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- PDB-7p11: Galectin-8 N-terminal carbohydrate recognition domain in complex ... -

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Basic information

Entry
Database: PDB / ID: 7p11
TitleGalectin-8 N-terminal carbohydrate recognition domain in complex with quinoline D-galactal ligand
Components
  • Galectin-8
  • Isoform 2 of Galectin-8
KeywordsSUGAR BINDING PROTEIN / Inhibitor / complex / Galectin / Lectin / D-galactal
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-5KM / Galectin-8
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHassan, M. / Hakansson, M. / Nilsson, J.U. / Kovacic, R.
Funding support Sweden, 1items
OrganizationGrant numberCountry
H2020 Marie Curie Actions of the European Commission765581 Sweden
CitationJournal: 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.
History
DepositionJul 1, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 15, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 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: Galectin-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7475
Polymers34,0492
Non-polymers6983
Water2,882160
1
A: Isoform 2 of Galectin-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,3343
Polymers16,9671
Non-polymers3672
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Galectin-8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,4132
Polymers17,0821
Non-polymers3311
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.620, 61.394, 85.242
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.: 1
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: Protein Galectin-8 / Gal-8 / Po66 carbohydrate-binding protein / Po66-CBP / Prostate carcinoma tumor antigen 1 / PCTA-1


Mass: 17081.572 Da / Num. of mol.: 1
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
#3: Chemical ChemComp-5KM / 2-[[(2~{R},3~{R},4~{R})-2-(hydroxymethyl)-3-oxidanyl-3,4-dihydro-2~{H}-pyran-4-yl]oxymethyl]quinoline-7-carboxylic acid


Mass: 331.320 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H17NO6 / Feature type: SUBJECT OF INVESTIGATION
#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.: 160 / 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: 2.1→46.03 Å / Num. obs: 16364 / % possible obs: 99.91 % / Redundancy: 6.4 % / Rmerge(I) obs: 0.144 / Net I/σ(I): 8.8
Reflection shellResolution: 2.1→2.103 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: 2.1→46.03 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.943 / SU B: 26.772 / SU ML: 0.271 / Cross valid method: THROUGHOUT / ESU R: 0.296 / ESU R Free: 0.226 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26304 860 5 %RANDOM
Rwork0.20512 ---
obs0.20826 16364 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.102 Å2
Baniso -1Baniso -2Baniso -3
1--2.2 Å20 Å20 Å2
2--4.99 Å2-0 Å2
3----2.78 Å2
Refinement stepCycle: 1 / Resolution: 2.1→46.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2386 0 49 160 2595
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0132551
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172359
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.6713466
X-RAY DIFFRACTIONr_angle_other_deg1.2341.5975490
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9295312
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.38922.409137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.8115431
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7871516
X-RAY DIFFRACTIONr_chiral_restr0.0650.2336
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.022851
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02551
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_it1.5812.9471220
X-RAY DIFFRACTIONr_mcbond_other1.5822.9451217
X-RAY DIFFRACTIONr_mcangle_it2.6194.4081525
X-RAY DIFFRACTIONr_mcangle_other2.6194.4091526
X-RAY DIFFRACTIONr_scbond_it1.723.1831331
X-RAY DIFFRACTIONr_scbond_other1.7193.1841332
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.8144.6881937
X-RAY DIFFRACTIONr_long_range_B_refined5.22233.3132714
X-RAY DIFFRACTIONr_long_range_B_other5.16433.2892693
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 4399 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.103→2.157 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.396 56 -
Rwork0.366 1179 -
obs--99.76 %
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)
12.6364-0.5652-0.22142.32810.45781.9283-0.08640.06920.03950.27960.01010.01720.1111-0.08190.07630.1289-0.0765-0.02630.078-0.01340.11415.5987-0.2456-1.5532
23.0630.1583-1.62752.4139-0.18462.77980.02340.39980.0784-0.2488-0.04980.04050.0909-0.28180.02640.11960.0508-0.01630.12160.0250.095742.04561.9699-21.1782
30.2995-0.1345-0.26440.3583-0.01590.5555-0.01510.0720.1268-0.02610.00360.03180.1746-0.04420.01150.30640.00390.00140.0340.03380.319526.8046-0.2-7.9072
400000000000000-00.4592-0.0138-0.20080.0276-0.06720.285231.833-5.54-7.409
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A14 - 201
2X-RAY DIFFRACTION2B13 - 201
3X-RAY DIFFRACTION3D6 - 402
4X-RAY DIFFRACTION4C1

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