide S]]