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- PDB-3wlu: Crystal Structure of human galectin-9 NCRD with Selenolactose -

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Basic information

Entry
Database: PDB / ID: 3wlu
TitleCrystal Structure of human galectin-9 NCRD with Selenolactose
ComponentsGalectin-9
KeywordsSUGAR BINDING PROTEIN / selenolactose / beta sandwich / galectin / carbohydrate binding
Function / homology
Function and homology information


positive regulation of activated T cell autonomous cell death / : / Interleukin-2 family signaling / positive regulation of dendritic cell apoptotic process / negative regulation of T-helper 1 type immune response / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / negative regulation of mast cell degranulation / natural killer cell tolerance induction / positive regulation of transforming growth factor beta production / positive regulation of dendritic cell chemotaxis ...positive regulation of activated T cell autonomous cell death / : / Interleukin-2 family signaling / positive regulation of dendritic cell apoptotic process / negative regulation of T-helper 1 type immune response / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / negative regulation of mast cell degranulation / natural killer cell tolerance induction / positive regulation of transforming growth factor beta production / positive regulation of dendritic cell chemotaxis / positive regulation of dendritic cell differentiation / galactoside binding / oligosaccharide binding / galactose binding / disaccharide binding / negative regulation of chemokine production / positive regulation of interleukin-13 production / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of monocyte chemotactic protein-1 production / negative regulation of activated T cell proliferation / p38MAPK cascade / positive regulation of interleukin-4 production / negative regulation of type II interferon production / positive regulation of interleukin-10 production / negative regulation of tumor necrosis factor production / maternal process involved in female pregnancy / positive regulation of T cell migration / ERK1 and ERK2 cascade / positive regulation of interleukin-12 production / response to interleukin-1 / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / female pregnancy / positive regulation of non-canonical NF-kappaB signal transduction / : / cellular response to virus / positive regulation of interleukin-6 production / cellular response to type II interferon / : / positive regulation of type II interferon production / chemotaxis / positive regulation of tumor necrosis factor production / carbohydrate binding / response to lipopolysaccharide / positive regulation of viral entry into host cell / positive regulation of canonical NF-kappaB signal transduction / positive regulation of ERK1 and ERK2 cascade / inflammatory response / receptor ligand activity / negative regulation of gene expression / positive regulation of gene expression / enzyme binding / extracellular space / nucleus / cytoplasm / cytosol
Similarity search - Function
Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-LSE / Galectin-9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.4 Å
AuthorsMakyio, H. / Suzuki, T. / Ando, H. / Yamada, Y. / Ishida, H. / Kiso, M. / Wakatsuki, S. / Kato, R.
CitationJournal: Bioorg.Med.Chem. / Year: 2014
Title: Expanded potential of seleno-carbohydrates as a molecular tool for X-ray structural determination of a carbohydrate-protein complex with single/multi-wavelength anomalous dispersion phasing
Authors: Suzuki, T. / Makyio, H. / Ando, H. / Komura, N. / Menjo, M. / Yamada, Y. / Imamura, A. / Ishida, H. / Wakatsuki, S. / Kato, R. / Kiso, M.
History
DepositionNov 14, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 5, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galectin-9
B: Galectin-9
C: Galectin-9
D: Galectin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7658
Polymers63,6874
Non-polymers2,0784
Water15,655869
1
A: Galectin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4412
Polymers15,9221
Non-polymers5201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Galectin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4412
Polymers15,9221
Non-polymers5201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Galectin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4412
Polymers15,9221
Non-polymers5201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Galectin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4412
Polymers15,9221
Non-polymers5201
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)35.732, 68.167, 224.156
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological unit is a monomer. There are 4 biological units in the asymmetric unit (chains A,B,C and D)

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Components

#1: Protein
Galectin-9 / Gal-9 / Ecalectin / Tumor antigen HOM-HD-21


Mass: 15921.826 Da / Num. of mol.: 4 / Fragment: ligand binding domain, UNP residues 5-148
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS9 / Plasmid: pGEX4T-1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O00182
#2: Chemical
ChemComp-LSE / 2-(trimethylsilyl)ethyl 4-O-beta-D-galactopyranosyl-6-Se-methyl-6-seleno-beta-D-glucopyranoside


Mass: 519.518 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C18H36O10SeSi
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 869 / 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: 2.14 Å3/Da / Density % sol: 42.61 %
Crystal growTemperature: 289 K / Method: vapor diffusion / pH: 7.5
Details: PEG 6000, 100mM Tris-HCl, pH 7.5, VAPOR DIFFUSION, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 0.97889 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 31, 2011
RadiationMonochromator: Si(111) double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97889 Å / Relative weight: 1
ReflectionResolution: 1.4→43.3 Å / Num. all: 109389 / Num. obs: 109285 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14 % / Rmerge(I) obs: 0.086 / Net I/σ(I): 19.3
Reflection shellResolution: 1.4→1.42 Å / Redundancy: 13.7 % / Rmerge(I) obs: 0.885 / Mean I/σ(I) obs: 3.3 / Num. unique all: 5393 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHENIXmodel building
REFMAC5.7.0032refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.4→40 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.958 / SU B: 1.895 / SU ML: 0.04 / Cross valid method: THROUGHOUT / ESU R: 0.063 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.194 5463 5 %RANDOM
Rwork0.17224 ---
obs0.17332 103811 99.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.248 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2---0.49 Å20 Å2
3---0.32 Å2
Refinement stepCycle: LAST / Resolution: 1.4→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4456 0 120 869 5445
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.024708
X-RAY DIFFRACTIONr_bond_other_d0.0010.024292
X-RAY DIFFRACTIONr_angle_refined_deg1.7361.9386396
X-RAY DIFFRACTIONr_angle_other_deg0.8052.9879844
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1045564
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13623.793232
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.84915680
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.6381524
X-RAY DIFFRACTIONr_chiral_restr0.1090.2692
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215384
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021232
X-RAY DIFFRACTIONr_mcbond_it0.6930.7912268
X-RAY DIFFRACTIONr_mcbond_other0.6930.792267
X-RAY DIFFRACTIONr_mcangle_it1.0281.1882832
X-RAY DIFFRACTIONr_mcangle_other1.0281.1882833
X-RAY DIFFRACTIONr_scbond_it1.5490.9632440
X-RAY DIFFRACTIONr_scbond_other1.5480.9632441
X-RAY DIFFRACTIONr_scangle_other2.2061.3933565
X-RAY DIFFRACTIONr_long_range_B_refined5.4679.2975743
X-RAY DIFFRACTIONr_long_range_B_other5.4669.2975744
LS refinement shellResolution: 1.4→1.436 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.313 424 -
Rwork0.288 7548 -
obs--100 %
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)
10.82240.13910.30571.12630.16671.78960.0113-0.0125-0.02520.0064-0.00590.07750.0254-0.0218-0.00550.02930.00380.01450.01060.00310.028139.41818.5316153.287
20.79130.10680.1411.1648-0.13412.2635-0.016-0.0117-0.01640.0032-0.0812-0.07230.02360.14290.09720.00190.0020.00770.0140.01340.045322.999623.1463125.1234
30.95270.29530.09171.1981-0.51221.80690.0052-0.0209-0.00860.0151-0.0559-0.0723-0.00270.11740.05070.0126-0.00830.00260.01350.00190.022720.762256.0242125.3283
40.97710.08470.04851.1025-0.01761.97410.00020.02140.06870.0373-0.01280.0494-0.0199-0.01860.01260.0124-0.0030.01290.0103-0.00380.020438.193751.4827154.043
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A7 - 148
2X-RAY DIFFRACTION2B7 - 148
3X-RAY DIFFRACTION3C7 - 148
4X-RAY DIFFRACTION4D7 - 148

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