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- PDB-8z0a: Human GYS1-GYG2 complex (apo) -

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Basic information

Entry
Database: PDB / ID: 8z0a
TitleHuman GYS1-GYG2 complex (apo)
Components
  • Glycogen [starch] synthase, muscle
  • Glycogenin-2
KeywordsTRANSFERASE / Glycogen / Glycogenin / Glycogen synthase
Function / homology
Function and homology information


Glycogen storage disease type 0 (liver GYS2) / Glycogen storage disease type IV (GBE1) / glycogen synthase activity, transferring glucose-1-phosphate / Glycogen storage disease type XV (GYG1) / Glycogen storage disease type 0 (muscle GYS1) / glycogen(starch) synthase / glycogenin glucosyltransferase / glycogenin glucosyltransferase activity / alpha-1,4-glucan glucosyltransferase (UDP-glucose donor) activity / D-glucose binding ...Glycogen storage disease type 0 (liver GYS2) / Glycogen storage disease type IV (GBE1) / glycogen synthase activity, transferring glucose-1-phosphate / Glycogen storage disease type XV (GYG1) / Glycogen storage disease type 0 (muscle GYS1) / glycogen(starch) synthase / 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 / heart development / metal ion binding / nucleus / membrane / cytoplasm / cytosol
Similarity search - Function
Glycogen synthase / Glycogen synthase / : / Glycosyl transferase, family 8 / Glycosyl transferase family 8 / Nucleotide-diphospho-sugar transferases
Similarity search - Domain/homology
Glycogenin-2 / Glycogen [starch] synthase, muscle
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 2.84 Å
AuthorsChen, P.P. / Hsia, K.C.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Academia Sinica (Taiwan) Taiwan
CitationJournal: To Be Published
Title: Human GYS1-GYG2 complex (apo)
Authors: Chen, P.P. / Hsia, K.C.
History
DepositionApr 9, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0Apr 9, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2025Group: Data collection / Category: em_admin / em_software / Item: _em_admin.last_update / _em_software.name
Revision 1.1Jul 2, 2025Data content type: EM metadata / Data content type: EM metadata / EM metadata / Group: Data processing / Experimental summary / Data content type: EM metadata / EM metadata / Category: em_admin / em_software / Data content type: EM metadata / EM metadata / Item: _em_admin.last_update / _em_software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycogen [starch] synthase, muscle
B: Glycogen [starch] synthase, muscle
C: Glycogen [starch] synthase, muscle
D: Glycogen [starch] synthase, muscle
E: Glycogenin-2
F: Glycogenin-2
G: Glycogenin-2
H: Glycogenin-2


Theoretical massNumber of molelcules
Total (without water)568,7818
Polymers568,7818
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: electron microscopy, not applicable
TypeNameSymmetry operationNumber
identity operation1_5551

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Components

#1: Protein
Glycogen [starch] synthase, muscle / Glycogen synthase 1


Mass: 86987.781 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GYS1, GYS / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P13807, glycogen(starch) synthase
#2: Protein
Glycogenin-2 / GN-2 / GN2


Mass: 55207.566 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GYG2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O15488, glycogenin glucosyltransferase
Has protein modificationN

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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: Human GYS1-GYG2 complex (apo) / Type: COMPLEX / Entity ID: all / Source: RECOMBINANT
Molecular weightExperimental value: NO
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Spodoptera frugiperda (fall armyworm)
Buffer solutionpH: 7.4
Details: 50 mM K-phosphate buffer pH7.4, 150 mM NaCl, 1 mM beta-Me
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE / Humidity: 100 % / Chamber temperature: 298 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 defocus max: 1800 nm / Nominal defocus min: 1200 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 (6k x 4k)

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Processing

EM softwareName: PHENIX / Category: model refinement
CTF correctionType: NONE
3D reconstructionResolution: 2.84 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 238004 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00421212
ELECTRON MICROSCOPYf_angle_d0.51628724
ELECTRON MICROSCOPYf_dihedral_angle_d3.9992808
ELECTRON MICROSCOPYf_chiral_restr0.0413048
ELECTRON MICROSCOPYf_plane_restr0.0043704

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