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- EMDB-8193: Cryo-EM structure of isocitrate dehydrogenase (IDH1) in complex w... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-8193 | |||||||||
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Title | Cryo-EM structure of isocitrate dehydrogenase (IDH1) in complex with ML309 inhibitor | |||||||||
![]() | Isocitrate dehydrogenase (IDH1) in complex with ML309 inhibitor | |||||||||
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![]() | isocitrate dehydrogenase / small metabolic complex / small molecule inhibitor / OXIDOREDUCTASE | |||||||||
Function / homology | ![]() Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate / regulation of phospholipid catabolic process / NADPH regeneration / regulation of phospholipid biosynthetic process / NFE2L2 regulating TCA cycle genes / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process ...Abnormal conversion of 2-oxoglutarate to 2-hydroxyglutarate / regulation of phospholipid catabolic process / NADPH regeneration / regulation of phospholipid biosynthetic process / NFE2L2 regulating TCA cycle genes / isocitrate metabolic process / isocitrate dehydrogenase (NADP+) / isocitrate dehydrogenase (NADP+) activity / 2-oxoglutarate metabolic process / NADP metabolic process / glyoxylate cycle / response to steroid hormone / female gonad development / peroxisomal matrix / tricarboxylic acid cycle / glutathione metabolic process / Peroxisomal protein import / NAD binding / tertiary granule lumen / peroxisome / NADP binding / secretory granule lumen / response to oxidative stress / ficolin-1-rich granule lumen / cadherin binding / Neutrophil degranulation / magnesium ion binding / protein homodimerization activity / mitochondrion / extracellular exosome / extracellular region / identical protein binding / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
![]() | Merk A / Bartesaghi A | |||||||||
![]() | ![]() Title: Breaking Cryo-EM Resolution Barriers to Facilitate Drug Discovery. Authors: Alan 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 / ![]() Abstract: 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. ...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. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 26.8 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 19.3 KB 19.3 KB | Display Display | ![]() |
Images | ![]() | 52.8 KB | ||
Filedesc metadata | ![]() | 6.2 KB | ||
Others | ![]() ![]() | 27.2 MB 27.5 MB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5k11MC ![]() 8191C ![]() 8192C ![]() 8194C ![]() 5k0zC ![]() 5k10C ![]() 5k12C C: citing same article ( M: atomic model generated by this map |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Isocitrate dehydrogenase (IDH1) in complex with ML309 inhibitor | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 0.495 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Additional map: Map sharpened using a B-factor of -180
File | emd_8193_additional_1.map | ||||||||||||
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Annotation | Map sharpened using a B-factor of -180 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Additional map: Reconstruction obtained without imposing symmetry
File | emd_8193_additional_2.map | ||||||||||||
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Annotation | Reconstruction obtained without imposing symmetry | ||||||||||||
Projections & Slices |
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Density Histograms |
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Sample components
-Entire : Isocitrate dehydrogenase R132C mutant in complex with ML309
Entire | Name: Isocitrate dehydrogenase R132C mutant in complex with ML309 |
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Components |
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-Supramolecule #1: Isocitrate dehydrogenase R132C mutant in complex with ML309
Supramolecule | Name: Isocitrate dehydrogenase R132C mutant in complex with ML309 type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 93 KDa |
-Macromolecule #1: Isocitrate dehydrogenase [NADP] cytoplasmic
Macromolecule | Name: Isocitrate dehydrogenase [NADP] cytoplasmic / type: protein_or_peptide / ID: 1 / Number of copies: 2 / Enantiomer: LEVO / EC number: isocitrate dehydrogenase (NADP+) |
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Source (natural) | Organism: ![]() |
Molecular weight | Theoretical: 46.334742 KDa |
Recombinant expression | Organism: ![]() |
Sequence | String: KKISGGSVVE MQGDEMTRII WELIKEKLIF PYVELDLHSY DLGIENRDAT NDQVTKDAAE AIKKHNVGVK CATITPDEKR VEEFKLKQM WKSPNGTIRN ILGGTVFREA IICKNIPRLV SGWVKPIIIG CHAYGDQYRA TDFVVPGPGK VEITYTPSDG T QKVTYLVH ...String: KKISGGSVVE MQGDEMTRII WELIKEKLIF PYVELDLHSY DLGIENRDAT NDQVTKDAAE AIKKHNVGVK CATITPDEKR VEEFKLKQM WKSPNGTIRN ILGGTVFREA IICKNIPRLV SGWVKPIIIG CHAYGDQYRA TDFVVPGPGK VEITYTPSDG T QKVTYLVH NFEEGGGVAM GMYNQDKSIE DFAHSSFQMA LSKGWPLYLS TKNTILKKYD GRFKDIFQEI YDKQYKSQFE AQ KIWYEHR LIDDMVAQAM KSEGGFIWAC KNYDGDVQSD SVAQGYGSLG MMTSVLVCPD GKTVEAEAAH GTVTRHYRMY QKG QETSTN PIASIFAWTR GLAHRAKLDN NKELAFFANA LEEVSIETIE AGFMTKDLAA CIKGLPNVQR SDYLNTFEFM DKLG ENLKI KLAQAK UniProtKB: Isocitrate dehydrogenase [NADP] cytoplasmic |
-Macromolecule #2: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Macromolecule | Name: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE type: ligand / ID: 2 / Number of copies: 2 / Formula: NDP |
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Molecular weight | Theoretical: 745.421 Da |
Chemical component information | ![]() ChemComp-NDP: |
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Concentration | 2.8 mg/mL | ||||||||||||
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Buffer | pH: 7.5 Component:
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Grid | Model: Quantifoil R1.2/1.3 / Material: COPPER / Mesh: 300 / Support film - Material: CARBON / Support film - topology: HOLEY / Pretreatment - Type: PLASMA CLEANING | ||||||||||||
Vitrification | Cryogen name: ETHANE / Instrument: LEICA EM GP / Details: Plunged into liquid ethane (LEICA EM GP). |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Temperature | Min: 79.6 K / Max: 79.8 K |
Specialist optics | Energy filter - Name: GIF Quantum / Energy filter - Lower energy threshold: 0 eV / Energy filter - Upper energy threshold: 20 eV |
Image recording | Film or detector model: GATAN K2 QUANTUM (4k x 4k) / Detector mode: SUPER-RESOLUTION / Digitization - Frames/image: 0-29 / Number real images: 820 / Average exposure time: 0.2 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: ![]() |
Electron optics | Calibrated magnification: 101000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.6 µm / Nominal defocus min: 0.7000000000000001 µm / Nominal magnification: 270000 |
Sample stage | Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER / Cooling holder cryogen: NITROGEN |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |
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Image processing
-Atomic model buiding 1
Refinement | Space: REAL / Protocol: FLEXIBLE FIT |
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Output model | ![]() PDB-5k11: |