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- PDB-1vcu: Structure of the human cytosolic sialidase Neu2 in complex with t... -

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Basic information

Entry
Database: PDB / ID: 1vcu
TitleStructure of the human cytosolic sialidase Neu2 in complex with the inhibitor DANA
ComponentsSialidase 2
KeywordsHYDROLASE / sialidase / neuraminidase / ganglioside / dana / sialic acid
Function / homology
Function and homology information


Sialic acid metabolism / glycosphingolipid catabolic process / glycoprotein catabolic process / Glycosphingolipid catabolism / ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase / exo-alpha-sialidase activity / catalytic complex / lysosome ...Sialic acid metabolism / glycosphingolipid catabolic process / glycoprotein catabolic process / Glycosphingolipid catabolism / ganglioside catabolic process / oligosaccharide catabolic process / exo-alpha-sialidase / exo-alpha-sialidase activity / catalytic complex / lysosome / membrane / cytoplasm / cytosol
Similarity search - Function
BNR repeat-like domain / Sialidase family / Sialidase / Neuraminidase - #10 / Sialidase superfamily / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / Sialidase-2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsChavas, L.M.G. / Fusi, P. / Tringali, C. / Venerando, B. / Tettamanti, G. / Kato, R. / Monti, E. / Wakatsuki, S.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal Structure of the Human Cytosolic Sialidase Neu2: EVIDENCE FOR THE DYNAMIC NATURE OF SUBSTRATE RECOGNITION
Authors: Chavas, L.M.G. / Tringali, C. / Fusi, P. / Venerando, B. / Tettamanti, G. / Kato, R. / Monti, E. / Wakatsuki, S.
History
DepositionMar 12, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 2, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Database references / Derived calculations
Category: chem_comp / struct_ref_seq_dif ...chem_comp / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.type / _struct_ref_seq_dif.details / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 25, 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

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Assembly

Deposited unit
A: Sialidase 2
B: Sialidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,3758
Polymers84,8392
Non-polymers1,5366
Water2,360131
1
A: Sialidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1874
Polymers42,4201
Non-polymers7683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sialidase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,1874
Polymers42,4201
Non-polymers7683
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)157.650, 74.000, 77.190
Angle α, β, γ (deg.)90.00, 90.64, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Sialidase 2 / Neu2 / Cytosolic sialidase / N-acetyl-alpha- neuraminidase 2


Mass: 42419.598 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-2T / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9Y3R4, exo-alpha-sialidase
#2: Sugar ChemComp-DAN / 2-DEOXY-2,3-DEHYDRO-N-ACETYL-NEURAMINIC ACID / Neu5Ac2en


Type: D-saccharide / Mass: 291.255 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H17NO8
#3: Chemical
ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / 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: 2.64 Å3/Da / Density % sol: 53.12 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2-deoxy-2,3-dehydro-N-acetyl neuraminic acid, 2-methyl-2,4-pentanediol, guanidine hydrochloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 0.97 Å
DetectorType: ADSC QUAMTUM 4r / Detector: CCD / Date: Jun 27, 2003
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.85→50 Å / Num. all: 20889 / Num. obs: 20807 / % possible obs: 99.7 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 11.5
Reflection shellResolution: 2.85→2.95 Å / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 2 / % possible all: 99.6

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
MOLREPphasing
CNSrefinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SNT

1snt


Resolution: 2.85→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1050 -RANDOM
Rwork0.195 ---
all0.199 20889 --
obs0.199 20807 99.7 %-
Refinement stepCycle: LAST / Resolution: 2.85→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5850 0 100 131 6081
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.396

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