9eep: Difference between revisions

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

~~The entry~~ 9eep is ~~ON HOLD until Paper~~ Publication

==Cryo-EM model of E. coli aspartate transcarbamoylase in the R-state complexed with CP and succinate==

== Structural highlights ==

<table><tr><td colspan='2'>[[9eep]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9EEP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9EEP 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]] 3.08Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CP:PHOSPHORIC+ACID+MONO(FORMAMIDE)ESTER'>CP</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=9eep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9eep OCA], [https://pdbe.org/9eep PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9eep RCSB], [https://www.ebi.ac.uk/pdbsum/9eep PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9eep ProSAT]</span></td></tr>

</table>

== Publication Abstract from PubMed ==

Aspartate transcarbamoylase (ATCase) from Escherichia coli catalyzes a key step in pyrimidine nucleotide biosynthesis and has long served as a model for allosteric regulation. Despite decades of study, how nucleotide binding at distant regulatory sites controls cooperativity between active sites remained unresolved. Here we show that ATCase does not simply interconvert between two conformations, as traditionally depicted, but instead samples a continuum of conformations that tune enzyme cooperativity. Using complementary cryo-electron microscopy, small-angle X-ray scattering, and crystallography under conditions that ensure full assembly of the allosteric sites, we show that ATCase behaves like a flexible balloon whose global "breathing" motions directly regulate activity: compression enforces high cooperativity, inhibiting the enzyme, whereas expansion relieves this cooperativity and activates the enzyme. We further show that all four ribonucleoside triphosphates act in symmetric pairs to tune this motion, with the pyrimidines CTP and UTP compressing the enzyme to limit further pyrimidine production, and the purines ATP and GTP expanding it to balance pyrimidine and purine pools. Together, these findings uncover a dynamic breathing mechanism for long-range allosteric communication in ATCase.

~~Authors: Patterson, M~~.G., Miller, ~~R.C.~~, Ando, N.

Cooperativity in E. coli aspartate transcarbamoylase is tuned by allosteric breathing.,Miller RC, Patterson MG, Bhatt N, Pei X, Ando N Nat Commun. 2026 Mar 20. doi: 10.1038/s41467-026-70909-y. PMID:41862478<ref>PMID:41862478</ref>

~~Description: Cryo-EM model~~ of E. ~~coli aspartate transcarbamoylase in the R~~-~~state complexed with CP and succinate~~

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

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

</div>

[[Category: ~~Miller, R.C~~]]

[[Category: Ando, N]]

== References ==

[[Category: Patterson~~, M.G~~]]

__TOC__

</StructureSection>

[[Category: Escherichia coli]]

[[Category: Large Structures]]

[[Category: Ando N]]

[[Category: Miller RC]]

[[Category: Patterson MG]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9eep is ON HOLD  until Paper Publication
+==Cryo-EM model of E. coli aspartate transcarbamoylase in the R-state complexed with CP and succinate==
+<StructureSection load='9eep' size='340' side='right'caption='[[9eep]], [[Resolution|resolution]] 3.08&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9eep]] is a 12 chain structure with sequence from [https://en.wikipedia.org/wiki/Escherichia_coli Escherichia coli]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9EEP OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9EEP 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]] 3.08&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CP:PHOSPHORIC+ACID+MONO(FORMAMIDE)ESTER'>CP</scene>, <scene name='pdbligand=SIN:SUCCINIC+ACID'>SIN</scene>, <scene name='pdbligand=ZN:ZINC+ION'>ZN</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=9eep FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9eep OCA], [https://pdbe.org/9eep PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9eep RCSB], [https://www.ebi.ac.uk/pdbsum/9eep PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9eep ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Aspartate transcarbamoylase (ATCase) from Escherichia coli catalyzes a key step in pyrimidine nucleotide biosynthesis and has long served as a model for allosteric regulation. Despite decades of study, how nucleotide binding at distant regulatory sites controls cooperativity between active sites remained unresolved. Here we show that ATCase does not simply interconvert between two conformations, as traditionally depicted, but instead samples a continuum of conformations that tune enzyme cooperativity. Using complementary cryo-electron microscopy, small-angle X-ray scattering, and crystallography under conditions that ensure full assembly of the allosteric sites, we show that ATCase behaves like a flexible balloon whose global "breathing" motions directly regulate activity: compression enforces high cooperativity, inhibiting the enzyme, whereas expansion relieves this cooperativity and activates the enzyme. We further show that all four ribonucleoside triphosphates act in symmetric pairs to tune this motion, with the pyrimidines CTP and UTP compressing the enzyme to limit further pyrimidine production, and the purines ATP and GTP expanding it to balance pyrimidine and purine pools. Together, these findings uncover a dynamic breathing mechanism for long-range allosteric communication in ATCase.
-Authors: Patterson, M.G., Miller, R.C., Ando, N.
+Cooperativity in E. coli aspartate transcarbamoylase is tuned by allosteric breathing.,Miller RC, Patterson MG, Bhatt N, Pei X, Ando N Nat Commun. 2026 Mar 20. doi: 10.1038/s41467-026-70909-y. PMID:41862478<ref>PMID:41862478</ref>
-Description: Cryo-EM model of E. coli aspartate transcarbamoylase in the R-state complexed with CP and succinate
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Miller, R.C]]
+<div class="pdbe-citations 9eep" style="background-color:#fffaf0;"></div>
-[[Category: Ando, N]]
+== References ==
-[[Category: Patterson, M.G]]
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Escherichia coli]]
+[[Category: Large Structures]]
+[[Category: Ando N]]
+[[Category: Miller RC]]
+[[Category: Patterson MG]]