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- PDB-4y1x: Complex of human Galectin-1 and Galbeta1-4(6OSO3)GlcNAc -

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Basic information

Entry
Database: PDB / ID: 4y1x
TitleComplex of human Galectin-1 and Galbeta1-4(6OSO3)GlcNAc
ComponentsGalectin-1
KeywordsSUGAR BINDING PROTEIN / Complex / Galectin-1 / sulfated LacNAc / Galbeta1-4(6OSO3)GlcNAc
Function / homology
Function and homology information


galectin complex / lactose binding / plasma cell differentiation / galactoside binding / myoblast differentiation / laminin binding / T cell costimulation / Post-translational protein phosphorylation / cell-cell adhesion / positive regulation of inflammatory response ...galectin complex / lactose binding / plasma cell differentiation / galactoside binding / 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 / collagen-containing extracellular matrix / positive regulation of viral entry into host cell / positive regulation of apoptotic process / endoplasmic reticulum lumen / apoptotic process / RNA binding / extracellular space / extracellular exosome / extracellular region / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.45 Å
AuthorsLin, H.Y. / Hsieh, T.J. / Lin, C.H.
Funding support Taiwan, 4items
OrganizationGrant numberCountry
Academia SinicaAS-022316 Taiwan
Ministry of Science and Technology103-2113-M-001-023-MY3 Taiwan
Ministry of Science and Technology102-2113-M-001-001-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 / 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_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

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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)34,7454
Polymers33,7902
Non-polymers9552
Water91951
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.579, 57.220, 110.945
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.: 2
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: Polysaccharide beta-D-galactopyranose-(1-4)-methyl 2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranoside


Mass: 477.439 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGalpb1-4DGlcpNAc[1Me,6S]b1-OMEGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_1*OC_2*NCC/3=O_6*OSO/3=O/3=O][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-GlcpNAc6SO3]{[(4+1)][b-D-Galp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / 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: 2.05 Å3/Da / Density % sol: 39.91 %
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: Aug 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.45→30 Å / Num. obs: 10845 / % possible obs: 99.7 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.068 / Χ2: 0.98 / Net I/av σ(I): 22.57 / Net I/σ(I): 12.5 / Num. measured all: 54812
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
2.45-2.545.10.49610550.90199.6
2.54-2.645.30.34710530.938100
2.64-2.765.30.2610850.973100
2.76-2.95.30.1810600.996100
2.9-3.095.30.13310620.99999.9
3.09-3.325.20.0910840.99399.9
3.32-3.665.20.05610740.938100
3.66-4.195.10.04710870.95199.8
4.19-5.274.70.04111111.08299.1
5.27-304.30.04211741.03698.5

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Processing

Software
NameVersionClassification
Blu-Icedata collection
HKL-2000data scaling
PHASERphasing
PHENIXmodel building
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.15data extraction
RefinementResolution: 2.45→25.293 Å / SU ML: 0.23 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.259 994 10.07 %
Rwork0.2097 --
obs0.2145 9873 91.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.64 Å2 / Biso mean: 29.0271 Å2 / Biso min: 5.6 Å2
Refinement stepCycle: final / Resolution: 2.45→25.293 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2046 0 62 51 2159
Biso mean--52.22 24.77 -
Num. residues----266
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)
14.9983-5.67820.29346.5291-1.06916.38170.16580.12330.1038-0.13080.03480.14470.32-0.1025-0.08160.18710.004-0.05860.1495-0.01330.27597.6967-17.4159-18.0171
24.74932.46825.62924.43391.7547.49020.2237-0.4248-0.13610.3791-0.0536-0.28130.0052-0.0192-0.1550.17470.00750.0150.15360.05590.175814.7047-11.042-3.9611
31.5054-0.0776-0.97621.9756-0.69323.3658-0.0054-0.13270.05750.14690.0743-0.366-0.70370.3211-0.02660.3066-0.02170.08220.1221-0.0180.093216.6921-3.9231-16.5695
41.97230.7382-0.30163.549-0.54572.44980.0086-0.16970.06170.46020.05830.502-0.4882-0.239-0.04220.21960.05840.09920.21370.00050.23337.8499-3.8069-9.3544
53.53640.3691-1.02243.1637-1.06120.58790.0207-0.25760.43840.31760.1050.558-0.2461-0.5136-0.16190.33620.1075-0.00930.2753-0.01730.21965.2643-4.6262-16.4671
64.13411.67372.58382.24041.99992.30430.0302-0.3840.04350.38210.114-0.31420.07830.28320.0480.21960.1077-0.0870.19440.01130.222417.4124-13.3182-13.4481
77.57824.6462.94492.89721.95251.6755-0.0271-0.17520.05190.3454-0.2426-0.18820.1803-0.17710.29230.17010.030.0390.19020.05930.2449.8925-17.5316-6.7973
87.6999-4.44112.84958.1036-5.93764.57580.0386-0.07290.15090.2101-0.0416-0.2094-0.05710.3334-0.07240.2685-0.0706-0.03290.1681-0.0010.199917.1631-26.3167-10.688
93.56970.80860.98582.42050.99322.0820.1186-0.29190.0866-0.4662-0.08870.8043-0.1217-0.76070.12470.17420.0574-0.07070.252-0.02660.46611.1547-31.4308-11.7442
102.21690.1647-0.3922.956-0.16912.9391-0.06040.34730.2239-0.50290.07410.11090.1827-0.0393-0.06260.12390.01940.00120.16170.03570.103113.3868-36.1185-16.0674
115.94760.67370.22370.4993-0.85572.7011-0.10930.5912-0.4709-0.39660.18440.73960.2713-0.77160.0460.1157-0.0791-0.03070.223-0.06510.43433.3526-44.934-16.6939
120.17850.1213-0.32550.2059-0.14460.98980.17340.09840.0812-0.14280.1053-0.0585-0.0874-0.07020.11720.30390.05460.58310.15080.0792-0.128618.6427-42.6076-19.9984
133.3179-0.49630.48513.21670.19764.0408-0.2562-0.3974-0.28750.3006-0.10040.9990.3046-0.60230.41040.3267-0.08340.05710.2303-0.08580.46661.7954-43.4715-9.803
144.44890.78261.25481.90360.80412.33550.0551-0.3144-0.15030.4476-0.00940.3275-0.0178-0.2141-0.09390.14750.00290.05490.26560.07160.133611.7777-35.993-3.9234
150.6904-0.4493-0.70950.88130.69452.59610.1369-0.66560.22880.49040.10730.56760.0116-0.0006-0.04170.2327-0.01280.12590.2485-0.04370.26258.4839-41.3984-2.7418
161.3732-1.75310.05093.0523-0.97461.0258-0.2251-0.06290.02750.0676-0.28-0.7138-0.00740.40820.02260.11290.09510.01530.22340.04060.372623.7869-35.5166-10.3022
173.11832.84670.14932.69290.35810.61040.26080.3681-0.1348-0.32850.04850.53450.1055-0.6377-0.160.14130.055-0.06370.29870.02310.32969.0355-30.6451-17.6172
188.08440.5208-1.11817.94380.22046.05770.47090.0951-0.20430.1560.29750.27590.2014-0.1599-0.58390.1619-0.05050.03680.2757-0.01540.08776.3398-25.251-8.8967
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 15 )A2 - 15
2X-RAY DIFFRACTION2chain 'A' and (resid 16 through 29 )A16 - 29
3X-RAY DIFFRACTION3chain 'A' and (resid 30 through 71 )A30 - 71
4X-RAY DIFFRACTION4chain 'A' and (resid 72 through 99 )A72 - 99
5X-RAY DIFFRACTION5chain 'A' and (resid 100 through 118 )A100 - 118
6X-RAY DIFFRACTION6chain 'A' and (resid 119 through 125 )A119 - 125
7X-RAY DIFFRACTION7chain 'A' and (resid 126 through 134 )A126 - 134
8X-RAY DIFFRACTION8chain 'B' and (resid 2 through 15 )B2 - 15
9X-RAY DIFFRACTION9chain 'B' and (resid 16 through 29 )B16 - 29
10X-RAY DIFFRACTION10chain 'B' and (resid 30 through 48 )B30 - 48
11X-RAY DIFFRACTION11chain 'B' and (resid 49 through 61 )B49 - 61
12X-RAY DIFFRACTION12chain 'B' and (resid 62 through 71 )B62 - 71
13X-RAY DIFFRACTION13chain 'B' and (resid 72 through 82 )B72 - 82
14X-RAY DIFFRACTION14chain 'B' and (resid 83 through 100 )B83 - 100
15X-RAY DIFFRACTION15chain 'B' and (resid 101 through 109 )B101 - 109
16X-RAY DIFFRACTION16chain 'B' and (resid 110 through 118 )B110 - 118
17X-RAY DIFFRACTION17chain 'B' and (resid 119 through 125 )B119 - 125
18X-RAY DIFFRACTION18chain 'B' and (resid 126 through 134 )B126 - 134

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