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- PDB-3wpd: Crystal structure of horse TLR9 in complex with inhibitory DNA4084 -

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Basic information

Entry
Database: PDB / ID: 3wpd
TitleCrystal structure of horse TLR9 in complex with inhibitory DNA4084
Components
  • DNA (5'-D(*CP*CP*TP*GP*GP*AP*TP*GP*GP*G)-3')
  • Toll-like receptor 9
KeywordsDNA BINDING PROTEIN/DNA / Leucine rich repeat / Receptor / Innate immunity / DNA binding / Glycosylation / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


regulation of B cell differentiation / endolysosome / positive regulation of toll-like receptor 9 signaling pathway / positive regulation of B cell activation / unmethylated CpG binding / siRNA binding / positive regulation of immunoglobulin production / toll-like receptor signaling pathway / pattern recognition receptor activity / positive regulation of interferon-alpha production ...regulation of B cell differentiation / endolysosome / positive regulation of toll-like receptor 9 signaling pathway / positive regulation of B cell activation / unmethylated CpG binding / siRNA binding / positive regulation of immunoglobulin production / toll-like receptor signaling pathway / pattern recognition receptor activity / positive regulation of interferon-alpha production / canonical NF-kappaB signal transduction / phagocytic vesicle / positive regulation of B cell proliferation / activation of innate immune response / positive regulation of interferon-beta production / positive regulation of interleukin-6 production / positive regulation of type II interferon production / defense response to virus / lysosome / positive regulation of MAPK cascade / inflammatory response / innate immune response / endoplasmic reticulum membrane / protein homodimerization activity / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Leucine-rich repeat unit / Leucine-rich repeat / TIR domain / Leucine Rich repeat / Leucine Rich Repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Toll - interleukin 1 - resistance / Leucine-rich repeats, bacterial type / TIR domain profile. ...Leucine-rich repeat unit / Leucine-rich repeat / TIR domain / Leucine Rich repeat / Leucine Rich Repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Toll - interleukin 1 - resistance / Leucine-rich repeats, bacterial type / TIR domain profile. / Alpha-Beta Horseshoe / Leucine-rich repeat, SDS22-like subfamily / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
DNA / Toll-like receptor 9
Similarity search - Component
Biological speciesEquus caballus (horse)
synthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsOhto, U. / Tanji, H. / Shimizu, T.
CitationJournal: Nature / Year: 2015
Title: Structural basis of CpG and inhibitory DNA recognition by Toll-like receptor 9
Authors: Ohto, U. / Shibata, T. / Tanji, H. / Ishida, H. / Krayukhina, E. / Uchiyama, S. / Miyake, K. / Shimizu, T.
History
DepositionJan 11, 2014Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1May 6, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_ref_seq_dif / 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_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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: Toll-like receptor 9
C: DNA (5'-D(*CP*CP*TP*GP*GP*AP*TP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,6848
Polymers92,5292
Non-polymers1,1556
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3330 Å2
ΔGint-13 kcal/mol
Surface area32430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.550, 117.080, 69.570
Angle α, β, γ (deg.)90.00, 105.46, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-903-

SO4

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Components

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Protein / DNA chain , 2 types, 2 molecules AC

#1: Protein Toll-like receptor 9


Mass: 89427.562 Da / Num. of mol.: 1 / Fragment: UNP residues 26-817
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: TLR9 / Cell (production host): SCHNEIDER 2(S2) / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: Q2EEY0
#2: DNA chain DNA (5'-D(*CP*CP*TP*GP*GP*AP*TP*GP*GP*G)-3')


Mass: 3101.027 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic (others)

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Sugars , 2 types, 3 molecules

#3: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#5: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 13 molecules

#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 2.49 Å3/Da / Density % sol: 50.67 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 14-10% PEG 3350, 0.2M ammonium sulfate, 0.1M Na acetate pH 4.5, 10% ethylene glycol , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NE3A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 11, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.75→67.05 Å / Num. obs: 23567 / Rsym value: 0.143

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.75→58.61 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.895 / SU B: 15.539 / SU ML: 0.307 / Cross valid method: THROUGHOUT / ESU R Free: 0.38 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25808 1212 5.1 %RANDOM
Rwork0.20062 ---
obs0.20364 22352 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 43.106 Å2
Baniso -1Baniso -2Baniso -3
1-4.17 Å2-0 Å2-2.19 Å2
2---3.28 Å2-0 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 2.75→58.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5909 206 71 10 6196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0196342
X-RAY DIFFRACTIONr_bond_other_d0.0010.025995
X-RAY DIFFRACTIONr_angle_refined_deg1.4261.9558680
X-RAY DIFFRACTIONr_angle_other_deg0.8423.00213716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2115750
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.46323.547265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.79515999
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.8691541
X-RAY DIFFRACTIONr_chiral_restr0.0730.2994
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0217000
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021502
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.753→2.824 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.35 98 -
Rwork0.288 1619 -
obs--99.77 %

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