+Open data
-Basic information
Entry | Database: PDB / ID: 6pdt | ||||||
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Title | cryoEM structure of yeast glucokinase filament | ||||||
Components | Glucokinase-1 | ||||||
Keywords | TRANSFERASE / filament | ||||||
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) | ||||||
Method | ELECTRON MICROSCOPY / helical reconstruction / cryo EM / Resolution: 3.8 Å | ||||||
Model details | MODEL GENERATED BY ROSETTA VERSION 2019.21.post.dev+31.master.d8f9b4a90a8 | ||||||
Authors | Lynch, E.M. / Dosey, A.M. / Farrell, D.P. / Stoddard, P.R. / Kollman, J.M. | ||||||
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 | Molecule: MolmilJmol/JSmol |
-Downloads & links
-Download
PDBx/mmCIF format | 6pdt.cif.gz | 636 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pdt.ent.gz | 524.9 KB | Display | PDB format |
PDBx/mmJSON format | 6pdt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pdt_validation.pdf.gz | 1004.5 KB | Display | wwPDB validaton report |
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Full document | 6pdt_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6pdt_validation.xml.gz | 57 KB | Display | |
Data in CIF | 6pdt_validation.cif.gz | 83.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pd/6pdt ftp://data.pdbj.org/pub/pdb/validation_reports/pd/6pdt | HTTPS FTP |
-Related structure data
Related structure data | 20309MC 6p4xC M: map data used to model this data C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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-Components
#1: Protein | Mass: 55446.258 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (yeast) Strain: ATCC 204508 / S288c / Gene: GLK1, HOR3, YCL040W, YCL312, YCL40W / Production host: Escherichia coli (E. coli) / References: UniProt: P17709, glucokinase #2: Sugar | ChemComp-GLC / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-ATP / Has ligand of interest | N | Has protein modification | Y | |
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-Experimental details
-Experiment
Experiment | Method: ELECTRON MICROSCOPY |
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EM experiment | Aggregation state: FILAMENT / 3D reconstruction method: helical reconstruction |
-Sample preparation
Component | Name: glucokinase-1 / Type: COMPLEX / Entity ID: #1 / Source: RECOMBINANT |
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Molecular weight | Experimental value: NO |
Source (natural) | Organism: Saccharomyces cerevisiae (brewer's yeast) |
Source (recombinant) | Organism: Escherichia coli (E. coli) |
Buffer solution | pH: 7.5 |
Specimen | Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES |
Vitrification | Cryogen name: ETHANE / Humidity: 100 % |
-Electron microscopy imaging
Experimental equipment | Model: Titan Krios / Image courtesy: FEI Company |
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Microscopy | Model: FEI TITAN KRIOS |
Electron gun | Electron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM |
Electron lens | Mode: BRIGHT FIELD |
Image recording | Electron dose: 90 e/Å2 / Detector mode: SUPER-RESOLUTION / Film or detector model: GATAN K2 SUMMIT (4k x 4k) |
-Processing
EM software |
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CTF correction | Type: PHASE FLIPPING AND AMPLITUDE CORRECTION | |||||||||||||||||||||||||||
Helical symmerty | Angular rotation/subunit: 120.4 ° / Axial rise/subunit: 60.1 Å / Axial symmetry: D1 | |||||||||||||||||||||||||||
3D reconstruction | Resolution: 3.8 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 56778 / Symmetry type: HELICAL |