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- EMDB-60043: Molecular Architecture of Human Glycogen Debranching Enzyme: Insi... -

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Basic information

Entry
Database: EMDB / ID: EMD-60043
TitleMolecular Architecture of Human Glycogen Debranching Enzyme: Insights into Glycogen Storage Disease III Pathogenesis
Map data
Sample
  • Organelle or cellular component: glycogen debranching enzyme
    • Protein or peptide: Glycogen debranching enzyme
Keywordsglycogen metabolism / glycogen debranching / CYTOSOLIC PROTEIN
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 / inclusion body / response to nutrient / response to glucocorticoid / 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)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.36 Å
AuthorsGuan H / Chen H
Funding support3 items
OrganizationGrant numberCountry
Other governmentZDSYS20220402111000001
Other governmentJCYJ20220530115214033
Other governmentKQTD20210811090115021
CitationJournal: Nat Commun / Year: 2025
Title: Molecular architecture and catalytic mechanism of human glycogen debranching enzyme.
Authors: Huiyi Guan / Huan Chen / He Geng / Ruifang Ma / Zhongmin Liu / Yong Wang / Yifang Chen / Kaige Yan /
Abstract: Glycogen, a key branched glucose polymer, acts as a vital energy reservoir in mammalian cells, particularly during intense activity or fasting. The glycogen debranching enzyme (GDE) plays a key role ...Glycogen, a key branched glucose polymer, acts as a vital energy reservoir in mammalian cells, particularly during intense activity or fasting. The glycogen debranching enzyme (GDE) plays a key role in glycogen degradation by removing branches, ensuring efficient glucose release. Dysfunction of GDE leads to the accumulation of limit dextrin and is implicated in the pathogenesis of Glycogen Storage Disease Type III (GSD III). We present the cryo-EM structure of human GDE (hsGDE) at 3.23 Å resolution, providing molecular insights into its substrate selectivity and catalytic mechanism. Our study further investigates the molecular consequences of disease-associated mutations by correlating structural data with enzymatic activities of representative GSD III-causing variants. We discover that these mutations induce GSD III through diverse mechanisms, including significant reductions in enzymatic activity, and disruptions to the glycogen-bound region and overall structural integrity. The elucidation of these pathways not only advances our understanding of hsGDE's role in substrate recognition and catalysis but also illuminates the molecular pathology of GSD III. Our findings pave the way for the development of targeted therapeutic strategies for this disease.
History
DepositionMay 6, 2024-
Header (metadata) releaseMay 14, 2025-
Map releaseMay 14, 2025-
UpdateDec 3, 2025-
Current statusDec 3, 2025Processing site: PDBc / Status: Released

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Structure visualization

Supplemental images

emd_60043.png

Downloads & links

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Map

FileDownload / File: emd_60043.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Projections & slices

Image control

Size
Brightness
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AxesZ (Sec.)Y (Row.)X (Col.)
0.92 Å/pix.
x 300 pix.
= 276. Å		0.92 Å/pix.
x 300 pix.
= 276. Å		0.92 Å/pix.
x 300 pix.
= 276. Å

Surface

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Images are generated by Spider.

Voxel sizeX=Y=Z: 0.92 Å
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Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.3
Minimum - Maximum-1.9132282 - 3.2047033
Average (Standard dev.)0.00033307442 (±0.06576407)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 276.0 Å
α=β=γ: 90.0 °

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Supplemental data

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Half map: #2

Fileemd_60043_half_map_1.map
Projections & Slices
AxesZYX

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Slices (1/2)
Density Histograms

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Half map: #1

Fileemd_60043_half_map_2.map
Projections & Slices
AxesZYX

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Sample components

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Entire : glycogen debranching enzyme

EntireName: glycogen debranching enzyme
Components
  • Organelle or cellular component: glycogen debranching enzyme
    • Protein or peptide: Glycogen debranching enzyme

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Supramolecule #1: glycogen debranching enzyme

SupramoleculeName: glycogen debranching enzyme / type: organelle_or_cellular_component / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Homo sapiens (human)

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Macromolecule #1: Glycogen debranching enzyme

MacromoleculeName: Glycogen debranching enzyme / type: protein_or_peptide / ID: 1 / Number of copies: 1 / Enantiomer: LEVO / EC number: 4-alpha-glucanotransferase
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 174.974875 KDa
Recombinant expressionOrganism: Eukaryota (eukaryotes)
SequenceString: MGHSKQIRIL LLNEMEKLEK TLFRLEQGYE LQFRLGPTLQ GKAVTVYTNY PFPGETFNRE KFRSLDWENP TEREDDSDKY CKLNLQQSG SFQYYFLQGN EKSGGGYIVV DPILRVGADN HVLPLDCVTL QTFLAKCLGP FDEWESRLRV AKESGYNMIH F TPLQTLGL ...String:
MGHSKQIRIL LLNEMEKLEK TLFRLEQGYE LQFRLGPTLQ GKAVTVYTNY PFPGETFNRE KFRSLDWENP TEREDDSDKY CKLNLQQSG SFQYYFLQGN EKSGGGYIVV DPILRVGADN HVLPLDCVTL QTFLAKCLGP FDEWESRLRV AKESGYNMIH F TPLQTLGL SRSCYSLANQ LELNPDFSRP NRKYTWNDVG QLVEKLKKEW NVICITDVVY NHTAANSKWI QEHPECAYNL VN SPHLKPA WVLDRALWRF SCDVAEGKYK EKGIPALIEN DHHMNSIRKI IWEDIFPKLK LWEFFQVDVN KAVEQFRRLL TQE NRRVTK SDPNQHLTII QDPEYRRFGC TVDMNIALTT FIPHDKGPAA IEECCNWFHK RMEELNSEKH RLINYHQEQA VNCL LGNVF YERLAGHGPK LGPVTRKHPL VTRYFTFPFE EIDFSMEESM IHLPNKACFL MAHNGWVMGD DPLRNFAEPG SEVYL RREL ICWGDSVKLR YGNKPEDCPY LWAHMKKYTE ITATYFQGVR LDNCHSTPLH VAEYMLDAAR NLQPNLYVVA ELFTGS EDL DNVFVTRLGI SSLIREAMSA YNSHEEGRLV YRYGGEPVGS FVQPCLRPLM PAIAHALFMD ITHDNECPIV HRSAYDA LP STTIVSMACC ASGSTRGYDE LVPHQISVVS EERFYTKWNP EALPSNTGEV NFQSGIIAAR CAISKLHQEL GAKGFIQV Y VDQVDEDIVA VTRHSPSIHQ SVVAVSRTAF RNPKTSFYSK EVPQMCIPGK IEEVVLEART IERNTKPYRK DENSINGTP DITVEIREHI QLNESKIVKQ AGVATKGPNE YIQEIEFENL SPGSVIIFRV SLDPHAQVAV GILRNHLTQF SPHFKSGSLA VDNADPILK IPFASLASRL TLAELNQILY RCESEEKEDG GGCYDIPNWS ALKYAGLQGL MSVLAEIRPK NDLGHPFCNN L RSGDWMID YVSNRLISRS GTIAEVGKWL QAMFFYLKQI PRYLIPCYFD AILIGAYTTL LDTAWKQMSS FVQNGSTFVK HL SLGSVQL CGVGKFPSLP ILSPALMDVP YRLNEITKEK EQCCVSLAAG LPHFSSGIFR CWGRDTFIAL RGILLITGRY VEA RNIILA FAGTLRHGLI PNLLGEGIYA RYNCRDAVWW WLQCIQDYCK MVPNGLDILK CPVSRMYPTD DSAPLPAGTL DQPL FEVIQ EAMQKHMQGI QFRERNAGPQ IDRNMKDEGF NITAGVDEET GFVYGGNRFN CGTWMDKMGE SDRARNRGIP ATPRD GSAV EIVGLSKSAV RWLLELSKKN IFPYHEVTVK RHGKAIKVSY DEWNRKIQDN FEKLFHVSED PSDLNEKHPN LVHKRG IYK DSYGASSPWC DYQLRPNFTI AMVVAPELFT TEKAWKALEI AEKKLLGPLG MKTLDPDDMV YCGIYDNALD NDNYNLA KG FNYHQGPEWL WPIGYFLRAK LYFSRLMGPE TTAKTIVLVK NVLSRHYVHL ERSPWKGLPE LTNENAQYCP FSCETQAW S IATILETLYD L

UniProtKB: Glycogen debranching enzyme

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Experimental details

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Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI/PHILIPS CM300FEG/HE
Image recordingFilm or detector model: GATAN K3 BIOQUANTUM (6k x 4k) / Average electron dose: 50.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: BRIGHT FIELD / Nominal defocus max: 2.0 µm / Nominal defocus min: 1.0 µm

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Image processing

CTF correctionType: PHASE FLIPPING AND AMPLITUDE CORRECTION
Startup modelType of model: NONE
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.36 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 1228386
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: MAXIMUM LIKELIHOOD
FSC plot (resolution estimation)

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