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- PDB-8du5: Murine sialidase-1 (NEU1) -

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Basic information

Entry
Database: PDB / ID: 8du5
TitleMurine sialidase-1 (NEU1)
ComponentsSialidase-1
KeywordsHYDROLASE / sialic acid / sialidase / glycosidase / lysosome
Function / homology
Function and homology information


regulation of myoblast proliferation / Sialic acid metabolism / : / : / : / Glycosphingolipid catabolism / ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase / exo-alpha-sialidase activity ...regulation of myoblast proliferation / Sialic acid metabolism / : / : / : / Glycosphingolipid catabolism / ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase / exo-alpha-sialidase activity / Neutrophil degranulation / lysosomal lumen / positive regulation of neuron projection development / cell junction / cytoplasmic vesicle / lysosome / lysosomal membrane / cell surface / membrane / plasma membrane / cytoplasm
Similarity search - Function
BNR repeat-like domain / Sialidase family / Sialidase / Sialidase superfamily
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsGorelik, A. / Illes, K. / Nagar, B.
Funding support Canada, 2items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)PJT-173264 Canada
Canadian Institutes of Health Research (CIHR)MFE-164773 Canada
CitationJournal: Sci Adv / Year: 2023
Title: Structure of the immunoregulatory sialidase NEU1.
Authors: Gorelik, A. / Illes, K. / Mazhab-Jafari, M.T. / Nagar, B.
History
DepositionJul 26, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sialidase-1
B: Sialidase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,7348
Polymers83,1652
Non-polymers2,5696
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimer at low concentration, multimer at high concentration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4910 Å2
ΔGint30 kcal/mol
Surface area29670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)221.346, 221.346, 131.748
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number80
Space group name H-MI41
Space group name HallI4bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: -y+1,x+1/2,z+5/4
#7: y+1,-x+1/2,z+5/4
#8: -x+1/2,-y+1/2,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 44 through 424)
d_2ens_1chain "B"

NCS domain segments:

Ens-ID: ens_1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ASPASPLEULEUAA44 - 40913 - 378
d_12NAGNAGNAGNAGCC1
d_13NAGNAGNAGNAGCC1
d_14NAGNAGNAGNAGDD1
d_15BMABMABMABMACC3
d_16NAGNAGNAGNAGAF501
d_21ASPASPLEULEUBB44 - 40913 - 378
d_22NAGNAGNAGNAGEE1
d_23NAGNAGNAGNAGEE1
d_24NAGNAGNAGNAGBG501
d_25BMABMABMABMAEE3
d_26NAGNAGNAGNAGBH502

NCS oper: (Code: givenMatrix: (-0.675802317767, 0.736026649554, 0.0394461461725), (0.732139552836, 0.664120317925, 0.151379914428), (0.0852226640893, 0.131182980854, -0.987688272209)Vector: 130. ...NCS oper: (Code: given
Matrix: (-0.675802317767, 0.736026649554, 0.0394461461725), (0.732139552836, 0.664120317925, 0.151379914428), (0.0852226640893, 0.131182980854, -0.987688272209)
Vector: 130.777797528, -57.0787896259, -7.00340161376)

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Components

#1: Protein Sialidase-1 / G9 sialidase / Lysosomal sialidase / N-acetyl-alpha-neuraminidase 1


Mass: 41582.492 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Neu1, Neu / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: O35657, exo-alpha-sialidase
#2: 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
#3: 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-Glycam 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
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}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-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
#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.: 3 / 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
Has ligand of interestN
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

Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6
Details: precipitant: sodium acetate; buffer: bis-tris-HCl pH6; cryoprotectant: sodium malonate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.98 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jul 17, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 38652 / % possible obs: 96.4 % / Redundancy: 4 % / Biso Wilson estimate: 75.63 Å2 / CC1/2: 0.987 / CC star: 0.997 / Rpim(I) all: 0.1 / Rrim(I) all: 0.21 / Net I/σ(I): 7
Reflection shellResolution: 3.5→3.63 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 0.85 / Num. unique obs: 3888 / CC1/2: 0.446 / CC star: 0.786 / Rpim(I) all: 0.854 / Rrim(I) all: 1.808 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1SNT

1snt


Resolution: 3.5→43.41 Å / SU ML: 0.3227 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 19.7842
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.1991 2022 6.66 %
Rwork0.1746 28328 -
obs0.1762 30350 75.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 93.91 Å2
Refinement stepCycle: LAST / Resolution: 3.5→43.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5642 0 169 0 5811
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0035951
X-RAY DIFFRACTIONf_angle_d0.6038100
X-RAY DIFFRACTIONf_chiral_restr0.0448931
X-RAY DIFFRACTIONf_plane_restr0.0051041
X-RAY DIFFRACTIONf_dihedral_angle_d10.58882181
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.885008001901 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.5-3.590.2808590.2753820X-RAY DIFFRACTION30.64
3.59-3.680.3435770.26111060X-RAY DIFFRACTION39.51
3.68-3.790.30261000.25411350X-RAY DIFFRACTION51.16
3.79-3.910.30781130.24911579X-RAY DIFFRACTION59.72
3.92-4.060.25681290.2181791X-RAY DIFFRACTION66.76
4.06-4.220.24141460.1922008X-RAY DIFFRACTION76.09
4.22-4.410.18311580.16272197X-RAY DIFFRACTION82.06
4.41-4.640.17421610.14982305X-RAY DIFFRACTION86.47
4.64-4.930.14971710.14242408X-RAY DIFFRACTION90.14
4.93-5.310.15441800.14382493X-RAY DIFFRACTION92.43
5.31-5.840.21051810.16882594X-RAY DIFFRACTION96.15
5.85-6.690.18581810.17342543X-RAY DIFFRACTION95.44
6.69-8.420.19241810.17442601X-RAY DIFFRACTION95.9
8.42-43.410.17431850.15812579X-RAY DIFFRACTION93.89

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