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Yorodumi- EMDB-8191: Cryo-EM structure of lactate dehydrogenase (LDH) in complex with ... -
+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-8191 | |||||||||
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Title | Cryo-EM structure of lactate dehydrogenase (LDH) in complex with GSK2837808A | |||||||||
Map data | Lactate dehydrogenase (LDH) in complex with GSK2837808A | |||||||||
Sample |
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Keywords | lactate dehydrogenase / small metabolic complex / small molecule inhibitor / OXIDOREDUCTASE | |||||||||
Function / homology | Function and homology information Pyruvate metabolism / Pyruvate metabolism / L-lactate dehydrogenase / carboxylic acid metabolic process / L-lactate dehydrogenase activity / carbohydrate metabolic process / cytosol Similarity search - Function | |||||||||
Biological species | Gallus gallus (chicken) | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 2.8 Å | |||||||||
Authors | Merk A / Bartesaghi A | |||||||||
Citation | Journal: Cell / Year: 2016 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 |
Movie viewer |
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Structure viewer | EM map: SurfViewMolmilJmol/JSmol |
Supplemental images |
-Downloads & links
-EMDB archive
Map data | emd_8191.map.gz | 19.7 MB | EMDB map data format | |
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Header (meta data) | emd-8191-v30.xml emd-8191.xml | 16.6 KB 16.6 KB | Display Display | EMDB header |
Images | emd_8191.png | 169.7 KB | ||
Filedesc metadata | emd-8191.cif.gz | 6.1 KB | ||
Others | emd_8191_additional.map.gz | 19.9 MB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-8191 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-8191 | HTTPS FTP |
-Validation report
Summary document | emd_8191_validation.pdf.gz | 505.5 KB | Display | EMDB validaton report |
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Full document | emd_8191_full_validation.pdf.gz | 505 KB | Display | |
Data in XML | emd_8191_validation.xml.gz | 5.6 KB | Display | |
Data in CIF | emd_8191_validation.cif.gz | 6.3 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8191 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-8191 | HTTPS FTP |
-Related structure data
Related structure data | 5k0zMC 8192C 8193C 8194C 5k10C 5k11C 5k12C C: citing same article (ref.) M: atomic model generated by this map |
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Similar structure data |
-Links
EMDB pages | EMDB (EBI/PDBe) / EMDataResource |
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Related items in Molecule of the Month |
-Map
File | Download / File: emd_8191.map.gz / Format: CCP4 / Size: 22.2 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | Lactate dehydrogenase (LDH) in complex with GSK2837808A | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 -150
File | emd_8191_additional.map | ||||||||||||
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Annotation | Map sharpened using a B-factor of -150 | ||||||||||||
Projections & Slices |
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Density Histograms |
-Sample components
-Entire : Lactate dehydrogenase (LDH) in complex with GSK2837808A
Entire | Name: Lactate dehydrogenase (LDH) in complex with GSK2837808A |
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Components |
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-Supramolecule #1: Lactate dehydrogenase (LDH) in complex with GSK2837808A
Supramolecule | Name: Lactate dehydrogenase (LDH) in complex with GSK2837808A type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Gallus gallus (chicken) |
Molecular weight | Theoretical: 145 KDa |
-Macromolecule #1: L-lactate dehydrogenase B chain
Macromolecule | Name: L-lactate dehydrogenase B chain / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: L-lactate dehydrogenase |
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Source (natural) | Organism: Gallus gallus (chicken) |
Molecular weight | Theoretical: 36.115656 KDa |
Recombinant expression | Organism: Bacteria (eubacteria) |
Sequence | String: ATLKEKLITP VAAGSTVPSN KITVVGVGQV GMACAISILG KGLCDELALV DVLEDKLKGE MMDLQHGSLF LQTHKIVADK DYAVTANSK IVVVTAGVRQ QEGESRLNLV QRNVNVFKFI IPQIVKYSPN CTILVVSNPV DILTYVTWKL SGLPKHRVIG S GCNLDTAR ...String: ATLKEKLITP VAAGSTVPSN KITVVGVGQV GMACAISILG KGLCDELALV DVLEDKLKGE MMDLQHGSLF LQTHKIVADK DYAVTANSK IVVVTAGVRQ QEGESRLNLV QRNVNVFKFI IPQIVKYSPN CTILVVSNPV DILTYVTWKL SGLPKHRVIG S GCNLDTAR FRYLMAERLG IHPTSCHGWI LGEHGDSSVA VWSGVNVAGV SLQELNPAMG TDKDSENWKE VHKQVVESAY EV IRLKGYT NWAIGLSVAE LCETMLKNLY RVHSVSTLVK GTYGIENDVF LSLPCVLSAS GLTSVINQKL KDDEVAQLKK SAD TLWSIQ KDLKD UniProtKB: L-lactate dehydrogenase B chain |
-Macromolecule #2: water
Macromolecule | Name: water / type: ligand / ID: 2 / Number of copies: 41 / Formula: HOH |
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Molecular weight | Theoretical: 18.015 Da |
Chemical component information | ChemComp-HOH: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | single particle reconstruction |
Aggregation state | particle |
-Sample preparation
Concentration | 1.5 mg/mL |
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Buffer | pH: 7.4 / Component - Name: PBS / Details: Phosphate-buffered saline |
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 (LEICE EM GP). |
-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: 1707 / Average exposure time: 0.2 sec. / Average electron dose: 60.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Calibrated magnification: 101000 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.2 µm / Nominal defocus min: 0.8 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 |