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

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Basic information

Entry
Database: PDB / ID: 9gtl
TitleCrystal structure of human lysosomal acid-alpha-glucosidase, GAA, in complex with iminosugar compound 4j
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: 2 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)109,22323
Polymers105,4481
Non-polymers3,77522
Water8,737485
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5320 Å2
ΔGint-47 kcal/mol
Surface area30780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.315, 102.670, 126.808
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, 4 molecules

#2: 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
#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 alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: 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

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Non-polymers , 8 types, 503 molecules

#6: Chemical ChemComp-A1IO9 / (2~{R},3~{R},4~{R},5~{S})-2-(hydroxymethyl)-2-(3-phenylpropyl)piperidine-3,4,5-triol


Mass: 281.347 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H23NO4
#7: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#8: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Cl
#9: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#10: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3 / Feature type: SUBJECT OF INVESTIGATION
#11: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#12: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#13: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 485 / 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: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.978565 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 23, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978565 Å / Relative weight: 1
ReflectionResolution: 2→47.58 Å / Num. obs: 83802 / % possible obs: 100 % / Redundancy: 13.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.04 / Rrim(I) all: 0.149 / Χ2: 1 / Net I/σ(I): 12.2 / Num. measured all: 1148153
Reflection shellResolution: 2→2.04 Å / % possible obs: 100 % / Redundancy: 14.1 % / Rmerge(I) obs: 2.436 / Num. measured all: 64160 / Num. unique obs: 4536 / CC1/2: 0.505 / Rpim(I) all: 0.669 / Rrim(I) all: 2.527 / Χ2: 0.98 / Net I/σ(I) obs: 1.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
Aimlessdata scaling
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→47.2 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.963 / SU B: 4.368 / SU ML: 0.111 / Cross valid method: THROUGHOUT / ESU R: 0.132 / ESU R Free: 0.124 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19975 4183 5 %Taken over from parent data set
Rwork0.16752 ---
obs0.16914 79540 99.95 %-
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: 40.695 Å2
Baniso -1Baniso -2Baniso -3
1-2.74 Å2-0 Å20 Å2
2---2.17 Å20 Å2
3----0.57 Å2
Refinement stepCycle: 1 / Resolution: 2→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6631 0 238 485 7354
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0137153
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176491
X-RAY DIFFRACTIONr_angle_refined_deg1.3191.6839795
X-RAY DIFFRACTIONr_angle_other_deg1.2511.59915003
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1085858
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.11722.151358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.466151045
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5951541
X-RAY DIFFRACTIONr_chiral_restr0.0650.2940
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028003
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021663
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_it3.0274.033405
X-RAY DIFFRACTIONr_mcbond_other3.0244.0293404
X-RAY DIFFRACTIONr_mcangle_it4.0026.0264261
X-RAY DIFFRACTIONr_mcangle_other4.0026.0274262
X-RAY DIFFRACTIONr_scbond_it4.2434.5323748
X-RAY DIFFRACTIONr_scbond_other4.2424.5333749
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.2136.6645531
X-RAY DIFFRACTIONr_long_range_B_refined7.08548.3297894
X-RAY DIFFRACTIONr_long_range_B_other7.06548.0077792
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.336 297 -
Rwork0.306 5848 -
obs--99.87 %

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