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- PDB-2eak: Crystal structure of human galectin-9 N-terminal CRD in complex w... -

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Basic information

Entry
Database: PDB / ID: 2eak
TitleCrystal structure of human galectin-9 N-terminal CRD in complex with lactose
ComponentsGalectin-9
KeywordsSUGAR BINDING PROTEIN / beta sandwich / carbohydrate binding protein / galectin
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 / positive regulation of dendritic cell chemotaxis / negative regulation of mast cell degranulation / 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 / positive regulation of dendritic cell chemotaxis / negative regulation of mast cell degranulation / 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 / ERK1 and ERK2 cascade / positive regulation of interleukin-12 production / 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 / chemotaxis / positive regulation of interleukin-6 production / 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
alpha-lactose / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL / Galectin-9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsNagae, M. / Nakamura-Tsuruta, S. / Nishi, N. / Nakamura, T. / Hirabayashi, J. / Wakatsuki, S. / Kato, R.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structural analysis of the human galectin-9 N-terminal carbohydrate recognition domain reveals unexpected properties that differ from the mouse orthologue.
Authors: Nagae, M. / Nishi, N. / Nakamura-Tsuruta, S. / Hirabayashi, J. / Wakatsuki, S. / Kato, R.
History
DepositionJan 31, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Feb 22, 2012Group: Database references / Non-polymer description
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / 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 / 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.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galectin-9
B: Galectin-9
C: Galectin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0067
Polymers49,0753
Non-polymers9314
Water4,954275
1
A: Galectin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,8553
Polymers16,3581
Non-polymers4972
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Galectin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,4502
Polymers16,3581
Non-polymers921
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Galectin-9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7012
Polymers16,3581
Non-polymers3421
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)70.681, 118.687, 132.052
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

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


Mass: 16358.354 Da / Num. of mol.: 3 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pGEX4T-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O00182
#2: Polysaccharide beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose / alpha-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1a_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#3: Chemical ChemComp-DTV / (2S,3S)-1,4-DIMERCAPTOBUTANE-2,3-DIOL


Mass: 154.251 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2S2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 275 / 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: 2.82 Å3/Da / Density % sol: 56.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.2M ammonium fluoride, 20% PEG 3350, pH 7.2, 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 210 / Detector: CCD / Date: Nov 5, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.96→132.45 Å / Num. all: 36556 / Num. obs: 34714 / % possible obs: 91.8 % / Redundancy: 6.1 % / Rsym value: 0.075
Reflection shellResolution: 1.97→2.04 Å / Redundancy: 6.1 % / Num. unique all: 3595 / Rsym value: 0.313 / % possible all: 91.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→132.45 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.881 / SU B: 3.667 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.27846 1841 5 %RANDOM
Rwork0.22317 ---
obs0.22587 33289 91.36 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 22.062 Å2
Baniso -1Baniso -2Baniso -3
1--0.3 Å20 Å20 Å2
2---0.01 Å20 Å2
3---0.3 Å2
Refinement stepCycle: LAST / Resolution: 1.97→132.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3335 0 60 275 3670
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223507
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5351.944761
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.5885424
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.4123.757173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.94315509
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1691518
X-RAY DIFFRACTIONr_chiral_restr0.1140.2515
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022740
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.210.21512
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3120.22362
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2292
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1790.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3980.221
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0061.52184
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.54423427
X-RAY DIFFRACTIONr_scbond_it2.11131495
X-RAY DIFFRACTIONr_scangle_it3.1464.51334
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.964→2.015 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 131 -
Rwork0.228 2363 -
obs--85.53 %

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