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- PDB-8zeq: Molecular Architecture of Human Glycogen Debranching Enzyme: Insi... -

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Basic information

Entry
Database: PDB / ID: 8zeq
TitleMolecular Architecture of Human Glycogen Debranching Enzyme: Insights into Glycogen Storage Disease III Pathogenesis
ComponentsGlycogen debranching enzyme
KeywordsCYTOSOLIC PROTEIN / glycogen metabolism / glycogen debranching
Function / homology
Function and homology information


isoamylase complex / amylo-alpha-1,6-glucosidase / : / amylo-alpha-1,6-glucosidase activity / 4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / glycogen biosynthetic process / glycogen catabolic process / Glycogen breakdown (glycogenolysis) / polysaccharide binding ...isoamylase complex / amylo-alpha-1,6-glucosidase / : / amylo-alpha-1,6-glucosidase activity / 4-alpha-glucanotransferase / 4-alpha-glucanotransferase activity / glycogen biosynthetic process / glycogen catabolic process / Glycogen breakdown (glycogenolysis) / polysaccharide binding / polyubiquitin modification-dependent protein binding / response to glucocorticoid / inclusion body / response to nutrient / sarcoplasmic reticulum / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / extracellular region / nucleus / cytosol / cytoplasm
Similarity search - Function
Glycogen debranching enzyme, metazoa / Glycogen debranching enzyme / Eukaryotic glycogen debranching enzyme, N-terminal domain / Glycogen debranching enzyme, central domain / Glycogen debranching enzyme, C-terminal / Glycogen debranching enzyme, glucanotransferase domain / Amylo-alpha-1,6-glucosidase / N-terminal domain from the human glycogen debranching enzyme / Glycogen debranching enzyme, glucanotransferase domain / Central domain of human glycogen debranching enzyme ...Glycogen debranching enzyme, metazoa / Glycogen debranching enzyme / Eukaryotic glycogen debranching enzyme, N-terminal domain / Glycogen debranching enzyme, central domain / Glycogen debranching enzyme, C-terminal / Glycogen debranching enzyme, glucanotransferase domain / Amylo-alpha-1,6-glucosidase / N-terminal domain from the human glycogen debranching enzyme / Glycogen debranching enzyme, glucanotransferase domain / Central domain of human glycogen debranching enzyme / Six-hairpin glycosidase superfamily / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Glycogen debranching enzyme
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodELECTRON MICROSCOPY / single particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsGuan, H. / Chen, H.
Funding support3items
OrganizationGrant numberCountry
Other governmentZDSYS20220402111000001
Other governmentJCYJ20220530115214033
Other governmentKQTD20210811090115021
CitationJournal: To Be Published
Title: Molecular Architecture of Human Glycogen Debranching Enzyme: Insights into Glycogen Storage Disease III Pathogenesis
Authors: Guan, H. / Chen, H. / Gang, H. / Ma, R.
History
DepositionMay 6, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0May 14, 2025Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: EM metadata / Data content type: EM metadata / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: FSC / Data content type: FSC / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 1 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Half map / Part number: 2 / Data content type: Half map / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Image / Data content type: Image / Provider: repository / Type: Initial release
Revision 1.0May 14, 2025Data content type: Primary map / Data content type: Primary map / Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycogen debranching enzyme


Theoretical massNumber of molelcules
Total (without water)174,9751
Polymers174,9751
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 debranching enzyme / Glycogen debrancher


Mass: 174974.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AGL, GDE / Production host: Eukaryota (eucaryotes)
References: UniProt: P35573, 4-alpha-glucanotransferase, amylo-alpha-1,6-glucosidase
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: glycogen debranching enzyme / Type: ORGANELLE OR CELLULAR COMPONENT / Entity ID: all / Source: RECOMBINANT
Source (natural)Organism: Homo sapiens (human)
Source (recombinant)Organism: Eukaryota (eucaryotes)
Buffer solutionpH: 7.5
SpecimenEmbedding applied: NO / Shadowing applied: NO / Staining applied: NO / Vitrification applied: YES
VitrificationCryogen name: ETHANE

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Electron microscopy imaging

MicroscopyModel: FEI/PHILIPS CM300FEG/HE
Electron gunElectron source: FIELD EMISSION GUN / Accelerating voltage: 300 kV / Illumination mode: OTHER
Electron lensMode: BRIGHT FIELD / Nominal defocus max: 2000 nm / Nominal defocus min: 1000 nm
Image recordingElectron dose: 50 e/Å2 / Film or detector model: GATAN K3 BIOQUANTUM (6k x 4k)

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Processing

EM softwareName: PHENIX / Version: 1.21.1_5286: / Category: model refinement
CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
3D reconstructionResolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Num. of particles: 1228386 / Symmetry type: POINT
Refine LS restraints
Refine-IDTypeDev idealNumber
ELECTRON MICROSCOPYf_bond_d0.00212614
ELECTRON MICROSCOPYf_angle_d0.4317122
ELECTRON MICROSCOPYf_dihedral_angle_d2.251681
ELECTRON MICROSCOPYf_chiral_restr0.0391837
ELECTRON MICROSCOPYf_plane_restr0.0032226

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