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- PDB-3nv2: Crystal structure of human galectin-9 C-terminal CRD in complex w... -

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Basic information

Entry
Database: PDB / ID: 3nv2
TitleCrystal structure of human galectin-9 C-terminal CRD in complex with N-acetyllactosamine
ComponentsGalectin 9 short isoform variant
KeywordsSUGAR BINDING PROTEIN / Sugar binding
Function / homology
Function and homology information


positive regulation of activated T cell autonomous cell death / Interleukin-2 family signaling / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response / positive regulation of dendritic cell apoptotic process / disaccharide binding / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / negative regulation of mast cell degranulation / positive regulation of dendritic cell chemotaxis / positive regulation of dendritic cell differentiation / galactoside binding ...positive regulation of activated T cell autonomous cell death / Interleukin-2 family signaling / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response / positive regulation of dendritic cell apoptotic process / disaccharide binding / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / negative regulation of mast cell degranulation / positive regulation of dendritic cell chemotaxis / positive regulation of dendritic cell differentiation / galactoside binding / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway / positive regulation of transforming growth factor beta production / galactose binding / negative regulation of chemokine production / positive regulation of CD4-positive, alpha-beta T cell proliferation / negative regulation of CD4-positive, alpha-beta T cell proliferation / positive regulation of monocyte chemotactic protein-1 production / natural killer cell tolerance induction / negative regulation of natural killer cell mediated cytotoxicity / positive regulation of interleukin-13 production / p38MAPK cascade / negative regulation of activated T cell proliferation / positive regulation of interleukin-10 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / maternal process involved in female pregnancy / positive regulation of interleukin-4 production / ERK1 and ERK2 cascade / positive regulation of interleukin-12 production / response to interleukin-1 / positive regulation of interleukin-1 beta production / female pregnancy / positive regulation of interleukin-8 production / cellular response to virus / cellular response to type II interferon / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / chemotaxis / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / positive regulation of NF-kappaB transcription factor activity / carbohydrate binding / collagen-containing extracellular matrix / positive regulation of canonical NF-kappaB signal transduction / response to lipopolysaccharide / positive regulation of viral entry into host cell / positive regulation of ERK1 and ERK2 cascade / inflammatory response / negative regulation of gene expression / positive regulation of gene expression / enzyme binding / extracellular space / nucleus / 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
N-acetyl-alpha-lactosamine / NICKEL (II) ION / Galectin-9 / Galectin-9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsYoshida, H. / Kamitori, S.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: X-ray structures of human galectin-9 C-terminal domain in complexes with a biantennary oligosaccharide and sialyllactose
Authors: Yoshida, H. / Teraoka, M. / Nishi, N. / Nakakita, S. / Nakamura, T. / Hirashima, M. / Kamitori, S.
History
DepositionJul 7, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
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 / entity_name_com / 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_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _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 1, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galectin 9 short isoform variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1723
Polymers15,7301
Non-polymers4422
Water2,522140
1
A: Galectin 9 short isoform variant
hetero molecules

A: Galectin 9 short isoform variant
hetero molecules

A: Galectin 9 short isoform variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5169
Polymers47,1903
Non-polymers1,3266
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area2780 Å2
ΔGint-22 kcal/mol
Surface area17740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.805, 70.805, 50.209
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
Components on special symmetry positions
IDModelComponents
11A-401-

NI

DetailsAUTHOR STATES THAT THE BIOLOGICAL ASSEMBLY IS UNKNOWN.

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Components

#1: Protein Galectin 9 short isoform variant / Galectin-9


Mass: 15729.982 Da / Num. of mol.: 1
Fragment: C-terminal carbohydrate recognition domain, residues 186-323
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX-4T-2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q53FQ0, UniProt: O00182*PLUS
#2: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose / N-acetyl-alpha-lactosamine


Type: oligosaccharide, Oligosaccharide / Class: Glycan component / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: N-acetyl-alpha-lactosamine
DescriptorTypeProgram
DGalpb1-4DGlcpNAca1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5_2*NCC/3=O][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 140 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE LIGANDS GAL AND NDG FORM N-ACETYLLACTOSAMINE.

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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: 2.31 Å3/Da / Density % sol: 46.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 20% PEG MME 2000, 0.1M Tris pH 8.5, 0.01M nickel chloride hexahydrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 28, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.34→50 Å / Num. obs: 6135 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11.2 % / Biso Wilson estimate: 24.1 Å2 / Rmerge(I) obs: 0.075 / Net I/σ(I): 8.7 / Num. measured all: 68565
Reflection shellResolution: 2.34→2.38 Å / Redundancy: 11.2 % / Rmerge(I) obs: 0.385 / Mean I/σ(I) obs: 7.4 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3KOE

3koe
PDB Unreleased entry


Resolution: 2.34→38.85 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 40669.38 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.231 659 11 %RANDOM
Rwork0.179 ---
all0.185 5989 --
obs0.179 5989 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.142 Å2 / ksol: 0.364624 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.56 Å22.79 Å20 Å2
2--1.56 Å20 Å2
3----3.12 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2.34→38.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1090 0 27 140 1257
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d27.2
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 2.34→2.49 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.256 108 11.5 %
Rwork0.171 829 -
obs-829 92.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4water_rep.paramwater.top

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