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- PDB-3wpe: Crystal structure of bovine TLR9 in complex with agonistic DNA166... -

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Basic information

Entry
Database: PDB / ID: 3wpe
TitleCrystal structure of bovine TLR9 in complex with agonistic DNA1668_12mer
Components
  • DNA (5'-D(*CP*AP*TP*GP*AP*CP*GP*TP*TP*CP*CP*T)-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 / early phagosome / positive regulation of immunoglobulin production / toll-like receptor signaling pathway / pattern recognition receptor activity ...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 / early phagosome / 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 / 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 / endosome / positive regulation of MAPK cascade / inflammatory response / innate immune response / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / plasma membrane
Similarity search - Function
Leucine-rich repeat unit / Leucine-rich repeat / Leucine Rich repeat / Leucine Rich Repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeats, bacterial type / TIR domain profile. / Alpha-Beta Horseshoe / Leucine-rich repeat, SDS22-like subfamily ...Leucine-rich repeat unit / Leucine-rich repeat / Leucine Rich repeat / Leucine Rich Repeat / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / 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 / DNA (> 10) / Toll-like receptor 9
Similarity search - Component
Biological speciesBos taurus (domestic cattle)
synthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.38 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 1.2Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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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*AP*TP*GP*AP*CP*GP*TP*TP*CP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)92,9372
Polymers92,9372
Non-polymers00
Water55831
1
A: Toll-like receptor 9
C: DNA (5'-D(*CP*AP*TP*GP*AP*CP*GP*TP*TP*CP*CP*T)-3')

A: Toll-like receptor 9
C: DNA (5'-D(*CP*AP*TP*GP*AP*CP*GP*TP*TP*CP*CP*T)-3')


Theoretical massNumber of molelcules
Total (without water)185,8744
Polymers185,8744
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area7580 Å2
ΔGint-43 kcal/mol
Surface area56480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.820, 113.080, 67.430
Angle α, β, γ (deg.)90.00, 100.61, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Toll-like receptor 9


Mass: 89323.531 Da / Num. of mol.: 1 / Fragment: Extracellular domain, UNP residues 25-815
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: TLR9 / Cell (production host): SCHNEIDER 2(S2) / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: Q5I2M5
#2: DNA chain DNA (5'-D(*CP*AP*TP*GP*AP*CP*GP*TP*TP*CP*CP*T)-3')


Mass: 3613.366 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 31 / Source method: isolated from a natural source / Formula: H2O
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: 2.33 Å3/Da / Density % sol: 47.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 3-5% PEG 4000, 0.2M Na acetate, 0.1M Na citrate pH 5.5, 15% DMSO , VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Apr 21, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.38→48.11 Å / Num. obs: 34012 / Rmerge(I) obs: 0.113

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.7.0029refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.38→43.05 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.895 / SU B: 21.279 / SU ML: 0.224 / Cross valid method: THROUGHOUT / ESU R: 0.418 / ESU R Free: 0.281 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27365 1717 5 %RANDOM
Rwork0.21702 ---
obs0.21981 32294 99.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 50.268 Å2
Baniso -1Baniso -2Baniso -3
1-2.85 Å20 Å22.53 Å2
2---2.02 Å20 Å2
3----1.22 Å2
Refinement stepCycle: LAST / Resolution: 2.38→43.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5628 124 0 31 5783
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0195903
X-RAY DIFFRACTIONr_bond_other_d0.0020.025654
X-RAY DIFFRACTIONr_angle_refined_deg1.1661.9518050
X-RAY DIFFRACTIONr_angle_other_deg0.7793.00212954
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2915709
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.45423.398256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.08715963
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1681540
X-RAY DIFFRACTIONr_chiral_restr0.0640.2924
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0216558
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021414
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: 2.383→2.445 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.367 143 -
Rwork0.309 2334 -
obs--99.16 %
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)
10.09970.0021-0.06740.06160.02860.0604-0.00770.005-0.0077-0.02050.00170.0108-0.0024-0.00180.0060.035-0.003-0.05550.08930.00450.1026.3606-0.033316.4411
22.17210.09461.34990.27050.23750.9675-0.11950.19080.15480.26990.01740.00870.09950.0890.1020.29820.018-0.01110.14050.04530.11717.2549-18.315329.1743
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 792
2X-RAY DIFFRACTION2C4 - 9

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