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- PDB-3tv8: Pharmacological Chaperoning in Human alpha-Galactosidase -

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Basic information

Entry
Database: PDB / ID: 3tv8
TitlePharmacological Chaperoning in Human alpha-Galactosidase
ComponentsAlpha-galactosidase A
KeywordsHYDROLASE / pharmacological chaperone / (beta/alpha)8 barrel / carbohydrate-binding protein / glycosidase / glycoprotein / n-linked glycosylation / lysosome
Function / homology
Function and homology information


glycosylceramide catabolic process / negative regulation of nitric-oxide synthase activity / alpha-galactosidase / alpha-galactosidase activity / glycosphingolipid catabolic process / oligosaccharide metabolic process / glycoside catabolic process / galactoside binding / negative regulation of nitric oxide biosynthetic process / Glycosphingolipid catabolism ...glycosylceramide catabolic process / negative regulation of nitric-oxide synthase activity / alpha-galactosidase / alpha-galactosidase activity / glycosphingolipid catabolic process / oligosaccharide metabolic process / glycoside catabolic process / galactoside binding / negative regulation of nitric oxide biosynthetic process / Glycosphingolipid catabolism / catalytic activity / lysosomal lumen / azurophil granule lumen / lysosome / hydrolase activity / signaling receptor binding / Neutrophil degranulation / Golgi apparatus / protein homodimerization activity / extracellular exosome / extracellular region / cytoplasm
Similarity search - Function
Alpha galactosidase A, C-terminal beta-sandwich domain / Alpha galactosidase A C-terminal beta sandwich domain / Alpha galactosidase A / Glycoside hydrolase, family 27 / Glycoside hydrolase family 27/36, conserved site / Alpha-galactosidase signature. / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Aldolase class I / Aldolase-type TIM barrel ...Alpha galactosidase A, C-terminal beta-sandwich domain / Alpha galactosidase A C-terminal beta sandwich domain / Alpha galactosidase A / Glycoside hydrolase, family 27 / Glycoside hydrolase family 27/36, conserved site / Alpha-galactosidase signature. / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Aldolase class I / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-DGJ / Alpha-galactosidase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.639 Å
AuthorsRogich, J.J. / Guce, A.I. / Clark, N.E. / Garman, S.C.
CitationJournal: Chem.Biol. / Year: 2011
Title: The molecular basis of pharmacological chaperoning in human alpha-galactosidase
Authors: Guce, A.I. / Clark, N.E. / Rogich, J.J. / Garman, S.C.
History
DepositionSep 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 4, 2012Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_unobs_or_zero_occ_atoms / software / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _software.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-galactosidase A
B: Alpha-galactosidase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,43716
Polymers92,3592
Non-polymers4,07814
Water1,15364
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-20 kcal/mol
Surface area30520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.465, 90.465, 216.544
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111LEULEUGLUGLU1AA32 - 481 - 17
211LEULEUGLUGLU1BB32 - 481 - 17
121ILEILESERSER1AA64 - 6533 - 34
221ILEILESERSER1BB64 - 6533 - 34
131ALAALATRPTRP1AA73 - 8142 - 50
231ALAALATRPTRP1BB73 - 8142 - 50
141ALAALAARGARG1AA84 - 10053 - 69
241ALAALAARGARG1BB84 - 10053 - 69
151LEULEUGLNGLN1AA106 - 10775 - 76
251LEULEUGLNGLN1BB106 - 10775 - 76
161VALVALASPASP1AA124 - 13693 - 105
261VALVALASPASP1BB124 - 13693 - 105
171THRTHRCYSCYS1AA141 - 174110 - 143
271THRTHRCYSCYS1BB141 - 174110 - 143
181LEULEUASNASN1AA180 - 192149 - 161
281LEULEUASNASN1BB180 - 192149 - 161
191THRTHRGLYGLY1AA194 - 195163 - 164
291THRTHRGLYGLY1BB194 - 195163 - 164
1101SERSERLEULEU1AA197 - 206166 - 175
2101SERSERLEULEU1BB197 - 206166 - 175
1111TYRTYRILEILE1AA216 - 239185 - 208
2111TYRTYRILEILE1BB216 - 239185 - 208
1121SERSERGLNGLN1AA241 - 250210 - 219
2121SERSERGLNGLN1BB241 - 250210 - 219
1131ILEILEASPASP1AA253 - 313222 - 282
2131ILEILEASPASP1BB253 - 313222 - 282
1141ASPASPPROPRO1AA315 - 323284 - 292
2141ASPASPPROPRO1BB315 - 323284 - 292
1151GLNGLNGLYGLY1AA327 - 328296 - 297
2151GLNGLNGLYGLY1BB327 - 328296 - 297
1161PHEPHECYSCYS4AA50 - 5619 - 25
2161PHEPHECYSCYS4BB50 - 5619 - 25
112TYRTYRASPASP1AA329 - 335298 - 304
212TYRTYRASPASP1BB329 - 335298 - 304
122PHEPHEGLYGLY1AA337 - 346306 - 315
222PHEPHEGLYGLY1BB337 - 346306 - 315
132ALAALAGLYGLY1AA350 - 375319 - 344
232ALAALAGLYGLY1BB350 - 375319 - 344
142ALAALATHRTHR1AA377 - 385346 - 354
242ALAALATHRTHR1BB377 - 385346 - 354
152LEULEUARGARG1AA387 - 392356 - 361
252LEULEUARGARG1BB387 - 392356 - 361
162LEULEUTRPTRP1AA394 - 399363 - 368
262LEULEUTRPTRP1BB394 - 399363 - 368
172SERSERLEULEU1AA405 - 415374 - 384
272SERSERLEULEU1BB405 - 415374 - 384
182LEULEUASNASN1AA417 - 419386 - 388
282LEULEUASNASN1BB417 - 419386 - 388

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alpha-galactosidase A / Alpha-D-galactosidase A / Alpha-D-galactoside galactohydrolase / Melibiase


Mass: 46179.406 Da / Num. of mol.: 2 / Fragment: UNP Residues 32-429 / Mutation: D170A
Source method: isolated from a genetically manipulated source
Details: Selected with blastocidin / Source: (gene. exp.) Homo sapiens (human) / Gene: GLA / Plasmid: pIB/V5-His-TOPO TA / Production host: TRICHOPLUSIA NI (cabbage looper) / Strain (production host): HI-FIVE / References: UniProt: P06280, alpha-galactosidase

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Sugars , 3 types, 6 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#3: 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: 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.: 4
Source method: isolated from a genetically manipulated source
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 , 4 types, 72 molecules

#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#7: Chemical ChemComp-DGJ / (2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol / 1-deoxygalactonojirimycin


Mass: 163.172 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: medication, Galafold*YM
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 64 / Source method: isolated from a natural source / Formula: H2O

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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: 2.77 Å3/Da / Density % sol: 55.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 20% PEG 4000, 200mM Ammonium Sulfate, 100mM Sodium Acetate, pH 4.6, vapor diffusion, hanging drop, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 16, 2010 / Details: TOROIDAL FOCUSING MIRROR
RadiationMonochromator: SI(111) CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 2.639→50 Å / Num. obs: 31099 / % possible obs: 99.8 % / Redundancy: 5.8 % / Biso Wilson estimate: 55.5 Å2 / Rmerge(I) obs: 0.172 / Χ2: 1.017 / Net I/σ(I): 3.9
Reflection shellResolution: 2.639→2.69 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.685 / Num. unique all: 1518 / Χ2: 0.921 / % possible all: 99.8

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 3HG2

3hg2


Resolution: 2.639→44.54 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.91 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 20.342 / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.762 / ESU R Free: 0.303 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2388 1582 5.1 %RANDOM
Rwork0.2014 ---
obs0.2033 30933 99.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 93.1 Å2 / Biso mean: 36.3518 Å2 / Biso min: 7.27 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20.01 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.639→44.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6247 0 197 64 6508
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0226642
X-RAY DIFFRACTIONr_bond_other_d0.0030.024485
X-RAY DIFFRACTIONr_angle_refined_deg1.1551.9689034
X-RAY DIFFRACTIONr_angle_other_deg0.846310842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9635781
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.16424.259317
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.699151051
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5741538
X-RAY DIFFRACTIONr_chiral_restr0.0660.2955
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217317
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021367
X-RAY DIFFRACTIONr_mcbond_it1.66563885
X-RAY DIFFRACTIONr_mcbond_other0.48161586
X-RAY DIFFRACTIONr_mcangle_it2.92286225
X-RAY DIFFRACTIONr_scbond_it4.656122757
X-RAY DIFFRACTIONr_scangle_it6.885182809
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
12963TIGHT POSITIONAL0.040.05
191MEDIUM POSITIONAL0.020.5
12963TIGHT THERMAL2.5510
191MEDIUM THERMAL2.420
21036TIGHT POSITIONAL0.050.05
21036TIGHT THERMAL2.2310
LS refinement shellResolution: 2.639→2.708 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.337 91 -
Rwork0.353 2120 -
all-2211 -
obs--98.14 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.67250.24640.07760.12940.12060.27490.0019-0.03290.0548-0.0102-0.03190.02490.017-0.03610.030.0626-0.01-0.0060.0607-0.0010.0522-16.132252.7636109.6355
20.67320.0650.81420.176-0.13351.26080.08430.0564-0.02250.03900.0480.04880.1066-0.08440.07310.02260.01140.0834-0.00090.017114.218450.9507114.1166
30.48180.0070.26260.1992-0.22360.4389-0.02570.08110.04150.0166-0.0416-0.029-0.01860.07420.06730.03730.00110.00910.07750.05690.068920.629963.09979.9935
40.80760.11050.43210.03290.07671.8826-0.05720.00110.0233-0.03650.04630.02310.0329-0.16150.01090.102-0.0347-0.02230.08030.04240.0265-8.718456.097273.3799
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A32 - 328
2X-RAY DIFFRACTION2A329 - 420
3X-RAY DIFFRACTION3B32 - 328
4X-RAY DIFFRACTION4B329 - 420

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