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- PDB-1np0: Human lysosomal beta-hexosaminidase isoform B in complex with int... -

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Basic information

Entry
Database: PDB / ID: 1np0
TitleHuman lysosomal beta-hexosaminidase isoform B in complex with intermediate analogue NAG-thiazoline
Components
  • (Beta-hexosaminidase subunit beta chain ...Hexosaminidase) x 2
  • Beta-hexosaminidase subunit betaHexosaminidase
KeywordsHYDROLASE / (beta/alpha)8-barrel / homodimer / family 20 glycosidase
Function / homology
Function and homology information


beta-N-acetylhexosaminidase complex / Defective HEXB causes GM2G2 / chondroitin sulfate catabolic process / Keratan sulfate degradation / dermatan sulfate catabolic process / glycosaminoglycan metabolic process / CS/DS degradation / Hyaluronan uptake and degradation / penetration of zona pellucida / maintenance of location in cell ...beta-N-acetylhexosaminidase complex / Defective HEXB causes GM2G2 / chondroitin sulfate catabolic process / Keratan sulfate degradation / dermatan sulfate catabolic process / glycosaminoglycan metabolic process / CS/DS degradation / Hyaluronan uptake and degradation / penetration of zona pellucida / maintenance of location in cell / male courtship behavior / ganglioside catabolic process / cortical granule / acetylglucosaminyltransferase activity / astrocyte cell migration / oligosaccharide catabolic process / hyaluronan catabolic process / phospholipid biosynthetic process / beta-N-acetylhexosaminidase / beta-N-acetylhexosaminidase activity / N-acetyl-beta-D-galactosaminidase activity / lipid storage / Glycosphingolipid catabolism / azurophil granule / oogenesis / lysosome organization / single fertilization / neuromuscular process controlling balance / myelination / lysosomal lumen / acrosomal vesicle / locomotory behavior / skeletal system development / sensory perception of sound / intracellular calcium ion homeostasis / neuron cellular homeostasis / azurophil granule lumen / regulation of cell shape / lysosome / Neutrophil degranulation / positive regulation of transcription by RNA polymerase II / extracellular exosome / extracellular region / membrane / identical protein binding
Similarity search - Function
Beta-hexosaminidase, eukaryotic type, N-terminal / beta-acetyl hexosaminidase like / Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Beta-hexosaminidase-like, domain 2 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chem-NGT / Beta-hexosaminidase subunit beta
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.5 Å
AuthorsMark, B.L. / Mahuran, D.J. / Cherney, M.M. / Zhao, D. / Knapp, S. / James, M.N.G.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Crystal structure of Human beta-hexosaminidase B: Understanding the molecular basis of Sandhoff and Tay-Sachs disease
Authors: Mark, B.L. / Mahuran, D.J. / Cherney, M.M. / Zhao, D. / Knapp, S. / James, M.N.G.
History
DepositionJan 16, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Derived calculations / Version format compliance
Revision 2.0Aug 16, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Database references / Derived calculations / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / entity ...atom_site / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_nat / pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_sheet_hbond / pdbx_unobs_or_zero_occ_residues / struct_conf / struct_conn / struct_ref / struct_ref_seq / struct_sheet_range / 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.label_asym_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _pdbx_struct_sheet_hbond.range_1_auth_asym_id / _pdbx_struct_sheet_hbond.range_1_label_asym_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_asym_id / _pdbx_struct_sheet_hbond.range_2_label_asym_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _struct_conf.beg_auth_asym_id / _struct_conf.beg_label_asym_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_asym_id / _struct_conf.end_label_asym_id / _struct_conf.end_label_seq_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_seq_id / _struct_sheet_range.beg_auth_asym_id / _struct_sheet_range.beg_label_asym_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_auth_asym_id / _struct_sheet_range.end_label_asym_id / _struct_sheet_range.end_label_seq_id / _struct_site_gen.auth_asym_id / _struct_site_gen.label_asym_id / _struct_site_gen.label_seq_id
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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 / struct_asym / struct_conn / 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 / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.1Aug 16, 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Beta-hexosaminidase subunit beta
C: Beta-hexosaminidase subunit beta chain B
D: Beta-hexosaminidase subunit beta chain A
B: Beta-hexosaminidase subunit beta
E: Beta-hexosaminidase subunit beta chain B
F: Beta-hexosaminidase subunit beta chain A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,43714
Polymers111,7776
Non-polymers1,6608
Water4,396244
1
A: Beta-hexosaminidase subunit beta
C: Beta-hexosaminidase subunit beta chain B
D: Beta-hexosaminidase subunit beta chain A
hetero molecules

A: Beta-hexosaminidase subunit beta
C: Beta-hexosaminidase subunit beta chain B
D: Beta-hexosaminidase subunit beta chain A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,43314
Polymers111,7776
Non-polymers1,6568
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area29170 Å2
ΔGint-157 kcal/mol
Surface area36640 Å2
MethodPISA
2
B: Beta-hexosaminidase subunit beta
E: Beta-hexosaminidase subunit beta chain B
F: Beta-hexosaminidase subunit beta chain A
hetero molecules

B: Beta-hexosaminidase subunit beta
E: Beta-hexosaminidase subunit beta chain B
F: Beta-hexosaminidase subunit beta chain A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,44014
Polymers111,7776
Non-polymers1,6648
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area29220 Å2
ΔGint-166 kcal/mol
Surface area36430 Å2
MethodPISA
3
A: Beta-hexosaminidase subunit beta
C: Beta-hexosaminidase subunit beta chain B
D: Beta-hexosaminidase subunit beta chain A
B: Beta-hexosaminidase subunit beta
E: Beta-hexosaminidase subunit beta chain B
F: Beta-hexosaminidase subunit beta chain A
hetero molecules

A: Beta-hexosaminidase subunit beta
C: Beta-hexosaminidase subunit beta chain B
D: Beta-hexosaminidase subunit beta chain A
B: Beta-hexosaminidase subunit beta
E: Beta-hexosaminidase subunit beta chain B
F: Beta-hexosaminidase subunit beta chain A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)226,87328
Polymers223,55412
Non-polymers3,31916
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/61
Buried area64000 Å2
ΔGint-345 kcal/mol
Surface area67450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.414, 112.414, 397.232
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Beta-hexosaminidase subunit beta chain ... , 2 types, 4 molecules CEDF

#2: Protein Beta-hexosaminidase subunit beta chain B / Hexosaminidase / Beta-N-acetylhexosaminidase subunit beta / Hexosaminidase subunit B / Cervical cancer proto- ...Beta-N-acetylhexosaminidase subunit beta / Hexosaminidase subunit B / Cervical cancer proto-oncogene 7 protein / HCC-7 / N-acetyl-beta-glucosaminidase subunit beta


Mass: 21653.576 Da / Num. of mol.: 2 / Fragment: residues 122-311 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: placenta / References: UniProt: P07686, beta-N-acetylhexosaminidase
#3: Protein Beta-hexosaminidase subunit beta chain A / Hexosaminidase / Beta-N-acetylhexosaminidase subunit beta / Hexosaminidase subunit B / Cervical cancer proto- ...Beta-N-acetylhexosaminidase subunit beta / Hexosaminidase subunit B / Cervical cancer proto-oncogene 7 protein / HCC-7 / N-acetyl-beta-glucosaminidase subunit beta


Mass: 27818.477 Da / Num. of mol.: 2 / Fragment: residues 316-556 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: placenta / References: UniProt: P07686, beta-N-acetylhexosaminidase

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Protein / Sugars , 2 types, 4 molecules AB

#1: Protein Beta-hexosaminidase subunit beta / Hexosaminidase / Beta-N-acetylhexosaminidase subunit beta / Hexosaminidase subunit B / Cervical cancer proto- ...Beta-N-acetylhexosaminidase subunit beta / Hexosaminidase subunit B / Cervical cancer proto-oncogene 7 protein / HCC-7 / N-acetyl-beta-glucosaminidase subunit beta


Mass: 6416.366 Da / Num. of mol.: 2 / Fragment: Propeptide residues 50-107 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / Organ: placenta / References: UniProt: P07686
#4: 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.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE

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Non-polymers , 4 types, 250 molecules

#5: Chemical ChemComp-NGT / 3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL


Mass: 219.258 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H13NO4S
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#7: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#8: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 244 / 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: 3.19 Å3/Da / Density % sol: 61.16 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 5 mg/ml HexB [final], 50% saturated ammonium sulfate, 50 mM potassium phosphate, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 6, 2001 / Details: bent conical Si-mirror (Rh coating)
RadiationMonochromator: bent cylindrical Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.5→37 Å / Num. obs: 52315 / Observed criterion σ(I): -3

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1NOU

1nou


Resolution: 2.5→36.76 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.927 / SU B: 11.156 / SU ML: 0.256 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.346 / ESU R Free: 0.233 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22671 2597 5 %RANDOM
Rwork0.1982 ---
obs0.19964 49713 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.379 Å2
Baniso -1Baniso -2Baniso -3
1-2.47 Å21.23 Å20 Å2
2--2.47 Å20 Å2
3----3.7 Å2
Refinement stepCycle: LAST / Resolution: 2.5→36.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7756 0 107 244 8107
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0218097
X-RAY DIFFRACTIONr_bond_other_d0.0030.027159
X-RAY DIFFRACTIONr_angle_refined_deg1.5571.93811009
X-RAY DIFFRACTIONr_angle_other_deg1.1752.98316665
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2973954
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.192151389
X-RAY DIFFRACTIONr_chiral_restr0.0920.21200
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028852
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021702
X-RAY DIFFRACTIONr_nbd_refined0.1810.31542
X-RAY DIFFRACTIONr_nbd_other0.1420.36936
X-RAY DIFFRACTIONr_nbtor_other0.480.52
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.5930
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0660.54
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1240.317
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1470.389
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1470.521
X-RAY DIFFRACTIONr_symmetry_hbond_other0.0730.51
X-RAY DIFFRACTIONr_mcbond_it0.4751.54798
X-RAY DIFFRACTIONr_mcangle_it0.92127788
X-RAY DIFFRACTIONr_scbond_it1.49233299
X-RAY DIFFRACTIONr_scangle_it2.3684.53221
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.279 206
Rwork0.223 3503
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)
10.3345-0.09110.01790.40970.03831.28840.02440.01760.02140.03910.05680.0363-0.023-0.1369-0.08120.04990.03740.00320.12440.04520.122713.981829.430423.4003
20.37190.0412-0.37650.5155-0.32291.19940.03650.06610.07980.13570.02510.0286-0.15090.0201-0.06160.0968-0.07510.02330.06410.01090.147948.947252.279631.8443
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A55 - 107
2X-RAY DIFFRACTION1C122 - 311
3X-RAY DIFFRACTION1D316 - 552
4X-RAY DIFFRACTION2B55 - 107
5X-RAY DIFFRACTION2E122 - 311
6X-RAY DIFFRACTION2F316 - 552

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