5k0z: Difference between revisions

Revision as of 22:17, 20 September 2023

Cryo-EM structure of lactate dehydrogenase (LDH) in inhibitor-bound stateCryo-EM structure of lactate dehydrogenase (LDH) in inhibitor-bound state

5k0z, resolution 2.80Å

Structural highlights

5k0z is a 4 chain structure with sequence from Gallus gallus. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance.
Method:	Electron Microscopy, Resolution 2.8Å
Experimental data:	Check
Resources:	FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT

Function

LDHB_CHICK

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^[1]

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

References

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

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OCA

[1] Merk A, Bartesaghi A, Banerjee S, Falconieri V, Rao P, Davis MI, Pragani R, Boxer MB, Earl LA, Milne JL, Subramaniam S. Breaking Cryo-EM Resolution Barriers to Facilitate Drug Discovery. Cell. 2016 Jun 16;165(7):1698-707. doi: 10.1016/j.cell.2016.05.040. Epub 2016 May, 26. PMID:27238019 doi:http://dx.doi.org/10.1016/j.cell.2016.05.040

[1]

@@ Line 3: / Line 3: @@
 <SX load='5k0z' size='340' side='right' viewer='molstar' caption='[[5k0z]], [[Resolution|resolution]] 2.80&Aring;' scene=''>
 == Structural highlights ==
-<table><tr><td colspan='2'>[[5k0z]] is a 4 chain structure with sequence from [http://en.wikipedia.org/wiki/Chick Chick]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K0Z OCA]. For a <b>guided tour on the structure components</b> use [http://proteopedia.org/fgij/fg.htm?mol=5K0Z FirstGlance]. <br>
+<table><tr><td colspan='2'>[[5k0z]] is a 4 chain structure with sequence from [https://en.wikipedia.org/wiki/Gallus_gallus Gallus gallus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5K0Z OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5K0Z FirstGlance]. <br>
-</td></tr><tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[5k10|5k10]], [[5k11|5k11]], [[5k12|5k12]]</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]] 2.8&#8491;</td></tr>
-<tr id='gene'><td class="sblockLbl"><b>[[Gene|Gene:]]</b></td><td class="sblockDat">LDHB ([http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&srchmode=5&id=9031 CHICK])</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=5k0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k0z OCA], [https://pdbe.org/5k0z PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5k0z RCSB], [https://www.ebi.ac.uk/pdbsum/5k0z PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5k0z ProSAT]</span></td></tr>
-<tr id='activity'><td class="sblockLbl"><b>Activity:</b></td><td class="sblockDat"><span class='plainlinks'>[http://en.wikipedia.org/wiki/L-lactate_dehydrogenase L-lactate dehydrogenase], with EC number [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.1.1.27 1.1.1.27] </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=5k0z FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5k0z OCA], [http://pdbe.org/5k0z PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5k0z RCSB], [http://www.ebi.ac.uk/pdbsum/5k0z PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5k0z ProSAT]</span></td></tr>
 </table>
+== Function ==
+[https://www.uniprot.org/uniprot/LDHB_CHICK LDHB_CHICK]
 <div style="background-color:#fffaf0;">
 == Publication Abstract from PubMed ==
@@ Line 25: / Line 25: @@
 __TOC__
 </SX>
-[[Category: Chick]]
+[[Category: Gallus gallus]]
-[[Category: L-lactate dehydrogenase]]
 [[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: Lactate dehydrogenase]]
-[[Category: Oxidoreductase]]
-[[Category: Small metabolic complex]]
-[[Category: Small molecule inhibitor]]

5k0z: Difference between revisions

Revision as of 22:17, 20 September 2023

Cryo-EM structure of lactate dehydrogenase (LDH) in inhibitor-bound stateCryo-EM structure of lactate dehydrogenase (LDH) in inhibitor-bound state

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Contents

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5k0z: Difference between revisions

Revision as of 22:17, 20 September 2023

Cryo-EM structure of lactate dehydrogenase (LDH) in inhibitor-bound stateCryo-EM structure of lactate dehydrogenase (LDH) in inhibitor-bound state

Structural highlights

Function

Publication Abstract from PubMed

See Also

References

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Navigation menu

Search