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- PDB-4xbl: Crystal Structure of Human Galectin-1 in Complex with Type 1 N-ac... -

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Basic information

Entry
Database: PDB / ID: 4xbl
TitleCrystal Structure of Human Galectin-1 in Complex with Type 1 N-acetyllactosamine
ComponentsGalectin-1
KeywordsSUGAR BINDING PROTEIN / Complex / Human Galectin-1 / Type 1 LacNAc
Function / homology
Function and homology information


galectin complex / lactose binding / 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) ...galectin complex / lactose binding / 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 / positive regulation of apoptotic process / endoplasmic reticulum lumen / apoptotic process / RNA binding / extracellular space / 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: 1.931 Å
AuthorsHsieh, T.J. / Lin, H.Y. / 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: Plos One / Year: 2015
Title: Structural Basis Underlying the Binding Preference of Human Galectins-1, -3 and -7 for Gal beta 1-3/4GlcNAc.
Authors: Hsieh, T.J. / Lin, H.Y. / Tu, Z. / Huang, B.S. / Wu, S.C. / Lin, C.H.
History
DepositionDec 17, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 20, 2015Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_radiation_wavelength / entity / entity_src_gen / 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.name / _chem_comp.type / _entity_src_gen.pdbx_alt_source_flag / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _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 / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
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
A: Galectin-1
B: Galectin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8294
Polymers34,0622
Non-polymers7672
Water1,892105
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2420 Å2
ΔGint8 kcal/mol
Surface area12060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.265, 58.211, 111.401
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11CHAIN A
21CHAIN B

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: ASP / End label comp-ID: ASP / Auth seq-ID: 2 - 134 / Label seq-ID: 22 - 154

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1CHAIN AAA
2CHAIN BBB

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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: 17031.201 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS1 / Plasmid: pET15b / Production host: Escherichia coli (E. coli) / References: UniProt: P09382
#2: Polysaccharide beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 2 / Source method: obtained synthetically
DescriptorTypeProgram
DGalpb1-3DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a3-b1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(3+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 105 / 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: 2.06 Å3/Da / Density % sol: 40.27 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M Tris pH 8.0, 0.2M Lithium Sulfate, 30% (w/v) PEG3350, TEMPERATURE 298 K

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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: 1.93→30 Å / Num. obs: 21733 / % possible obs: 99.5 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.056 / Rsym value: 0.056 / Net I/av σ(I): 29.67 / Net I/σ(I): 29.67
Reflection shellResolution: 1.93→2 Å / Rmerge(I) obs: 0.246 / Mean I/σ(I) obs: 7.1 / % possible all: 96.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
PHASER2.5.3phasing
PHENIXmodel building
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1W6N

1w6n


Resolution: 1.931→25.363 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.26 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2349 1932 9.16 %
Rwork0.1957 --
obs0.1993 21103 96.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.931→25.363 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2066 0 52 105 2223
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082164
X-RAY DIFFRACTIONf_angle_d1.2072926
X-RAY DIFFRACTIONf_dihedral_angle_d16.668798
X-RAY DIFFRACTIONf_chiral_restr0.052324
X-RAY DIFFRACTIONf_plane_restr0.006384
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1124X-RAY DIFFRACTION6.036TORSIONAL
12B1124X-RAY DIFFRACTION6.036TORSIONAL
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.931-1.97930.33651100.24771186X-RAY DIFFRACTION85
1.9793-2.03280.26781290.23351289X-RAY DIFFRACTION92
2.0328-2.09260.23231300.22141311X-RAY DIFFRACTION94
2.0926-2.16010.27181340.21621324X-RAY DIFFRACTION96
2.1601-2.23720.26521340.20951322X-RAY DIFFRACTION96
2.2372-2.32680.22571380.20541368X-RAY DIFFRACTION97
2.3268-2.43260.30141390.2171377X-RAY DIFFRACTION98
2.4326-2.56070.27291400.22871368X-RAY DIFFRACTION98
2.5607-2.7210.21681440.20811397X-RAY DIFFRACTION99
2.721-2.93080.2721420.20971401X-RAY DIFFRACTION99
2.9308-3.22520.22861440.20041416X-RAY DIFFRACTION100
3.2252-3.69070.22181460.18581431X-RAY DIFFRACTION100
3.6907-4.64520.21341470.15211448X-RAY DIFFRACTION100
4.6452-25.3650.21550.19131533X-RAY DIFFRACTION100
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)
14.4725-0.31422.5234.29020.0427.51320.17780.2392-0.441-0.39830.09280.34520.4379-0.1187-0.20350.2891-0.0227-0.02520.13940.04210.31096.931-17.5147-17.5574
24.09833.80354.95017.59282.29697.28220.2503-0.2032-0.75540.9707-0.0141-0.8541-0.12060.0189-0.22410.38250.0058-0.04960.23910.03860.264815.9593-11.1799-3.4262
32.2314-0.1677-0.6675.1948-0.29966.39640.0722-0.06960.0610.1313-0.0366-0.1904-0.63940.239-0.05210.3157-0.03250.03360.1625-0.00040.154516.4374-4.1912-16.7817
42.40470.60810.74785.977-1.28143.1587-0.033-0.1433-0.0270.57440.12340.2639-0.5639-0.3319-0.12290.36310.08070.08420.24440.00350.2357.9214-4.0596-9.5212
53.98811.218-1.37770.9009-0.19610.6744-0.0605-0.39660.25950.60290.46730.8042-0.2307-0.1946-0.32110.65840.18540.00720.32990.00650.30035.2239-4.9848-16.3915
65.00064.9936-1.01238.4416-1.16384.80660.2888-0.5206-0.34970.7623-0.1827-0.4030.08370.3565-0.02540.30480.0412-0.00060.20110.05490.253212.7438-16.0494-9.4549
78.8731-4.53373.65725.5301-6.82849.22620.1934-0.27480.30410.4581-0.2354-0.3053-0.08870.40650.0430.3645-0.0451-0.05410.1612-0.0480.28217.2039-26.9908-10.5707
84.52581.75882.50396.96822.85346.95590.3371-0.21660.081-0.4486-0.27811.1793-0.0841-0.8272-0.02770.31820.0641-0.07280.26130.00480.39311.2983-31.9618-11.7788
94.97530.2654-1.54385.6696-0.58732.8392-0.20670.1519-0.1172-0.47020.02780.45260.3512-0.25020.13830.2789-0.0212-0.01990.1818-0.00040.15929.3387-41.5388-15.5306
104.872-2.8804-1.30556.4489-0.42022.6551-0.4253-0.1755-0.08770.48950.21310.1151-0.0245-0.08140.21130.3425-0.0068-0.0110.22890.02230.18412.3863-36.8086-3.7939
113.4388-0.7391-1.52996.671-0.1624.4428-0.0269-0.1759-0.17390.5973-0.1278-0.17670.05480.21540.27490.27030.0322-0.04210.15450.0210.158215.8356-39.2069-6.532
123.62644.73642.56527.40951.83668.90020.64010.1710.3258-0.5067-0.35890.6611-0.0314-1.0162-0.28660.34840.0587-0.05240.33440.01330.23739.1177-31.3302-17.6811
136.82793.34143.50333.3044.62867.68040.44310.10180.07080.15790.07620.3340.5329-0.0542-0.39320.29930.034-0.00710.21170.00940.28816.2111-25.6891-8.6655
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A and (resid 2 through 16 )
2X-RAY DIFFRACTION2chain A and (resid 17 through 29 )
3X-RAY DIFFRACTION3chain A and (resid 30 through 71 )
4X-RAY DIFFRACTION4chain A and (resid 72 through 99 )
5X-RAY DIFFRACTION5chain A and (resid 100 through 118 )
6X-RAY DIFFRACTION6chain A and (resid 119 through 134 )
7X-RAY DIFFRACTION7chain B and (resid 2 through 15 )
8X-RAY DIFFRACTION8chain B and (resid 16 through 29 )
9X-RAY DIFFRACTION9chain B and (resid 30 through 83 )
10X-RAY DIFFRACTION10chain B and (resid 84 through 100 )
11X-RAY DIFFRACTION11chain B and (resid 101 through 118 )
12X-RAY DIFFRACTION12chain B and (resid 119 through 125 )
13X-RAY DIFFRACTION13chain B and (resid 126 through 134 )

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