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- PDB-3wpg: Crystal structure of mouse TLR9 in complex with inhibitory DNA408... -

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Basic information

Entry
Database: PDB / ID: 3wpg
TitleCrystal structure of mouse TLR9 in complex with inhibitory DNA4084 (form 1)
Components
  • DNA (5'-D(*CP*CP*TP*GP*GP*AP*TP*GP*GP*GP*AP*A)-3')
  • Toll-like receptor 9
KeywordsDNA BINDING PROTEIN/DNA / Leucine rich repeat / Receptor / Innate immunity / DNA binding / Glycosylation / CpG motif / DNA BINDING PROTEIN-DNA complex
Function / homology
Function and homology information


Toll Like Receptor 9 (TLR9) Cascade / cellular response to chloroquine / positive regulation of intestinal epithelial cell development / regulation of B cell activation / Trafficking and processing of endosomal TLR / PI3K Cascade / detection of molecule of bacterial origin / cellular response to metal ion / regulation of B cell differentiation / endolysosome ...Toll Like Receptor 9 (TLR9) Cascade / cellular response to chloroquine / positive regulation of intestinal epithelial cell development / regulation of B cell activation / Trafficking and processing of endosomal TLR / PI3K Cascade / detection of molecule of bacterial origin / cellular response to metal ion / regulation of B cell differentiation / endolysosome / positive regulation of toll-like receptor 9 signaling pathway / regulation of dendritic cell cytokine production / maintenance of gastrointestinal epithelium / positive regulation of B cell activation / positive regulation of interleukin-18 production / unmethylated CpG binding / toll-like receptor 9 signaling pathway / siRNA binding / early phagosome / interleukin-1 receptor binding / positive regulation of granulocyte macrophage colony-stimulating factor production / MyD88-dependent toll-like receptor signaling pathway / positive regulation of immunoglobulin production / pattern recognition receptor activity / positive regulation of interferon-alpha production / positive regulation of interleukin-10 production / canonical NF-kappaB signal transduction / positive regulation of chemokine production / phagocytic vesicle / positive regulation of B cell proliferation / positive regulation of interleukin-12 production / positive regulation of autophagy / activation of innate immune response / positive regulation of interferon-beta production / positive regulation of cytokine production / positive regulation of interleukin-8 production / positive regulation of JNK cascade / microglial cell activation / positive regulation of non-canonical NF-kappaB signal transduction / response to molecule of bacterial origin / negative regulation of ERK1 and ERK2 cascade / positive regulation of interleukin-6 production / response to virus / male gonad development / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / cellular response to lipopolysaccharide / regulation of inflammatory response / early endosome membrane / defense response to Gram-negative bacterium / basolateral plasma membrane / defense response to virus / lysosome / positive regulation of canonical NF-kappaB signal transduction / endosome / positive regulation of MAPK cascade / immune response / apical plasma membrane / innate immune response / endoplasmic reticulum membrane / endoplasmic reticulum / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / plasma membrane
Similarity search - Function
Leucine-rich repeat unit / Leucine-rich repeat / TIR domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Toll - interleukin 1 - resistance / TIR domain profile. / Alpha-Beta Horseshoe / Leucine-rich repeat, SDS22-like subfamily / Toll/interleukin-1 receptor homology (TIR) domain ...Leucine-rich repeat unit / Leucine-rich repeat / TIR domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Toll - interleukin 1 - resistance / 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 speciesMus musculus (house mouse)
synthetic (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.246 Å
AuthorsOhto, U. / 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 1.2Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / ndb_struct_conf_na / pdbx_chem_comp_identifier / pdbx_distant_solvent_atoms / pdbx_entity_nonpoly / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Nov 6, 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
B: DNA (5'-D(*CP*CP*TP*GP*GP*AP*TP*GP*GP*GP*AP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,6028
Polymers93,9002
Non-polymers7026
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-63 kcal/mol
Surface area31300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.230, 123.860, 130.440
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Toll-like receptor 9


Mass: 90172.562 Da / Num. of mol.: 1 / Fragment: Extracellular domain, UNP residues 26-818 / Mutation: N200Q, N242Q, N309Q, N495Q, N568Q, N695Q, N752Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tlr9 / Cell (production host): SCHNEIDER 2(S2) / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: Q9EQU3
#2: DNA chain DNA (5'-D(*CP*CP*TP*GP*GP*AP*TP*GP*GP*GP*AP*A)-3')


Mass: 3727.441 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic (others)
#3: 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.: 1
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
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 3.06 Å3/Da / Density % sol: 59.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 6-8% PEG 8000, 0.4M ammonium sulfate, 0.1M Tris pH 8.0, 10% DMSO , 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: Nov 3, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.246→55.94 Å / Num. obs: 55799 / Biso Wilson estimate: 39.13 Å2 / Rsym value: 0.12

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.1_1168refinement
PDB_EXTRACT3.14data extraction
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.246→35.615 Å / FOM work R set: 0.6952 / SU ML: 0.3 / σ(F): 1.34 / Phase error: 35.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.28 2823 5.07 %
Rwork0.2359 --
obs0.2382 55710 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 147.78 Å2 / Biso mean: 57.29 Å2 / Biso min: 18.42 Å2
Refinement stepCycle: LAST / Resolution: 2.246→35.615 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5757 227 39 77 6100
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046206
X-RAY DIFFRACTIONf_angle_d0.8888452
X-RAY DIFFRACTIONf_chiral_restr0.061985
X-RAY DIFFRACTIONf_plane_restr0.0031027
X-RAY DIFFRACTIONf_dihedral_angle_d16.3022275
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.246-2.28470.42591480.39282555270399
2.2847-2.32630.39181370.375526302767100
2.3263-2.3710.41691420.360226072749100
2.371-2.41940.40791350.340626052740100
2.4194-2.4720.37671440.319726212765100
2.472-2.52950.35381240.299426212745100
2.5295-2.59270.35661290.289226182747100
2.5927-2.66280.32451590.278526132772100
2.6628-2.74110.28541490.276126192768100
2.7411-2.82950.3061430.265626192762100
2.8295-2.93060.3671390.274226272766100
2.9306-3.04790.30651300.271226472777100
3.0479-3.18650.31591450.254426302775100
3.1865-3.35440.26391290.243626602789100
3.3544-3.56440.27121480.218426582806100
3.5644-3.83930.26011490.18826442793100
3.8393-4.22510.2481240.182326912815100
4.2251-4.83520.17561270.176927072834100
4.8352-6.08690.23941550.197827002855100
6.0869-35.61950.26021670.23442815298299
Refinement TLS params.Method: refined / Origin x: -2.9957 Å / Origin y: 4.8483 Å / Origin z: -25.3832 Å
111213212223313233
T0.2644 Å2-0.0414 Å20.0341 Å2--0.0046 Å20.0585 Å2--0.2995 Å2
L1.6389 °20.0283 °20.9177 °2-0.2309 °20.1224 °2--3.7257 °2
S-0.0441 Å °0.0916 Å °0.0571 Å °0.0233 Å °0.0593 Å °0.0049 Å °-0.1611 Å °-0.1384 Å °-0.0139 Å °
Refinement TLS groupSelection details: all

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