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- PDB-4y20: Complex of human Galectin-1 and NeuAcalpha2-3Galbeta1-4Glc -

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Basic information

Entry
Database: PDB / ID: 4y20
TitleComplex of human Galectin-1 and NeuAcalpha2-3Galbeta1-4Glc
Components(Galectin-1) x 2
KeywordsSUGAR BINDING PROTEIN / Complex / Galectin-1 / Lectin / NeuAcalpha2-3Galbeta1-4Glc
Function / homology
Function and homology information


galectin complex / lactose binding / negative regulation of T-helper 17 cell lineage commitment / plasma cell differentiation / myoblast differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / positive regulation of inflammatory response ...galectin complex / lactose binding / negative regulation of T-helper 17 cell lineage commitment / plasma cell differentiation / myoblast differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / positive regulation of inflammatory response / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / : / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / positive regulation of viral entry into host cell / positive regulation of apoptotic process / receptor ligand activity / endoplasmic reticulum lumen / apoptotic process / extracellular space / RNA binding / extracellular exosome / extracellular region / plasma membrane / cytosol / cytoplasm
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
3'-sialyl-alpha-lactose / Galectin-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.204 Å
AuthorsLin, H.Y. / Hsieh, T.J. / Lin, C.H.
Funding support Taiwan, 4items
OrganizationGrant numberCountry
Academia SinicaAS-022316 Taiwan
Ministry of Science and Technology102-2113-M-001-001-MY3 Taiwan
Ministry of Science and Technology103-2113-M-001-023-MY3 Taiwan
Ministry of Science and Technology102-2923-M-001-001-MY3 Taiwan
CitationJournal: To Be Published
Title: Structural basis of human galectin-1 inhibition with Ki values in the micro- to nanomolar range
Authors: Lin, H.Y. / Hsieh, T.J. / Tu, Z. / Huang, B.S. / Wu, S.C. / Chien, C.T. / Hsu, S.T. / Lin, C.H.
History
DepositionFeb 9, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 6, 2016Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_oper_list / 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_atom_id / _atom_site.label_comp_id / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.src_method / _entity.type / _pdbx_struct_oper_list.symmetry_operation
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Galectin-1
B: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,0734
Polymers33,8062
Non-polymers1,2672
Water88349
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.942, 58.345, 111.969
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Galectin-1 / Gal-1 / 14 kDa laminin-binding protein / HLBP14 / 14 kDa lectin / Beta-galactoside-binding lectin L- ...Gal-1 / 14 kDa laminin-binding protein / HLBP14 / 14 kDa lectin / Beta-galactoside-binding lectin L-14-I / Galaptin / HBL / HPL / Lactose-binding lectin 1 / Lectin galactoside-binding soluble 1 / Putative MAPK-activating protein PM12 / S-Lac lectin 1


Mass: 16894.965 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P09382
#2: Protein Galectin-1 / Gal-1 / 14 kDa laminin-binding protein / HLBP14 / 14 kDa lectin / Beta-galactoside-binding lectin L- ...Gal-1 / 14 kDa laminin-binding protein / HLBP14 / 14 kDa lectin / Beta-galactoside-binding lectin L-14-I / Galaptin / HBL / HPL / Lactose-binding lectin 1 / Lectin galactoside-binding soluble 1 / Putative MAPK-activating protein PM12 / S-Lac lectin 1


Mass: 16910.967 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P09382
#3: Polysaccharide N-acetyl-alpha-neuraminic acid-(2-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / 3'-sialyl-alpha-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 633.552 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: 3'-sialyl-alpha-lactose
DescriptorTypeProgram
DNeup5Aca2-3DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1a_1-5][a2112h-1b_1-5][Aad21122h-2a_2-6_5*NCC/3=O]/1-2-3/a4-b1_b3-c2WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{[(3+2)][a-D-Neup5Ac]{}}}LINUCSPDB-CARE
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
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

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.71 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris (pH 8.0), 0.2 M Li2SO4, 30% (w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.2→30 Å / Num. obs: 14339 / % possible obs: 96.7 % / Redundancy: 6.5 % / Biso Wilson estimate: 24.81 Å2 / Rmerge(I) obs: 0.052 / Rpim(I) all: 0.021 / Rrim(I) all: 0.056 / Χ2: 1.017 / Net I/av σ(I): 31.163 / Net I/σ(I): 16.7 / Num. measured all: 93161
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.2-2.286.20.20313220.9880.0840.221.02991.2
2.28-2.376.20.17413240.9890.0730.1891.02792
2.37-2.486.10.1513440.990.0640.1641.02393.6
2.48-2.6160.11714100.9940.050.1281.03695.7
2.61-2.7760.08414220.9970.0360.0911.01697.1
2.77-2.996.20.06714440.9980.0290.0731.02399
2.99-3.296.60.06314870.9980.0260.0681.00499.8
3.29-3.767.10.05414690.9980.0220.0581.02299.9
3.76-4.737.10.03415120.9990.0140.0371.00798.9
4.73-307.40.029160510.0110.0320.99899.6

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
Blu-Icedata collection
HKL-2000data scaling
PHASER2.5.3phasing
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.204→25.871 Å / FOM work R set: 0.796 / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 25.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.248 1404 10.02 %
Rwork0.2089 12608 -
obs0.2129 14012 94.64 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.31 Å2 / Biso mean: 30.28 Å2 / Biso min: 10.3 Å2
Refinement stepCycle: final / Resolution: 2.204→25.871 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2047 0 86 49 2182
Biso mean--47.45 33.18 -
Num. residues----266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0022181
X-RAY DIFFRACTIONf_angle_d0.6932963
X-RAY DIFFRACTIONf_chiral_restr0.032306
X-RAY DIFFRACTIONf_plane_restr0.004386
X-RAY DIFFRACTIONf_dihedral_angle_d17.566909
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2038-2.28250.30391230.25031080120383
2.2825-2.37380.27371290.23491144127388
2.3738-2.48180.28881310.24991169130090
2.4818-2.61250.3281360.23821230136693
2.6125-2.7760.27561410.22571258139995
2.776-2.990.28131410.23191287142898
2.99-3.29040.27921470.23051335148299
3.2904-3.76530.24391480.197613181466100
3.7653-4.73910.19411500.16491357150799
4.7391-25.87260.21121580.199814301588100
Refinement TLS params.Method: refined / Origin x: -10.9706 Å / Origin y: -6.7375 Å / Origin z: -12.816 Å
111213212223313233
T0.0906 Å20.0034 Å20.0013 Å2-0.1792 Å20.005 Å2--0.135 Å2
L0.1752 °2-0.1271 °20.2799 °2-3.9357 °20.563 °2--1.3803 °2
S0.0214 Å °0.0232 Å °-0.0249 Å °0.0048 Å °-0.0049 Å °-0.0717 Å °0.068 Å °0.0229 Å °-0.0128 Å °
Refinement TLS groupSelection details: all

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