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- PDB-7q12: Human GYS1-GYG1 complex activated state bound to glucose-6-phosphate -

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Basic information

Entry
Database: PDB / ID: 7q12
TitleHuman GYS1-GYG1 complex activated state bound to glucose-6-phosphate
Components
  • Glycogen [starch] synthase, muscle
  • Glycogenin-1
KeywordsTRANSFERASE / Glycogen / Complex / Phosphorylation
Function / homology
Function and homology information


glycogen synthase activity, transferring glucose-1-phosphate / Glycogen storage disease type XV (GYG1) / Glycogen storage disease type 0 (muscle GYS1) / glycogen(starch) synthase / Glycogen storage disease type II (GAA) / glycogenin glucosyltransferase / glycogenin glucosyltransferase activity / : / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / D-glucose binding ...glycogen synthase activity, transferring glucose-1-phosphate / Glycogen storage disease type XV (GYG1) / Glycogen storage disease type 0 (muscle GYS1) / glycogen(starch) synthase / Glycogen storage disease type II (GAA) / glycogenin glucosyltransferase / glycogenin glucosyltransferase activity / : / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / D-glucose binding / glycogen biosynthetic process / Glycogen breakdown (glycogenolysis) / glycosyltransferase activity / inclusion body / Myoclonic epilepsy of Lafora / Glycogen synthesis / lysosomal lumen / heart development / manganese ion binding / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / protein homodimerization activity / extracellular region / membrane / cytosol / cytoplasm
Similarity search - Function
Glycogen synthase / Glycogen synthase / : / Glycosyl transferase, family 8 / Glycosyl transferase family 8 / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
6-O-phosphono-alpha-D-glucopyranose / Glycogen [starch] synthase, muscle / Glycogenin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.7 Å
AuthorsMcCorvie, T.J. / Shrestha, L. / Froese, D.S. / Ferreira, I.M. / Yue, W.W.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: Nat Struct Mol Biol / Year: 2022
Title: Molecular basis for the regulation of human glycogen synthase by phosphorylation and glucose-6-phosphate.
Authors: Thomas J McCorvie / Paula M Loria / Meihua Tu / Seungil Han / Leela Shrestha / D Sean Froese / Igor M Ferreira / Allison P Berg / Wyatt W Yue /
Abstract: Glycogen synthase (GYS1) is the central enzyme in muscle glycogen biosynthesis. GYS1 activity is inhibited by phosphorylation of its amino (N) and carboxyl (C) termini, which is relieved by ...Glycogen synthase (GYS1) is the central enzyme in muscle glycogen biosynthesis. GYS1 activity is inhibited by phosphorylation of its amino (N) and carboxyl (C) termini, which is relieved by allosteric activation of glucose-6-phosphate (Glc6P). We present cryo-EM structures at 3.0-4.0 Å resolution of phosphorylated human GYS1, in complex with a minimal interacting region of glycogenin, in the inhibited, activated and catalytically competent states. Phosphorylations of specific terminal residues are sensed by different arginine clusters, locking the GYS1 tetramer in an inhibited state via intersubunit interactions. The Glc6P activator promotes conformational change by disrupting these interactions and increases the flexibility of GYS1, such that it is poised to adopt a catalytically competent state when the sugar donor UDP-glucose (UDP-glc) binds. We also identify an inhibited-like conformation that has not transitioned into the activated state, in which the locking interaction of phosphorylation with the arginine cluster impedes subsequent conformational changes due to Glc6P binding. Our results address longstanding questions regarding the mechanism of human GYS1 regulation.
History
DepositionOct 17, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2022Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / em_3d_fitting_list / em_admin / pdbx_initial_refinement_model
Item: _em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id ..._em_3d_fitting_list.accession_code / _em_3d_fitting_list.initial_refinement_model_id / _em_3d_fitting_list.source_name / _em_3d_fitting_list.type / _em_admin.last_update

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycogen [starch] synthase, muscle
E: Glycogenin-1
F: Glycogenin-1
G: Glycogenin-1
H: Glycogenin-1
B: Glycogen [starch] synthase, muscle
C: Glycogen [starch] synthase, muscle
D: Glycogen [starch] synthase, muscle
hetero molecules


Theoretical massNumber of molelcules
Total (without water)494,27312
Polymers493,2328
Non-polymers1,0414
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy
TypeNameSymmetry operationNumber
identity operation1_5551
Buried area21870 Å2
ΔGint-119 kcal/mol
Surface area105370 Å2

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Components

#1: Protein
Glycogen [starch] synthase, muscle


Mass: 83885.430 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Tissue: Muscle / Gene: GYS1, GYS / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P13807, glycogen(starch) synthase
#2: Protein
Glycogenin-1 / GN-1 / GN1


Mass: 39422.621 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GYG1, GYG / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P46976, glycogenin glucosyltransferase
#3: Sugar
ChemComp-G6P / 6-O-phosphono-alpha-D-glucopyranose / ALPHA-D-GLUCOSE-6-PHOSPHATE / 6-O-phosphono-alpha-D-glucose / 6-O-phosphono-D-glucose / 6-O-phosphono-glucose


Type: D-saccharide, alpha linking / Mass: 260.136 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13O9P / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
a-D-Glcp6PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: ELECTRON MICROSCOPY
EM experimentAggregation state: PARTICLE / 3D reconstruction method: single particle reconstruction

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Sample preparation

ComponentName: Ternary complex of phosphorylated full-length human glycogen synthase 1 in complex with minimum region of human glycogenin-1
Type: COMPLEX / Entity ID: #1-#2 / Source: RECOMBINANT
Molecular weightValue: 0.35 MDa
Source (natural)Organism: Homo sapiens (human) / Tissue: muscle
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.5
Details: 25 mM HEPES, pH 7.5, 200 mM NaCl, 2.0 mM TCEP, 0.05% (v/v) tween-20 filtered sterilised with 5 mM glucose-6-phosphate
Buffer component
IDConc.NameFormulaBuffer-ID
125 mMHEPESHEPES1
2200 mMsodium chlorideNaCl1
32 mMTCEPTCEP1
40.05 % (v/v)Tween-20TWEEN-201
55 mMGlucose-6-phosphateGlucose-6-phosphate1
SpecimenConc.: 0.75 mg/ml / Embedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
Specimen supportGrid material: GOLD / Grid mesh size: 200 divisions/in. / Grid type: Quantifoil R1.2/1.3
VitrificationInstrument: FEI VITROBOT MARK II / Cryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 277 K

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Electron microscopy imaging

Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company
MicroscopyModel: FEI TITAN KRIOS
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: FLOOD BEAM
Electron lensMode: BRIGHT FIELD / Nominal magnification: 81000 X / Nominal defocus max: 2300 nm / Nominal defocus min: 800 nm / Cs: 2.7 mm / C2 aperture diameter: 100 µm
Specimen holderCryogen: NITROGEN / Specimen holder model: FEI TITAN KRIOS AUTOGRID HOLDER
Image recordingAverage exposure time: 1.22 sec. / Electron dose: 55 e/Å2 / Film or detector model: GATAN K3 (6k x 4k) / Num. of grids imaged: 1

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Processing

EM software
IDNameVersionCategory
1RELION3.1.1.particle selection
2EPUimage acquisition
4CTFFIND4.1CTF correction
7MOLREPmodel fitting
9RELION3.1.1.initial Euler assignment
10RELION3.1.1.final Euler assignment
11RELION3.1.1classification
12RELION3.1.1.3D reconstruction
13PHENIXmodel refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Particle selectionNum. of particles selected: 4391867
SymmetryPoint symmetry: D2 (2x2 fold dihedral)
3D reconstructionResolution: 3.7 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 15379 / Algorithm: FOURIER SPACE / Symmetry type: POINT
Atomic model buildingB value: 116.12 / Protocol: FLEXIBLE FIT / Space: REAL / Target criteria: correlation coefficient
Atomic model building

3D fitting-ID: 1 / Source name: PDB / Type: experimental model

IDPDB-IDPdb chain-IDAccession codeInitial refinement model-IDPdb chain residue range
13NB0

3nb0

A3NB0122-659
24QLB

4qlb

E4QLB2268-301

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