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- PDB-4y1u: Complex of human Galectin-1 and Galbeta1-4GlcNAc -

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Basic information

Entry
Database: PDB / ID: 4y1u
TitleComplex of human Galectin-1 and Galbeta1-4GlcNAc
ComponentsGalectin-1
KeywordsSUGAR BINDING PROTEIN / Complex / Galectin-1 / Lectin / type 2 LacNAc
Function / homology
Function and homology information


galectin complex / 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) / carbohydrate binding ...galectin complex / 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) / carbohydrate binding / collagen-containing extracellular matrix / 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 / endoplasmic reticulum lumen / apoptotic process / extracellular space / RNA binding / extracellular exosome / extracellular region / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.762 Å
AuthorsLin, H.Y. / Hsieh, T.J. / Lin, C.H.
Funding support Taiwan, 4items
OrganizationGrant numberCountry
Academia SinicaAS-022316 Taiwan
Ministry of Science and Technology102-2923-M-001-001-MY3 Taiwan
Ministry of Science and Technology102-2113-M-001-001-MY3 Taiwan
Ministry of Science and Technology103-2113-M-001-023-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 / 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_prerelease_seq / pdbx_struct_assembly_gen / pdbx_struct_oper_list / 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.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_value_order / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 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
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)34,6174
Polymers33,8222
Non-polymers7952
Water2,720151
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.300, 58.234, 111.649
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: 16910.967 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The N-termius residues are missing due to disorder.
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P09382
#2: Polysaccharide beta-D-galactopyranose-(1-4)-methyl 2-acetamido-2-deoxy-beta-D-glucopyranoside


Type: oligosaccharide / Mass: 397.375 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAc[1Me]b1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_1*OC_2*NCC/3=O][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 151 / 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: 2.41 Å3/Da / Density % sol: 48.94 %
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 14, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.76→30 Å / Num. obs: 28643 / % possible obs: 99.8 % / Redundancy: 5.9 % / Biso Wilson estimate: 18.89 Å2 / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.02 / Rrim(I) all: 0.048 / Χ2: 1.005 / Net I/av σ(I): 34.698 / Net I/σ(I): 18 / Num. measured all: 167642
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.76-1.825.70.24227960.9830.1090.2661.00899.4
1.82-1.960.18328160.9880.0810.2011.009100
1.9-1.9860.1328170.9920.0570.1421.005100
1.98-2.0960.09128260.9960.040.11.003100
2.09-2.2260.06628330.9980.0290.0730.997100
2.22-2.3960.05328480.9990.0230.0581.003100
2.39-2.6360.04328480.9990.0190.0471.005100
2.63-3.015.90.0428870.9980.0180.0441.008100
3.01-3.795.50.04829130.9980.0220.0531.00899.9
3.79-305.50.02530590.9990.0120.0281.00499.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Blu-Icedata collection
HKL-2000data processing
HKL-2000data scaling
PHASER2.5.3phasing
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W6N

1w6n


Resolution: 1.762→23.615 Å / FOM work R set: 0.8286 / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 23.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2274 1956 6.99 %
Rwork0.1817 26012 -
obs0.1848 27968 97.51 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 111.64 Å2 / Biso mean: 30.34 Å2 / Biso min: 10.27 Å2
Refinement stepCycle: final / Resolution: 1.762→23.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2048 0 54 151 2253
Biso mean--35.67 39.49 -
Num. residues----266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142148
X-RAY DIFFRACTIONf_angle_d1.482910
X-RAY DIFFRACTIONf_chiral_restr0.076324
X-RAY DIFFRACTIONf_plane_restr0.008384
X-RAY DIFFRACTIONf_dihedral_angle_d20.345800
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7616-1.80560.27281260.2181644177087
1.8056-1.85440.28891300.20471740187094
1.8544-1.9090.241290.19281811194096
1.909-1.97060.24441380.181812195096
1.9706-2.0410.23691370.17661809194697
2.041-2.12260.23421410.1811861200299
2.1226-2.21920.2361410.17991873201499
2.2192-2.33610.23981400.17411861200199
2.3361-2.48230.22311420.19791880202299
2.4823-2.67370.26711450.198919062051100
2.6737-2.94230.24191420.197218952037100
2.9423-3.3670.2311450.193119242069100
3.367-4.23810.19941470.152919582105100
4.2381-23.61760.20151530.17792038219199
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)
16.5832-6.3792-1.70287.84120.92797.96810.39680.39980.2371-0.3635-0.1984-0.4747-0.39510.1989-0.13570.1855-0.05210.04060.0734-0.04310.2598-7.5114-11.2688-18.1327
26.79033.0635-6.56765.5673-1.97796.82570.2563-0.3030.47530.6009-0.01740.46240.34270.1015-0.19330.23160.0064-0.00780.1697-0.03330.1941-14.5802-17.7744-4.0408
32.18090.12540.15054.6413-0.23734.55980.1456-0.1439-0.05750.3367-0.00430.38740.7064-0.3811-0.14110.2505-0.0545-0.03180.1246-0.00220.1225-16.8115-24.3535-14.5026
42.75870.26750.83387.1677-0.91244.94220.02870.06360.1111-0.45420.03060.37860.6167-0.3091-0.11430.2984-0.0106-0.0840.14410.0120.1533-16.7372-26.7446-24.5968
52.99090.6847-0.61625.24620.61620.21950.1761-0.21430.11081.00560.19030.12960.81850.1675-0.20480.45430.0202-0.05180.17540.02430.2208-13.5976-29.5793-5.4424
63.24060.5955-1.07675.5531.17124.02550.1313-0.12650.13680.07290.2544-0.33140.54060.3083-0.35590.17760.0739-0.06540.2113-0.01990.2288-4.0449-22.0139-12.4382
72.49110.1091.0470.3628-0.50631.32650.1177-0.8164-0.60041.09650.4776-0.20570.3218-0.0144-0.33030.68010.133-0.12220.43250.04070.294-4.9366-28.1289-9.0846
83.96411.67861.88863.08820.70541.052-0.15120.5037-0.0768-1.36540.3431-0.9440.28920.3196-0.11520.34140.00230.1210.2078-0.00040.2384-5.5673-19.7319-25.4073
99.66377.4637-7.53368.0994-7.13896.67060.13310.06480.03620.42170.22630.4385-0.0478-0.661-0.41140.1854-0.00590.00150.21340.03690.2082-17.3489-15.423-13.559
105.01274.1616-3.54833.9045-3.16392.67520.0336-0.48880.0103-0.1275-0.20840.7281-0.14220.06440.16450.2409-0.0422-0.01130.1912-0.05680.2936-9.8545-11.3181-6.9215
117.9498-4.6702-3.96797.73547.89578.82950.1049-0.0928-0.32640.3563-0.22250.16610.028-0.28850.19470.1927-0.00660.04350.10160.04990.245-16.9765-2.0503-10.6082
127.36490.9606-2.43031.964-0.48231.9430.3578-0.2009-0.0539-0.4548-0.3802-0.9497-0.10640.62090.19190.19930.00990.15160.21260.01470.3745-1.23742.9056-11.8406
134.46560.00341.46084.11610.19323.0769-0.11080.29990.0512-0.45460.0155-0.2044-0.25330.23490.07720.1510.00190.01190.1226-0.00090.097-11.404911.8515-17.3148
143.3895-1.24281.06334.6325-1.13622.9607-0.09820.29660.17080.3786-0.2095-0.942-0.30.44060.24910.2011-0.0501-0.04640.22330.01720.2725-4.077110.4807-8.0203
152.6358-0.72980.17975.4806-0.04043.4401-0.2715-0.1740.11380.56630.04790.1751-0.144-0.10930.14790.19340.01990.01480.127-0.01260.1343-15.69410.3631-5.4092
164.3675.5288-1.41577.4844-1.02735.69760.08190.2462-0.3074-0.7688-0.1639-0.8685-0.01170.59860.20030.1970.05360.06770.19030.0120.263-9.04682.2631-17.7328
173.34562.5017-3.69432.1841-2.77264.08930.37810.03330.1866-0.2774-0.1521-0.2424-0.45280.4339-0.41440.18590.01840.01950.17940.00550.2169-6.2252-3.4267-9.0365
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 15 )
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 29 )
3X-RAY DIFFRACTION3chain 'A' and (resid 30 through 61 )
4X-RAY DIFFRACTION4chain 'A' and (resid 62 through 71 )
5X-RAY DIFFRACTION5chain 'A' and (resid 72 through 82 )
6X-RAY DIFFRACTION6chain 'A' and (resid 83 through 99 )
7X-RAY DIFFRACTION7chain 'A' and (resid 100 through 109 )
8X-RAY DIFFRACTION8chain 'A' and (resid 110 through 118 )
9X-RAY DIFFRACTION9chain 'A' and (resid 119 through 125 )
10X-RAY DIFFRACTION10chain 'A' and (resid 126 through 134 )
11X-RAY DIFFRACTION11chain 'B' and (resid 2 through 15 )
12X-RAY DIFFRACTION12chain 'B' and (resid 16 through 29 )
13X-RAY DIFFRACTION13chain 'B' and (resid 30 through 71 )
14X-RAY DIFFRACTION14chain 'B' and (resid 72 through 91 )
15X-RAY DIFFRACTION15chain 'B' and (resid 92 through 118 )
16X-RAY DIFFRACTION16chain 'B' and (resid 119 through 125 )
17X-RAY DIFFRACTION17chain 'B' and (resid 126 through 134 )

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