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- PDB-4y1v: Complex of human Galectin-1 and Galbeta1-3GlcNAc -

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Basic information

Entry
Database: PDB / ID: 4y1v
TitleComplex of human Galectin-1 and Galbeta1-3GlcNAc
ComponentsGalectin-1
KeywordsSUGAR BINDING PROTEIN / Complex / Galectin-1 / lectin / type 1 LacNAc
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) / collagen-containing extracellular matrix / regulation of apoptotic process / positive regulation of canonical NF-kappaB signal transduction / positive regulation of viral entry into host cell / receptor ligand activity / positive regulation of apoptotic process / endoplasmic reticulum lumen / apoptotic process / RNA binding / extracellular space / 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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.32 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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / _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_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.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_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_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
Revision 2.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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)34,6174
Polymers33,8222
Non-polymers7952
Water1,08160
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.715, 58.291, 111.591
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-terminus 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-(1-3)-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
DGalpb1-3DGlcpNAc[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/a3-b1WURCSPDB2Glycan 1.1.0
[][methyl]{[(1+1)][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 2.43 Å3/Da / Density % sol: 49.45 %
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: Nov 3, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 2.32→30 Å / Num. obs: 12886 / % possible obs: 99.2 % / Redundancy: 4.5 % / Biso Wilson estimate: 28.79 Å2 / Rmerge(I) obs: 0.041 / Rpim(I) all: 0.022 / Rrim(I) all: 0.047 / Χ2: 0.907 / Net I/av σ(I): 30.454 / Net I/σ(I): 18.2 / Num. measured all: 57534
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.32-2.43.80.20812140.9660.1230.2430.99795.2
2.4-2.54.40.20312650.9650.1120.2330.97199.9
2.5-2.614.60.16712670.9750.0890.190.94699.8
2.61-2.754.70.1112640.9890.0570.1250.92399.8
2.75-2.924.70.07812940.9940.0410.0890.90699.5
2.92-3.154.70.05712670.9960.030.0650.8799.6
3.15-3.464.60.03712890.9980.020.0420.803100
3.46-3.964.60.02712980.9990.0140.030.75699.9
3.96-4.994.40.0313220.9990.0150.0331.02499.3
4.99-304.10.02714060.9980.0150.0310.90998.8

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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
PHENIXmodel building
PHENIXrefinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W6N

1w6n


Resolution: 2.32→25.833 Å / FOM work R set: 0.8109 / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 0.15 / Phase error: 24.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2677 1247 10.03 %
Rwork0.2171 11183 -
obs0.222 12430 96.14 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 130.15 Å2 / Biso mean: 38.4 Å2 / Biso min: 16.76 Å2
Refinement stepCycle: final / Resolution: 2.32→25.833 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2048 0 54 60 2162
Biso mean--50.84 41.24 -
Num. residues----266
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062148
X-RAY DIFFRACTIONf_angle_d0.9712910
X-RAY DIFFRACTIONf_chiral_restr0.039304
X-RAY DIFFRACTIONf_plane_restr0.004384
X-RAY DIFFRACTIONf_dihedral_angle_d26.121866
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3185-2.41120.34871220.27761083120586
2.4112-2.52090.33131310.26951170130193
2.5209-2.65370.28941340.25871208134295
2.6537-2.81980.27691380.24431229136797
2.8198-3.03720.32141410.25451251139297
3.0372-3.34220.26041400.22551279141999
3.3422-3.82450.26791420.193112831425100
3.8245-4.81340.22081450.16451312145799
4.8134-25.83490.2521540.22031368152299
Refinement TLS params.Method: refined / Origin x: 11.3375 Å / Origin y: -22.3516 Å / Origin z: -12.6699 Å
111213212223313233
T0.129 Å20.0127 Å20.0051 Å2-0.2895 Å2-0.0127 Å2--0.1323 Å2
L0.1879 °2-0.2681 °2-0.2989 °2-6.155 °2-1.0302 °2--1.0393 °2
S0.061 Å °-0.0155 Å °0.0089 Å °0.0336 Å °-0.0248 Å °0.2076 Å °-0.0703 Å °-0.0592 Å °-0.015 Å °
Refinement TLS groupSelection details: all

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