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TitleBreaking Cryo-EM Resolution Barriers to Facilitate Drug Discovery.
Journal, issue, pagesCell, Vol. 165, Issue 7, Page 1698-1707, Year 2016
Publish dateJun 16, 2016
AuthorsAlan Merk / Alberto Bartesaghi / Soojay Banerjee / Veronica Falconieri / Prashant Rao / Mindy I Davis / Rajan Pragani / Matthew B Boxer / Lesley A Earl / Jacqueline L S Milne / Sriram Subramaniam /
PubMed AbstractRecent advances in single-particle cryoelecton microscopy (cryo-EM) are enabling generation of numerous near-atomic resolution structures for well-ordered protein complexes with sizes ≥ ∼200 kDa. ...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 ≥ ∼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 Å 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-Å- and 1.8-Å-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 Å 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.
External linksCell / PubMed:27238019 / PubMed Central
MethodsEM (single particle)
Resolution1.8 - 3.8 Å
Structure data

8191

5k0z

EMDB-8191: Cryo-EM structure of lactate dehydrogenase (LDH) in complex with GSK2837808A
PDB-5k0z: Cryo-EM structure of lactate dehydrogenase (LDH) in inhibitor-bound state
Method: EM (single particle) / Resolution: 2.8 Å

8192

5k10

EMDB-8192, PDB-5k10:
Cryo-EM structure of isocitrate dehydrogenase (IDH1)
Method: EM (single particle) / Resolution: 3.8 Å

8193

5k11

EMDB-8193: Cryo-EM structure of isocitrate dehydrogenase (IDH1) in complex with ML309 inhibitor
PDB-5k11: Cryo-EM structure of isocitrate dehydrogenase (IDH1) in inhibitor-bound state
Method: EM (single particle) / Resolution: 3.8 Å

8194

5k12

EMDB-8194, PDB-5k12:
Cryo-EM structure of glutamate dehydrogenase at 1.8 A resolution
Method: EM (single particle) / Resolution: 1.8 Å

Chemicals

ChemComp-HOH:
WATER

ChemComp-NDP:
NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Source
  • gallus gallus (chicken)
  • homo sapiens (human)
  • bos taurus (cattle)
KeywordsOXIDOREDUCTASE / lactate dehydrogenase / small metabolic complex / small molecule inhibitor / isocitrate dehydrogenase / glutamate dehydrogenase

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