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- PDB-3lse: N-Domain of human adhesion/growth-regulatory galectin-9 in comple... -

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Basic information

Entry
Database: PDB / ID: 3lse
TitleN-Domain of human adhesion/growth-regulatory galectin-9 in complex with lactose
ComponentsGalectin-9
KeywordsSUGAR BINDING PROTEIN / MAINLY BETA / Alternative splicing / Cytoplasm / Lectin / Polymorphism / Secreted
Function / homology
Function and homology information


positive regulation of activated T cell autonomous cell death / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response / Interleukin-2 family signaling / positive regulation of dendritic cell apoptotic process / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / natural killer cell tolerance induction / negative regulation of mast cell degranulation / positive regulation of dendritic cell chemotaxis / positive regulation of dendritic cell differentiation / positive regulation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway ...positive regulation of activated T cell autonomous cell death / positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response / Interleukin-2 family signaling / positive regulation of dendritic cell apoptotic process / positive regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / natural killer cell tolerance induction / negative regulation of mast cell degranulation / positive regulation of dendritic cell chemotaxis / positive regulation of dendritic cell differentiation / 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 natural killer cell mediated cytotoxicity / disaccharide binding / galactoside binding / positive regulation of interleukin-13 production / 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 / positive regulation of interleukin-4 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-12 production / ERK1 and ERK2 cascade / response to interleukin-1 / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / female pregnancy / cellular response to virus / cellular response to type II interferon / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of interleukin-6 production / chemotaxis / positive regulation of tumor necrosis factor production / positive regulation of type II interferon production / positive regulation of NF-kappaB transcription factor activity / carbohydrate binding / positive regulation of canonical NF-kappaB signal transduction / collagen-containing extracellular matrix / 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 / cytoplasm / cytosol
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
beta-lactose / Galectin-9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.69 Å
AuthorsRuiz, F.M. / Romero, A.
CitationJournal: Int.J.Biochem.Cell Biol. / Year: 2010
Title: N-domain of human adhesion/growth-regulatory galectin-9: preference for distinct conformers and non-sialylated N-glycans and detection of ligand-induced structural changes in crystal and solution.
Authors: Solis, D. / Mate, M.J. / Lohr, M. / Ribeiro, J.P. / Lopez-Merino, L. / Andre, S. / Buzamet, E. / Canada, F.J. / Kaltner, H. / Lensch, M. / Ruiz, F.M. / Haroske, G. / Wollina, U. / Kloor, M. ...Authors: Solis, D. / Mate, M.J. / Lohr, M. / Ribeiro, J.P. / Lopez-Merino, L. / Andre, S. / Buzamet, E. / Canada, F.J. / Kaltner, H. / Lensch, M. / Ruiz, F.M. / Haroske, G. / Wollina, U. / Kloor, M. / Kopitz, J. / Saiz, J.L. / Menendez, M. / Jimenez-Barbero, J. / Romero, A. / Gabius, H.J.
History
DepositionFeb 12, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 5, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / database_PDB_caveat / 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_unobs_or_zero_occ_atoms / pdbx_validate_chiral / 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_atom_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_atom_id / _pdbx_validate_chiral.auth_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 6, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galectin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2072
Polymers15,8651
Non-polymers3421
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Galectin-9
hetero molecules

A: Galectin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,4144
Polymers31,7302
Non-polymers6852
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1900 Å2
ΔGint-1 kcal/mol
Surface area12890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)32.387, 32.387, 232.208
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Galectin-9 / Gal-9, HOM-HD-21, Ecalectin / Gal-9 / HOM-HD-21 / Ecalectin


Mass: 15864.775 Da / Num. of mol.: 1 / Fragment: N-terminal domain, residues 6-148
Source method: isolated from a genetically manipulated source
Details: Galectin-9-specific mRNA from human SW480 colon adenocarcinoma cells was used for cloning of full-length cDNA.
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS9 / Plasmid: pET-12a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: O00182
#2: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE

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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: 1.92 Å3/Da / Density % sol: 35.97 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 30 % PEG 2000, 0.1 M Hepes (pH 7.0), VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM16
DetectorType: ADSC QUANTUM 210r / Detector: CCD
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.69→58.03 Å / Num. obs: 3930 / % possible obs: 96.7 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 9.4 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 21.1
Reflection shellResolution: 2.69→2.75 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 5.1 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A3K

1a3k


Resolution: 2.69→58.03 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.834 / SU B: 54.215 / SU ML: 0.487 / Cross valid method: THROUGHOUT / ESU R Free: 0.551 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.35202 169 4.5 %RANDOM
Rwork0.22338 ---
obs0.22918 3588 95.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.253 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.06 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 2.69→58.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1119 0 23 0 1142
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221172
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9381.9441592
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.325142
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.14323.68457
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.67815169
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.762156
X-RAY DIFFRACTIONr_chiral_restr0.1460.2174
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021909
X-RAY DIFFRACTIONr_gen_planes_other
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_it0.5781.5707
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.02821142
X-RAY DIFFRACTIONr_scbond_it1.3133465
X-RAY DIFFRACTIONr_scangle_it2.1484.5450
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.694→2.764 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.926 7 -
Rwork0.374 207 -
obs--83.92 %
Refinement TLS params.Method: refined / Origin x: -5.001 Å / Origin y: -13.179 Å / Origin z: -15.01 Å
111213212223313233
T0.5176 Å20.0159 Å2-0.0208 Å2-0.0315 Å2-0.0099 Å2--0.0047 Å2
L4.5331 °21.9361 °20.3151 °2-9.6489 °2-0.7217 °2--10.859 °2
S0.035 Å °0.2022 Å °-0.0039 Å °-0.5395 Å °-0.1491 Å °0.1328 Å °0.8761 Å °-0.3526 Å °0.1141 Å °

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