9zg5: Difference between revisions

Line 1:

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

~~The entry~~ 9zg5 is ~~ON HOLD until Paper~~ Publication

==Structure of superfolder GFP bound to nanobody 15==

== Structural highlights ==

<table><tr><td colspan='2'>[[9zg5]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria] and [https://en.wikipedia.org/wiki/Lama_glama Lama glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9ZG5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9ZG5 FirstGlance]. <br>

</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.4Å</td></tr>

<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CRO:{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CRO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=9zg5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9zg5 OCA], [https://pdbe.org/9zg5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9zg5 RCSB], [https://www.ebi.ac.uk/pdbsum/9zg5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9zg5 ProSAT]</span></td></tr>

</table>

== Function ==

[https://www.uniprot.org/uniprot/A0A059PIQ0_AEQVI A0A059PIQ0_AEQVI]

== Publication Abstract from PubMed ==

The functional outcomes of biomolecular interactions depend on the kinetics of association and dissociation between proteins and their binding partners, ranging from small molecules to other proteins, and are fundamental to understanding cooperativity, allostery, and drug action. However, existing kinetic methods, such as surface plasmon resonance and biolayer interferometry (BLI), require immobilization or labeling of one binding partner and are often indirect measurements. Here, we introduce a transformative time-resolved native mass spectrometry (MS) approach that enables direct, label-free, and immobilization-free quantification of biomolecular kinetics across diverse interactions within minutes using only picomolar sample amounts. We benchmarked the approach using well-characterized systems and obtained kinetic parameters that agreed with those measured by BLI. We further demonstrate the utility of time-resolved native MS in quantifying the kinetics of protein-small-molecule interactions, including those involving an irreversible inhibitor. By capturing the association and dissociation of biomolecular interactions in real time, time-resolved native MS overcomes longstanding limitations of conventional kinetic assays and transforms native MS from a static technique to a dynamic, quantitative tool for probing biomolecular kinetics and mechanisms that underpin therapeutic discovery.

~~Authors:~~ Bahramimoghaddam, H., Laganowsky, A.

Time-Resolved Native Mass Spectrometry for Direct Measurement of Biomolecular Kinetics.,James VK, Stover L, Bahramimoghaddam H, Khandelwal T, Chang JY, Downing J, Scott E, Bailey KO, Russell DH, Baker LA, Laganowsky A J Am Chem Soc. 2026 May 20;148(19):19567-19577. doi: 10.1021/jacs.5c21842. Epub , 2026 May 9. PMID:42104933<ref>PMID:42104933</ref>

~~Description~~: ~~Structure of superfolder GFP bound to nanobody 15~~

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

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

</div>

[[Category: Bahramimoghaddam, H]]

[[Category: Laganowsky, A]]

== References ==

__TOC__

</StructureSection>

[[Category: Aequorea victoria]]

[[Category: Lama glama]]

[[Category: Large Structures]]

[[Category: Bahramimoghaddam H]]

[[Category: Laganowsky A]]

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@@ Line 1: / Line 1: @@
-'''Unreleased structure'''
-The entry 9zg5 is ON HOLD  until Paper Publication
+==Structure of superfolder GFP bound to nanobody 15==
+<StructureSection load='9zg5' size='340' side='right'caption='[[9zg5]], [[Resolution|resolution]] 3.40&Aring;' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[9zg5]] is a 8 chain structure with sequence from [https://en.wikipedia.org/wiki/Aequorea_victoria Aequorea victoria] and [https://en.wikipedia.org/wiki/Lama_glama Lama glama]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=9ZG5 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=9ZG5 FirstGlance]. <br>
+</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 3.4&#8491;</td></tr>
+<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=CRO:{2-[(1R,2R)-1-AMINO-2-HYDROXYPROPYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC+ACID'>CRO</scene>, <scene name='pdbligand=SO4:SULFATE+ION'>SO4</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=9zg5 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=9zg5 OCA], [https://pdbe.org/9zg5 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=9zg5 RCSB], [https://www.ebi.ac.uk/pdbsum/9zg5 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=9zg5 ProSAT]</span></td></tr>
+</table>
+== Function ==
+[https://www.uniprot.org/uniprot/A0A059PIQ0_AEQVI A0A059PIQ0_AEQVI]
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+The functional outcomes of biomolecular interactions depend on the kinetics of association and dissociation between proteins and their binding partners, ranging from small molecules to other proteins, and are fundamental to understanding cooperativity, allostery, and drug action. However, existing kinetic methods, such as surface plasmon resonance and biolayer interferometry (BLI), require immobilization or labeling of one binding partner and are often indirect measurements. Here, we introduce a transformative time-resolved native mass spectrometry (MS) approach that enables direct, label-free, and immobilization-free quantification of biomolecular kinetics across diverse interactions within minutes using only picomolar sample amounts. We benchmarked the approach using well-characterized systems and obtained kinetic parameters that agreed with those measured by BLI. We further demonstrate the utility of time-resolved native MS in quantifying the kinetics of protein-small-molecule interactions, including those involving an irreversible inhibitor. By capturing the association and dissociation of biomolecular interactions in real time, time-resolved native MS overcomes longstanding limitations of conventional kinetic assays and transforms native MS from a static technique to a dynamic, quantitative tool for probing biomolecular kinetics and mechanisms that underpin therapeutic discovery.
-Authors: Bahramimoghaddam, H., Laganowsky, A.
+Time-Resolved Native Mass Spectrometry for Direct Measurement of Biomolecular Kinetics.,James VK, Stover L, Bahramimoghaddam H, Khandelwal T, Chang JY, Downing J, Scott E, Bailey KO, Russell DH, Baker LA, Laganowsky A J Am Chem Soc. 2026 May 20;148(19):19567-19577. doi: 10.1021/jacs.5c21842. Epub , 2026 May 9. PMID:42104933<ref>PMID:42104933</ref>
-Description: Structure of superfolder GFP bound to nanobody 15
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-[[Category: Unreleased Structures]]
+</div>
-[[Category: Bahramimoghaddam, H]]
+<div class="pdbe-citations 9zg5" style="background-color:#fffaf0;"></div>
-[[Category: Laganowsky, A]]
+== References ==
+<references/>
+__TOC__
+</StructureSection>
+[[Category: Aequorea victoria]]
+[[Category: Lama glama]]
+[[Category: Large Structures]]
+[[Category: Bahramimoghaddam H]]
+[[Category: Laganowsky A]]