+Open data
-Basic information
Entry | Database: EMDB / ID: EMD-20309 | |||||||||
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Title | cryoEM structure of yeast glucokinase filament | |||||||||
Map data | cryoEM structure of yeast glucokinase filament | |||||||||
Sample |
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Keywords | filament / TRANSFERASE | |||||||||
Function / homology | Function and homology information Regulation of Glucokinase by Glucokinase Regulatory Protein / Synthesis of GDP-mannose / glucokinase / Glycolysis / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / mannose metabolic process / glucose 6-phosphate metabolic process / D-glucose binding ...Regulation of Glucokinase by Glucokinase Regulatory Protein / Synthesis of GDP-mannose / glucokinase / Glycolysis / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / mannose metabolic process / glucose 6-phosphate metabolic process / D-glucose binding / D-glucose import / intracellular glucose homeostasis / Neutrophil degranulation / glycolytic process / glucose metabolic process / mitochondrion / ATP binding / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | Saccharomyces cerevisiae (brewer's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) | |||||||||
Method | helical reconstruction / cryo EM / Resolution: 3.8 Å | |||||||||
Authors | Lynch EM / Dosey AM | |||||||||
Citation | Journal: Science / Year: 2020 Title: Polymerization in the actin ATPase clan regulates hexokinase activity in yeast. Authors: Patrick R Stoddard / Eric M Lynch / Daniel P Farrell / Annie M Dosey / Frank DiMaio / Tom A Williams / Justin M Kollman / Andrew W Murray / Ethan C Garner / Abstract: The actin fold is found in cytoskeletal polymers, chaperones, and various metabolic enzymes. Many actin-fold proteins, such as the carbohydrate kinases, do not polymerize. We found that Glk1, a ...The actin fold is found in cytoskeletal polymers, chaperones, and various metabolic enzymes. Many actin-fold proteins, such as the carbohydrate kinases, do not polymerize. We found that Glk1, a glucokinase, forms two-stranded filaments with ultrastructure that is distinct from that of cytoskeletal polymers. In cells, Glk1 polymerized upon sugar addition and depolymerized upon sugar withdrawal. Polymerization inhibits enzymatic activity; the Glk1 monomer-polymer equilibrium sets a maximum rate of glucose phosphorylation regardless of Glk1 concentration. A mutation that eliminated Glk1 polymerization alleviated concentration-dependent enzyme inhibition. Yeast containing nonpolymerizing Glk1 were less fit when growing on sugars and more likely to die when refed glucose. Glk1 polymerization arose independently from other actin-related filaments and may allow yeast to rapidly modulate glucokinase activity as nutrient availability changes. | |||||||||
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_20309.map.gz | 7.4 MB | EMDB map data format | |
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Header (meta data) | emd-20309-v30.xml emd-20309.xml | 11.1 KB 11.1 KB | Display Display | EMDB header |
Images | emd_20309.png | 137.1 KB | ||
Filedesc metadata | emd-20309.cif.gz | 5.5 KB | ||
Archive directory | http://ftp.pdbj.org/pub/emdb/structures/EMD-20309 ftp://ftp.pdbj.org/pub/emdb/structures/EMD-20309 | HTTPS FTP |
-Validation report
Summary document | emd_20309_validation.pdf.gz | 355.3 KB | Display | EMDB validaton report |
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Full document | emd_20309_full_validation.pdf.gz | 354.9 KB | Display | |
Data in XML | emd_20309_validation.xml.gz | 6.5 KB | Display | |
Data in CIF | emd_20309_validation.cif.gz | 7.5 KB | Display | |
Arichive directory | https://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20309 ftp://ftp.pdbj.org/pub/emdb/validation_reports/EMD-20309 | HTTPS FTP |
-Related structure data
Related structure data | 6pdtMC 6p4xC M: atomic model generated by this map C: citing same article (ref.) |
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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_20309.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES) | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Annotation | cryoEM structure of yeast glucokinase filament | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Projections & slices | Image control
Images are generated by Spider. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.05 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
-Sample components
-Entire : glucokinase-1
Entire | Name: glucokinase-1 |
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Components |
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-Supramolecule #1: glucokinase-1
Supramolecule | Name: glucokinase-1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1 |
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Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
-Macromolecule #1: Glucokinase-1
Macromolecule | Name: Glucokinase-1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: glucokinase |
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Source (natural) | Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c |
Molecular weight | Theoretical: 55.446258 KDa |
Recombinant expression | Organism: Escherichia coli (E. coli) |
Sequence | String: MSFDDLHKAT ERAVIQAVDQ ICDDFEVTPE KLDELTAYFI EQMEKGLAPP KEGHTLASDK GLPMIPAFVT GSPNGTERGV LLAADLGGT NFRICSVNLH GDHTFSMEQM KSKIPDDLLD DENVTSDDLF GFLARRTLAF MKKYHPDELA KGKDAKPMKL G FTFSYPVD ...String: MSFDDLHKAT ERAVIQAVDQ ICDDFEVTPE KLDELTAYFI EQMEKGLAPP KEGHTLASDK GLPMIPAFVT GSPNGTERGV LLAADLGGT NFRICSVNLH GDHTFSMEQM KSKIPDDLLD DENVTSDDLF GFLARRTLAF MKKYHPDELA KGKDAKPMKL G FTFSYPVD QTSLNSGTLI RWTKGFRIAD TVGKDVVQLY QEQLSAQGMP MIKVVALTND TVGTYLSHCY TSDNTDSMTS GE ISEPVIG CIFGTGTNGC YMEEINKITK LPQELRDKLI KEGKTHMIIN VEWGSFDNEL KHLPTTKYDV VIDQKLSTNP GFH LFEKRV SGMFLGEVLR NILVDLHSQG LLLQQYRSKE QLPRHLTTPF QLSSEVLSHI EIDDSTGLRE TELSLLQSLR LPTT PTERV QIQKLVRAIS RRSAYLAAVP LAAILIKTNA LNKRYHGEVE IGCDGSVVEY YPGFRSMLRH ALALSPLGAE GERKV HLKI AKDGSGVGAA LCALVA UniProtKB: Glucokinase-1 |
-Macromolecule #2: alpha-D-glucopyranose
Macromolecule | Name: alpha-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 4 / Formula: GLC |
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Molecular weight | Theoretical: 180.156 Da |
Chemical component information | ChemComp-GLC: |
-Macromolecule #3: MAGNESIUM ION
Macromolecule | Name: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: MG |
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Molecular weight | Theoretical: 24.305 Da |
-Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE
Macromolecule | Name: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 4 / Formula: ATP |
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Molecular weight | Theoretical: 507.181 Da |
Chemical component information | ChemComp-ATP: |
-Experimental details
-Structure determination
Method | cryo EM |
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Processing | helical reconstruction |
Aggregation state | filament |
-Sample preparation
Buffer | pH: 7.5 |
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Vitrification | Cryogen name: ETHANE / Chamber humidity: 100 % |
-Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 90.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN |
Electron optics | Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD |
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
-Image processing
Final reconstruction | Applied symmetry - Helical parameters - Δz: 60.1 Å Applied symmetry - Helical parameters - Δ&Phi: 120.4 ° Applied symmetry - Helical parameters - Axial symmetry: D1 (2x1 fold dihedral) Resolution.type: BY AUTHOR / Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION / Number images used: 56778 |
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Startup model | Type of model: OTHER |
Final angle assignment | Type: NOT APPLICABLE / Software - Name: RELION |