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- PDB-7aen: Galectin-8 N-terminal carbohydrate recognition domain in complex ... -

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Basic information

Entry
Database: PDB / ID: 7aen
TitleGalectin-8 N-terminal carbohydrate recognition domain in complex with methyl 3-O-((7-carboxy)quinolin-2-yl)-methoxy)-beta-D-galactopyranoside
ComponentsIsoform 2 of Galectin-8
KeywordsSUGAR BINDING PROTEIN / Inhibitor / complex
Function / homology
Function and homology information


lymphatic endothelial cell migration / xenophagy / cellular response to virus / integrin binding / carbohydrate binding / cytoplasmic vesicle / extracellular space / 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. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Chem-R8B / Galectin-8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHassan, M. / Klavern, V.S. / Hakansson, M. / Anderluh, M. / Tomasic, T. / Jakopin, Z. / Nilsson, J.U. / Kovacic, R. / Walse, B. / Diehl, C.
Funding support Sweden, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission765581 Sweden
Citation
Journal: Acs Med.Chem.Lett. / Year: 2021
Title: Structure-Guided Design of d-Galactal Derivatives with High Affinity and Selectivity for the Galectin-8 N-Terminal Domain
Authors: Hassan, M. / Baussiere, F. / Guzelj, S. / Sundin, A.P. / Hakansson, M. / Kovacic, R. / Leffler, H. / Tomasic, T. / Anderluh, M. / Jakopin, Z. / Nilsson, U.J.
#1: Journal: Chemmedchem / Year: 2021
Title: Selective Galectin-8N Ligands: The Design and Synthesis of Phthalazinone-d-Galactals
Authors: van Klaveren, S. / Sundin, A.P. / Jakopin, Z. / Anderluh, M. / Leffler, H. / Nilsson, U.J. / Tomasic, T.
#2: Journal: Chemmedchem / Year: 2021
Title: Selective Monovalent Galectin-8 Ligands Based on 3-Lactoylgalactoside
Authors: Girardi, B. / Manna, M. / Van Klaveren, S. / Tomasic, T. / Jakopin, Z. / Leffler, H. / Nilsson, U.J. / Ricklin, D. / Mravljak, J. / Schwardt, O. / Anderluh, M.
History
DepositionSep 17, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 28, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 9, 2022Group: Database references / Derived calculations / Structure summary
Category: chem_comp / citation ...chem_comp / citation / citation_author / database_2 / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Isoform 2 of Galectin-8
B: Isoform 2 of Galectin-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,8216
Polymers33,9352
Non-polymers8864
Water4,450247
1
A: Isoform 2 of Galectin-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4744
Polymers16,9671
Non-polymers5073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Isoform 2 of Galectin-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3472
Polymers16,9671
Non-polymers3791
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.452, 61.124, 84.712
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
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A14 - 160
2010B14 - 160

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Components

#1: Protein Isoform 2 of Galectin-8 / Gal-8 / Po66 carbohydrate-binding protein / Po66-CBP / Prostate carcinoma tumor antigen 1 / PCTA-1


Mass: 16967.467 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS8 / Production host: Escherichia coli (E. coli) / References: UniProt: O00214
#2: Chemical ChemComp-R8B / methyl 3-O-((7-carboxy) quinolin-2-yl)-methyl)-beta-D-galactopyranoside / 2-[[(2~{R},3~{S},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-methoxy-3,5-bis(oxidanyl)oxan-4-yl]oxymethyl]quinoline-7-carboxylic acid


Mass: 379.361 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H21NO8 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.01 Å3/Da / Density % sol: 38.85 %
Crystal growTemperature: 293.5 K / Method: liquid diffusion / pH: 8
Details: buffer (10mM Tris/HCl pH 8.0, 150 mM NaCl, 10 mm lactose and 1 mM TCEP) mixed with reservoir 25% (w/v) PEG 2000 monomethylethyer (MME), a cryo solution (10 mM Tris/HCl pH 8.0, 50 mM NaCl, 10 ...Details: buffer (10mM Tris/HCl pH 8.0, 150 mM NaCl, 10 mm lactose and 1 mM TCEP) mixed with reservoir 25% (w/v) PEG 2000 monomethylethyer (MME), a cryo solution (10 mM Tris/HCl pH 8.0, 50 mM NaCl, 10 mM lactose, 25% (w/v) PEG 2000 MME, 20% ethylene glycol (EG) and 1 mM TCEP) and flash-frozen in liquid nitrogen. A co-crystal with lactose, grown from a seeded drop with 24% (w/v) PEG 2000 MME in the reservoir, was used to soak in compound 1 by transferring crystals in three steps to different soaking drops. First to a 2 ul drop with glycerol ( 20% (v/v) glycerol, 25% (w/v PEG 2000 MME, 10 mM Tris/HCl pH 8.0, 50 mM NaCl and 1 mM TCEP) and secondly to a 2 ul drop with 10 mM compound 1 (10 mM Tris/HCl pH 8.0, 50 mM NaCl, 5 mM compound 1, 25% (w/v) PEG 2000 MME and 1 mM TCEP) and thirdly to a second drop with 5 mM compound 1 (same composition as before).

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Data collection

DiffractionMean temperature: 293.5 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1.00003 Å
DetectorType: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: Nov 8, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00003 Å / Relative weight: 1
ReflectionResolution: 1.6→49.57 Å / Num. obs: 35999 / % possible obs: 99.8 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.058 / Net I/σ(I): 16.4
Reflection shellResolution: 1.6→1.63 Å / Rmerge(I) obs: 1.69 / Num. unique obs: 0

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
Cootmodel building
PHASERphasing
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5GZD

5gzd


Resolution: 1.6→49.57 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.963 / SU B: 6.698 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.112 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21154 1910 5 %RANDOM
Rwork0.13924 ---
obs0.1428 35999 99.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.446 Å2
Baniso -1Baniso -2Baniso -3
1--1.25 Å20 Å20 Å2
2--1.37 Å20 Å2
3----0.12 Å2
Refinement stepCycle: 1 / Resolution: 1.6→49.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2378 0 61 247 2686
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132563
X-RAY DIFFRACTIONr_bond_other_d0.0020.0172393
X-RAY DIFFRACTIONr_angle_refined_deg1.8081.6753482
X-RAY DIFFRACTIONr_angle_other_deg1.3591.5995567
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5985313
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.48721.912136
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.57915436
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7211517
X-RAY DIFFRACTIONr_chiral_restr0.0770.2340
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022823
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02550
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.2573.0661212
X-RAY DIFFRACTIONr_mcbond_other5.2553.0671213
X-RAY DIFFRACTIONr_mcangle_it5.7354.5911513
X-RAY DIFFRACTIONr_mcangle_other5.7344.5931514
X-RAY DIFFRACTIONr_scbond_it6.5173.6071351
X-RAY DIFFRACTIONr_scbond_other6.5173.6061351
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.8475.221962
X-RAY DIFFRACTIONr_long_range_B_refined7.82137.3562766
X-RAY DIFFRACTIONr_long_range_B_other7.64736.882717
X-RAY DIFFRACTIONr_rigid_bond_restr4.02934956
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 4484 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 148 -
Rwork0.322 2602 -
obs--99.57 %

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