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- EMDB-20309: cryoEM structure of yeast glucokinase filament -

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Basic information

Entry
Database: EMDB / ID: EMD-20309
TitlecryoEM structure of yeast glucokinase filament
Map datacryoEM structure of yeast glucokinase filament
Sample
  • Complex: glucokinase-1
    • Protein or peptide: Glucokinase-1
  • Ligand: alpha-D-glucopyranose
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE
Function / homology
Function and homology information


Regulation of Glucokinase by Glucokinase Regulatory Protein / glucokinase / Glycolysis / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / glucose 6-phosphate metabolic process / mannose metabolic process / glucose binding / cellular glucose homeostasis ...Regulation of Glucokinase by Glucokinase Regulatory Protein / glucokinase / Glycolysis / fructokinase activity / carbohydrate phosphorylation / glucokinase activity / glucose 6-phosphate metabolic process / mannose metabolic process / glucose binding / cellular glucose homeostasis / glucose import / Neutrophil degranulation / glycolytic process / glucose metabolic process / mitochondrion / ATP binding / plasma membrane / cytosol
Similarity search - Function
Hexokinase / Hexokinase domain profile. / Hexokinase domain signature. / Hexokinase / Hexokinase / Hexokinase, C-terminal / Hexokinase, N-terminal / Hexokinase, binding site / ATPase, nucleotide binding domain
Similarity search - Domain/homology
Biological speciesSaccharomyces cerevisiae (baker's yeast) / Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (unknown)
Methodhelical reconstruction / cryo EM / Resolution: 3.8 Å
AuthorsLynch EM / Dosey AM / Farrell DP / Stoddard PR / Kollman JM
CitationJournal: 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
DepositionJun 19, 2019-
Header (metadata) releaseJul 17, 2019-
Map releaseMar 11, 2020-
UpdateJul 29, 2020-
Current statusJul 29, 2020Processing site: RCSB / Status: Released

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Structure visualization

Movie
  • Surface view with section colored by density value
  • Surface level: 0.026
  • Imaged by UCSF Chimera
  • Download
  • Surface view colored by cylindrical radius
  • Surface level: 0.026
  • Imaged by UCSF Chimera
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  • Surface view with fitted model
  • Atomic models: PDB-6pdt
  • Surface level: 0.026
  • Imaged by UCSF Chimera
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Movie viewer
Structure viewerEM map:
SurfViewMolmilJmol/JSmol
Supplemental images

Downloads & links

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Map

FileDownload / File: emd_20309.map.gz / Format: CCP4 / Size: 125 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationcryoEM structure of yeast glucokinase filament
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.05 Å/pix.
x 320 pix.
= 336. Å
1.05 Å/pix.
x 320 pix.
= 336. Å
1.05 Å/pix.
x 320 pix.
= 336. Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.05 Å
Density
Contour LevelBy AUTHOR: 0.026 / Movie #1: 0.026
Minimum - Maximum-0.07363354 - 0.12467296
Average (Standard dev.)0.0001642885 (±0.0026356839)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions320320320
Spacing320320320
CellA=B=C: 336.0 Å
α=β=γ: 90.0 °

CCP4 map header:

modeImage stored as Reals
Å/pix. X/Y/Z1.051.051.05
M x/y/z320320320
origin x/y/z0.0000.0000.000
length x/y/z336.000336.000336.000
α/β/γ90.00090.00090.000
start NX/NY/NZ-200-200-200
NX/NY/NZ401401401
MAP C/R/S123
start NC/NR/NS000
NC/NR/NS320320320
D min/max/mean-0.0740.1250.000

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Supplemental data

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Sample components

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Entire : glucokinase-1

EntireName: glucokinase-1
Components
  • Complex: glucokinase-1
    • Protein or peptide: Glucokinase-1
  • Ligand: alpha-D-glucopyranose
  • Ligand: MAGNESIUM ION
  • Ligand: ADENOSINE-5'-TRIPHOSPHATE

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Supramolecule #1: glucokinase-1

SupramoleculeName: glucokinase-1 / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1
Source (natural)Organism: Saccharomyces cerevisiae (baker's yeast)
Recombinant expressionOrganism: Escherichia coli (E. coli)

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Macromolecule #1: Glucokinase-1

MacromoleculeName: Glucokinase-1 / type: protein_or_peptide / ID: 1 / Number of copies: 4 / Enantiomer: LEVO / EC number: glucokinase
Source (natural)Organism: Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (unknown)
Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 55.446258 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: 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

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Macromolecule #2: alpha-D-glucopyranose

MacromoleculeName: alpha-D-glucopyranose / type: ligand / ID: 2 / Number of copies: 4 / Formula: GLC
Molecular weightTheoretical: 180.156 Da
Chemical component information

ChemComp-GLC:
alpha-D-glucopyranose / Glucose

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Macromolecule #3: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 3 / Number of copies: 4 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Macromolecule #4: ADENOSINE-5'-TRIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-TRIPHOSPHATE / type: ligand / ID: 4 / Number of copies: 4 / Formula: ATP
Molecular weightTheoretical: 507.181 Da
Chemical component information

ChemComp-ATP:
ADENOSINE-5'-TRIPHOSPHATE / ATP, energy-carrying molecule*YM / Adenosine triphosphate

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statefilament

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE / Chamber humidity: 100 %

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: SUPER-RESOLUTION / Average electron dose: 90.0 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

CTF correctionSoftware - Name: Gctf
Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION
Final reconstructionApplied 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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