5k12 - Revision history

OCA at 12:38, 6 March 2024

OCA — Wed, 06 Mar 2024 12:38:43 GMT

←Older revision		Revision as of 12:38, 6 March 2024
Line 9:		Line 9:
	== Function ==		== Function ==
	[https://www.uniprot.org/uniprot/DHE3_BOVIN DHE3_BOVIN] May be involved in learning and memory reactions by increasing the turnover of the excitatory neurotransmitter glutamate (By similarity).<ref>PMID:14659072</ref>		[https://www.uniprot.org/uniprot/DHE3_BOVIN DHE3_BOVIN] May be involved in learning and memory reactions by increasing the turnover of the excitatory neurotransmitter glutamate (By similarity).<ref>PMID:14659072</ref>
-	<div style="background-color:#fffaf0;">
-	== Publication Abstract from PubMed ==
-	Recent advances in single-particle cryoelecton microscopy (cryo-EM) are enabling generation of numerous near-atomic resolution structures for well-ordered protein complexes with sizes >/= approximately 200 kDa. Whether cryo-EM methods are equally useful for high-resolution structural analysis of smaller, dynamic protein complexes such as those involved in cellular metabolism remains an important question. Here, we present 3.8 A resolution cryo-EM structures of the cancer target isocitrate dehydrogenase (93 kDa) and identify the nature of conformational changes induced by binding of the allosteric small-molecule inhibitor ML309. We also report 2.8-A- and 1.8-A-resolution structures of lactate dehydrogenase (145 kDa) and glutamate dehydrogenase (334 kDa), respectively. With these results, two perceived barriers in single-particle cryo-EM are overcome: (1) crossing 2 A resolution and (2) obtaining structures of proteins with sizes < 100 kDa, demonstrating that cryo-EM can be used to investigate a broad spectrum of drug-target interactions and dynamic conformational states.
-
-	Breaking Cryo-EM Resolution Barriers to Facilitate Drug Discovery.,Merk A, Bartesaghi A, Banerjee S, Falconieri V, Rao P, Davis MI, Pragani R, Boxer MB, Earl LA, Milne JL, Subramaniam S Cell. 2016 Jun 16;165(7):1698-707. doi: 10.1016/j.cell.2016.05.040. Epub 2016 May, 26. PMID:27238019<ref>PMID:27238019</ref>
-
-	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	</div>
-	<div class="pdbe-citations 5k12" style="background-color:#fffaf0;"></div>

	==See Also==		==See Also==

OCA at 19:17, 20 September 2023

OCA — Wed, 20 Sep 2023 19:17:36 GMT

←Older revision		Revision as of 19:17, 20 September 2023
Line 3:		Line 3:
	<SX load='5k12' size='340' side='right' viewer='molstar' caption='[[5k12]], [[Resolution\|resolution]] 1.80Å' scene=''>		<SX load='5k12' size='340' side='right' viewer='molstar' caption='[[5k12]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k12]] is a 6 chain structure with sequence from [~~http~~://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K12 OCA]. For a <b>guided tour on the structure components</b> use [~~http~~://proteopedia.org/fgij/fg.htm?mol=5K12 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k12]] is a 6 chain structure with sequence from [https://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K12 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K12 FirstGlance]. <br>
-	</td></tr><tr id='~~related~~'><td class="sblockLbl"><b>[[~~Related_structure~~\|~~Related~~:]]</b></td><td class="sblockDat">~~[[5k0z\|5k0z]]~~, [[~~5k10~~\|~~5k10~~]]~~, [[5k11\|5k11]]</td></tr>~~	+	</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models\|Method:]]</b></td><td class="sblockDat" id="methodDat">Electron Microscopy, [[Resolution\|Resolution]] 1.8Å</td></tr>
-	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutamate_dehydrogenase_(NAD(P)(+)) Glutamate dehydrogenase (NAD(P)(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.~~4.1.3 1.4.1.3] </span>~~</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=5k12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k12 OCA], [https://pdbe.org/5k12 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k12 RCSB], [https://www.ebi.ac.uk/pdbsum/5k12 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k12 ProSAT]</span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[~~http~~://proteopedia.org/fgij/fg.htm?mol=5k12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k12 OCA], [~~http~~://pdbe.org/5k12 PDBe], [~~http~~://www.rcsb.org/pdb/explore.do?structureId=5k12 RCSB], [~~http~~://www.ebi.ac.uk/pdbsum/5k12 PDBsum], [~~http~~://prosat.h-its.org/prosat/prosatexe?pdbcode=5k12 ProSAT]</span></td></tr>	+
	</table>		</table>
	== Function ==		== Function ==
-	[~~[http~~://www.uniprot.org/uniprot/DHE3_BOVIN DHE3_BOVIN]] May be involved in learning and memory reactions by increasing the turnover of the excitatory neurotransmitter glutamate (By similarity).<ref>PMID:14659072</ref>	+	[https://www.uniprot.org/uniprot/DHE3_BOVIN DHE3_BOVIN] May be involved in learning and memory reactions by increasing the turnover of the excitatory neurotransmitter glutamate (By similarity).<ref>PMID:14659072</ref>
	<div style="background-color:#fffaf0;">		<div style="background-color:#fffaf0;">
	== Publication Abstract from PubMed ==		== Publication Abstract from PubMed ==
Line 28:		Line 27:
	[[Category: Bos taurus]]		[[Category: Bos taurus]]
	[[Category: Large Structures]]		[[Category: Large Structures]]
-	[[Category: Banerjee, S]]	+	[[Category: Banerjee S]]
-	[[Category: Bartesaghi, A]]	+	[[Category: Bartesaghi A]]
-	[[Category: Earl, L]]	+	[[Category: Earl L]]
-	[[Category: Falconieri, V]]	+	[[Category: Falconieri V]]
-	[[Category: Merk, A]]	+	[[Category: Merk A]]
-	[[Category: Milne, J]]	+	[[Category: Milne J]]
-	[[Category: Rao, P]]	+	[[Category: Rao P]]
-	[[Category: Subramaniam, S]]	+	[[Category: Subramaniam S]]
-	~~[[Category: Glutamate dehydrogenase]]~~	+
-	~~[[Category: Oxidoreductase]]~~	+
-	~~[[Category: Small metabolic complex~~]]	+

OCA at 20:27, 10 April 2020

OCA — Fri, 10 Apr 2020 20:27:59 GMT

←Older revision		Revision as of 20:27, 10 April 2020
Line 3:		Line 3:
	<SX load='5k12' size='340' side='right' viewer='molstar' caption='[[5k12]], [[Resolution\|resolution]] 1.80Å' scene=''>		<SX load='5k12' size='340' side='right' viewer='molstar' caption='[[5k12]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
-	<table><tr><td colspan='2'>[[5k12]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K12 OCA]. For a <b>guided tour on the structure components</b> use [http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5K12 FirstGlance]. <br>	+	<table><tr><td colspan='2'>[[5k12]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K12 OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5K12 FirstGlance]. <br>
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k0z\|5k0z]], [[5k10\|5k10]], [[5k11\|5k11]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k0z\|5k0z]], [[5k10\|5k10]], [[5k11\|5k11]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutamate_dehydrogenase_(NAD(P)(+)) Glutamate dehydrogenase (NAD(P)(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.3 1.4.1.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutamate_dehydrogenase_(NAD(P)(+)) Glutamate dehydrogenase (NAD(P)(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.3 1.4.1.3] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://~~oca~~.~~weizmann.ac.il/oca-docs~~/fgij/fg.htm?mol=5k12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k12 OCA], [http://pdbe.org/5k12 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k12 RCSB], [http://www.ebi.ac.uk/pdbsum/5k12 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k12 ProSAT]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://proteopedia.org/fgij/fg.htm?mol=5k12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k12 OCA], [http://pdbe.org/5k12 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k12 RCSB], [http://www.ebi.ac.uk/pdbsum/5k12 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k12 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 18:45, 6 March 2020

OCA — Fri, 06 Mar 2020 18:45:54 GMT

←Older revision		Revision as of 18:45, 6 March 2020
Line 1:		Line 1:

	==Cryo-EM structure of glutamate dehydrogenase at 1.8 A resolution==		==Cryo-EM structure of glutamate dehydrogenase at 1.8 A resolution==
-	<~~StructureSection~~ load='5k12' size='340' side='right' caption='[[5k12]], [[Resolution\|resolution]] 1.80Å' scene=''>	+	<SX load='5k12' size='340' side='right' viewer='molstar' caption='[[5k12]], [[Resolution\|resolution]] 1.80Å' scene=''>
	== Structural highlights ==		== Structural highlights ==
	<table><tr><td colspan='2'>[[5k12]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K12 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K12 FirstGlance]. <br>		<table><tr><td colspan='2'>[[5k12]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K12 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K12 FirstGlance]. <br>
Line 21:		Line 21:

	==See Also==		==See Also==
-	*[[Glutamate dehydrogenase\|Glutamate dehydrogenase]]	+	*[[Glutamate dehydrogenase 3D structures\|Glutamate dehydrogenase 3D structures]]
	== References ==		== References ==
	<references/>		<references/>
	__TOC__		__TOC__
-	</~~StructureSection~~>	+	</SX>
	[[Category: Bos taurus]]		[[Category: Bos taurus]]
		+	[[Category: Large Structures]]
	[[Category: Banerjee, S]]		[[Category: Banerjee, S]]
	[[Category: Bartesaghi, A]]		[[Category: Bartesaghi, A]]

OCA at 08:47, 18 July 2018

OCA — Wed, 18 Jul 2018 08:47:41 GMT

←Older revision		Revision as of 08:47, 18 July 2018
Line 19:		Line 19:
	</div>		</div>
	<div class="pdbe-citations 5k12" style="background-color:#fffaf0;"></div>		<div class="pdbe-citations 5k12" style="background-color:#fffaf0;"></div>
		+
		+	==See Also==
		+	*[[Glutamate dehydrogenase\|Glutamate dehydrogenase]]
	== References ==		== References ==
	<references/>		<references/>

OCA at 17:52, 12 July 2016

OCA — Tue, 12 Jul 2016 17:52:19 GMT

←Older revision		Revision as of 17:52, 12 July 2016
Line 6:		Line 6:
	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k0z\|5k0z]], [[5k10\|5k10]], [[5k11\|5k11]]</td></tr>		</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k0z\|5k0z]], [[5k10\|5k10]], [[5k11\|5k11]]</td></tr>
	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutamate_dehydrogenase_(NAD(P)(+)) Glutamate dehydrogenase (NAD(P)(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.3 1.4.1.3] </span></td></tr>		<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutamate_dehydrogenase_(NAD(P)(+)) Glutamate dehydrogenase (NAD(P)(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.3 1.4.1.3] </span></td></tr>
-	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5k12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k12 OCA], [http://pdbe.org/5k12 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k12 RCSB], [http://www.ebi.ac.uk/pdbsum/5k12 PDBsum]</span></td></tr>	+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5k12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k12 OCA], [http://pdbe.org/5k12 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k12 RCSB], [http://www.ebi.ac.uk/pdbsum/5k12 PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k12 ProSAT]</span></td></tr>
	</table>		</table>
	== Function ==		== Function ==

OCA at 15:29, 20 June 2016

OCA — Mon, 20 Jun 2016 15:29:00 GMT

←Older revision		Revision as of 15:29, 20 June 2016
Line 1:		Line 1:
-	'''Unreleased structure'''

-	~~The entry~~ 5k12 is ~~ON HOLD~~	+	==Cryo-EM structure of glutamate dehydrogenase at 1.8 A resolution==
		+	<StructureSection load='5k12' size='340' side='right' caption='[[5k12]], [[Resolution\|resolution]] 1.80Å' scene=''>
		+	== Structural highlights ==
		+	<table><tr><td colspan='2'>[[5k12]] is a 6 chain structure with sequence from [http://en.wikipedia.org/wiki/Bos_taurus Bos taurus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K12 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5K12 FirstGlance]. <br>
		+	</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure\|Related:]]</b></td><td class="sblockDat">[[5k0z\|5k0z]], [[5k10\|5k10]], [[5k11\|5k11]]</td></tr>
		+	<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/Glutamate_dehydrogenase_(NAD(P)(+)) Glutamate dehydrogenase (NAD(P)(+))], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.4.1.3 1.4.1.3] </span></td></tr>
		+	<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5k12 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k12 OCA], [http://pdbe.org/5k12 PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k12 RCSB], [http://www.ebi.ac.uk/pdbsum/5k12 PDBsum]</span></td></tr>
		+	</table>
		+	== Function ==
		+	[[http://www.uniprot.org/uniprot/DHE3_BOVIN DHE3_BOVIN]] May be involved in learning and memory reactions by increasing the turnover of the excitatory neurotransmitter glutamate (By similarity).<ref>PMID:14659072</ref>
		+	<div style="background-color:#fffaf0;">
		+	== Publication Abstract from PubMed ==
		+	Recent advances in single-particle cryoelecton microscopy (cryo-EM) are enabling generation of numerous near-atomic resolution structures for well-ordered protein complexes with sizes >/= approximately 200 kDa. Whether cryo-EM methods are equally useful for high-resolution structural analysis of smaller, dynamic protein complexes such as those involved in cellular metabolism remains an important question. Here, we present 3.8 A resolution cryo-EM structures of the cancer target isocitrate dehydrogenase (93 kDa) and identify the nature of conformational changes induced by binding of the allosteric small-molecule inhibitor ML309. We also report 2.8-A- and 1.8-A-resolution structures of lactate dehydrogenase (145 kDa) and glutamate dehydrogenase (334 kDa), respectively. With these results, two perceived barriers in single-particle cryo-EM are overcome: (1) crossing 2 A resolution and (2) obtaining structures of proteins with sizes < 100 kDa, demonstrating that cryo-EM can be used to investigate a broad spectrum of drug-target interactions and dynamic conformational states.

-	~~Authors:~~ Merk, A., Bartesaghi, A., Banerjee, S., Falconieri, V., Rao, P., ~~Earl~~, L., ~~Milne~~, J., ~~Subramaniam~~, S.	+	Breaking Cryo-EM Resolution Barriers to Facilitate Drug Discovery.,Merk A, Bartesaghi A, Banerjee S, Falconieri V, Rao P, Davis MI, Pragani R, Boxer MB, Earl LA, Milne JL, Subramaniam S Cell. 2016 Jun 16;165(7):1698-707. doi: 10.1016/j.cell.2016.05.040. Epub 2016 May, 26. PMID:27238019<ref>PMID:27238019</ref>

-	~~Description: Cryo-EM structure~~ of ~~glutamate dehydrogenase at 1~~.~~8 A resolution~~	+	From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>
-	~~[[Category: Unreleased Structures]]~~	+	</div>
-	~~[[Category~~: ~~Milne, J]]~~	+	<div class="pdbe-citations 5k12" style="background-color:#fffaf0;"></div>
-	~~[[Category: Merk, A]]~~	+	== References ==
-	~~[[Category: Falconieri, V]]~~	+	<references/>
-	[[Category: ~~Earl, L~~]]	+	__TOC__
		+	</StructureSection>
		+	[[Category: Bos taurus]]
	[[Category: Banerjee, S]]		[[Category: Banerjee, S]]
	[[Category: Bartesaghi, A]]		[[Category: Bartesaghi, A]]
		+	[[Category: Earl, L]]
		+	[[Category: Falconieri, V]]
		+	[[Category: Merk, A]]
		+	[[Category: Milne, J]]
	[[Category: Rao, P]]		[[Category: Rao, P]]
	[[Category: Subramaniam, S]]		[[Category: Subramaniam, S]]
		+	[[Category: Glutamate dehydrogenase]]
		+	[[Category: Oxidoreductase]]
		+	[[Category: Small metabolic complex]]

OCA: Protected "5k12" [edit=sysop:move=sysop]

OCA — Wed, 01 Jun 2016 14:10:15 GMT

Protected "5k12" [edit=sysop:move=sysop]

←Older revision

Revision as of 14:10, 1 June 2016

OCA: New page: '''Unreleased structure''' The entry 5k12 is ON HOLD Authors: Merk, A., Bartesaghi, A., Banerjee, S., Falconieri, V., Rao, P., Earl, L., Milne, J., Subramaniam, S. Description: Cryo-EM...

OCA — Wed, 01 Jun 2016 14:10:14 GMT

New page: '''Unreleased structure''' The entry 5k12 is ON HOLD Authors: Merk, A., Bartesaghi, A., Banerjee, S., Falconieri, V., Rao, P., Earl, L., Milne, J., Subramaniam, S. Description: Cryo-EM...

New page

'''Unreleased structure'''

The entry 5k12 is ON HOLD

Authors: Merk, A., Bartesaghi, A., Banerjee, S., Falconieri, V., Rao, P., Earl, L., Milne, J., Subramaniam, S.

Description: Cryo-EM structure of glutamate dehydrogenase at 1.8 A resolution
[[Category: Unreleased Structures]]
[[Category: Milne, J]]
[[Category: Merk, A]]
[[Category: Falconieri, V]]
[[Category: Earl, L]]
[[Category: Banerjee, S]]
[[Category: Bartesaghi, A]]
[[Category: Rao, P]]
[[Category: Subramaniam, S]]