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- PDB-9gtw: Crystal structure of human lysosomal acid-alpha-glucosidase, GAA,... -

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Basic information

Entry
Database: PDB / ID: 9gtw
TitleCrystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with iminosugar compound 3g
ComponentsLysosomal alpha-glucosidase
KeywordsHYDROLASE / acid-alpha-glucosidase / lysosomal / iminosugar / Pompe disease
Function / homology
Function and homology information


vacuolar sequestering / autolysosome lumen / maltose metabolic process / alpha-glucosidase activity / sucrose metabolic process / Glycogen storage disease type II (GAA) / alpha-1,4-glucosidase activity / alpha-glucosidase / neuromuscular process controlling posture / glycophagy ...vacuolar sequestering / autolysosome lumen / maltose metabolic process / alpha-glucosidase activity / sucrose metabolic process / Glycogen storage disease type II (GAA) / alpha-1,4-glucosidase activity / alpha-glucosidase / neuromuscular process controlling posture / glycophagy / tissue development / diaphragm contraction / regulation of the force of heart contraction / glycogen catabolic process / aorta development / lysosome organization / azurophil granule membrane / neuromuscular process controlling balance / Glycogen breakdown (glycogenolysis) / muscle cell cellular homeostasis / tertiary granule membrane / ficolin-1-rich granule membrane / heart morphogenesis / cardiac muscle contraction / lysosomal lumen / locomotory behavior / glucose metabolic process / carbohydrate binding / lysosome / lysosomal membrane / intracellular membrane-bounded organelle / Neutrophil degranulation / extracellular exosome / membrane / plasma membrane
Similarity search - Function
P-type trefoil, conserved site / P-type 'Trefoil' domain signature. / Trefoil (P-type) domain / P-type trefoil domain / P-type trefoil domain superfamily / P-type 'Trefoil' domain profile. / P or trefoil or TFF domain / Glycosyl hydrolases family 31, conserved site / Glycosyl hydrolases family 31 signature 2. / Glycosyl hydrolases family 31, active site ...P-type trefoil, conserved site / P-type 'Trefoil' domain signature. / Trefoil (P-type) domain / P-type trefoil domain / P-type trefoil domain superfamily / P-type 'Trefoil' domain profile. / P or trefoil or TFF domain / Glycosyl hydrolases family 31, conserved site / Glycosyl hydrolases family 31 signature 2. / Glycosyl hydrolases family 31, active site / Glycosyl hydrolases family 31 active site. / Glycoside hydrolase family 31, N-terminal domain / Glycosyl hydrolase 31 N-terminal galactose mutarotase-like domain / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Lysosomal alpha-glucosidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 Å
AuthorsSulzenbacher, G. / Roig-Zamboni, V. / Moracci, M. / Parenti, G. / Py, S.
Funding support France, 1items
OrganizationGrant numberCountry
Other government France
CitationJournal: J.Med.Chem. / Year: 2025
Title: C -Branched Iminosugars as Selective Pharmacological Chaperones of Lysosomal alpha-Glucosidase for the Treatment of Pompe Disease.
Authors: Vieira Da Cruz, A. / Perraudin, V. / Minopoli, N. / Iacono, R. / Roig-Zamboni, V. / Bossio, A. / Tangara, S. / Fayolle, M. / Kanazawa, A. / Philouze, C. / Tarallo, A. / Heming, J.J.A. / ...Authors: Vieira Da Cruz, A. / Perraudin, V. / Minopoli, N. / Iacono, R. / Roig-Zamboni, V. / Bossio, A. / Tangara, S. / Fayolle, M. / Kanazawa, A. / Philouze, C. / Tarallo, A. / Heming, J.J.A. / Artola, M. / Behr, J.B. / Overkleeft, H.S. / Moracci, M. / Sulzenbacher, G. / Parenti, G. / Py, S.
History
DepositionSep 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 1, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 8, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysosomal alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,92634
Polymers105,4481
Non-polymers4,47833
Water12,466692
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8480 Å2
ΔGint-7 kcal/mol
Surface area30480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.952, 101.938, 128.658
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Lysosomal alpha-glucosidase / Acid maltase / Aglucosidase alfa


Mass: 105448.477 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GAA / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P10253, alpha-glucosidase

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Sugars , 4 types, 5 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 570.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}LINUCSPDB-CARE
#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 8 types, 720 molecules

#6: Chemical ChemComp-A1IPC / (2~{S},3~{S},4~{S},5~{S})-2-heptyl-5-(hydroxymethyl)pyrrolidine-3,4-diol


Mass: 231.332 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H25NO3 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#8: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#10: Chemical
ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H14O4
#11: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#12: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 692 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 1.9 M AMMONIUM SULPHATE, 0.1 M HEPES, 2% V/V PEG400, PH 7
PH range: 7

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.976254 Å
DetectorType: DECTRIS EIGER2 X 9M / Detector: PIXEL / Date: Jun 8, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 1.75→101.94 Å / Num. obs: 128798 / % possible obs: 100 % / Redundancy: 6.2 % / CC1/2: 0.992 / Rmerge(I) obs: 0.176 / Rpim(I) all: 0.076 / Rrim(I) all: 0.192 / Χ2: 0.85 / Net I/σ(I): 5.6 / Num. measured all: 801670
Reflection shellResolution: 1.75→1.78 Å / % possible obs: 100 % / Redundancy: 6.3 % / Rmerge(I) obs: 1.261 / Num. measured all: 39750 / Num. unique obs: 6288 / CC1/2: 0.517 / Rpim(I) all: 0.543 / Rrim(I) all: 1.375 / Χ2: 0.66 / Net I/σ(I) obs: 1.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.75→77.55 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 2.432 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.086 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1921 6432 5 %Taken over from parent data set
Rwork0.16388 ---
obs0.16527 122147 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 31.771 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å2-0 Å2
2--0.39 Å2-0 Å2
3----0.26 Å2
Refinement stepCycle: 1 / Resolution: 1.75→77.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6635 0 284 692 7611
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137155
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176554
X-RAY DIFFRACTIONr_angle_refined_deg1.4091.6789748
X-RAY DIFFRACTIONr_angle_other_deg1.331.59515126
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.175855
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.78221.95359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.061151036
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.8451543
X-RAY DIFFRACTIONr_chiral_restr0.0740.2926
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.027940
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021666
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.0473.0223384
X-RAY DIFFRACTIONr_mcbond_other3.0463.0223383
X-RAY DIFFRACTIONr_mcangle_it3.5634.5134227
X-RAY DIFFRACTIONr_mcangle_other3.5634.5144228
X-RAY DIFFRACTIONr_scbond_it5.2733.5143771
X-RAY DIFFRACTIONr_scbond_other5.2723.5153772
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6625.0845514
X-RAY DIFFRACTIONr_long_range_B_refined7.22837.2347917
X-RAY DIFFRACTIONr_long_range_B_other7.13736.6047742
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 487 -
Rwork0.275 8907 -
obs--99.61 %

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