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- PDB-3wpi: Crystal structure of mouse TLR9 in complex with inhibitory DNA_super -

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Basic information

Entry
Database: PDB / ID: 3wpi
TitleCrystal structure of mouse TLR9 in complex with inhibitory DNA_super
Components
  • DNA (5'-D(*CP*CP*TP*CP*AP*AP*TP*AP*GP*GP*GP*TP*GP*AP*GP*GP*GP*G)-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 / positive regulation of MAPK cascade / endosome / 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 / ndb_struct_na_base_pair / ndb_struct_na_base_pair_step / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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 / _ndb_struct_na_base_pair.propeller / _ndb_struct_na_base_pair_step.inclination / _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 1.3Oct 16, 2024Group: 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
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*CP*AP*AP*TP*AP*GP*GP*GP*TP*GP*AP*GP*GP*GP*G)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0153
Polymers95,7942
Non-polymers2211
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1910 Å2
ΔGint1 kcal/mol
Surface area31450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)137.330, 129.720, 71.360
Angle α, β, γ (deg.)90.00, 92.17, 90.00
Int Tables number5
Space group name H-MC121

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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*CP*AP*AP*TP*AP*GP*GP*GP*TP*GP*AP*GP*GP*GP*G)-3')


Mass: 5621.641 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / 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: 3.32 Å3/Da / Density % sol: 62.9 %

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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: Dec 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.246→57.6 Å / Num. obs: 57648 / Biso Wilson estimate: 38.78 Å2 / Rsym value: 0.072

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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→36.341 Å / FOM work R set: 0.7277 / SU ML: 0.27 / σ(F): 1.35 / Phase error: 32.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.254 2906 5.05 %
Rwork0.2214 --
obs0.2231 57594 96.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 148.33 Å2 / Biso mean: 52.14 Å2 / Biso min: 18.18 Å2
Refinement stepCycle: LAST / Resolution: 2.246→36.341 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5750 183 14 102 6049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046129
X-RAY DIFFRACTIONf_angle_d0.9858334
X-RAY DIFFRACTIONf_chiral_restr0.066977
X-RAY DIFFRACTIONf_plane_restr0.0031024
X-RAY DIFFRACTIONf_dihedral_angle_d15.9892251
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.246-2.28280.36071190.34342274239387
2.2828-2.32220.4021390.35122589272896
2.3222-2.36440.38971360.34222640277697
2.3644-2.40990.35891490.31742586273597
2.4099-2.45910.35721470.30572581272897
2.4591-2.51250.37371240.29222610273498
2.5125-2.5710.30241360.27442603273997
2.571-2.63520.26951610.25552599276097
2.6352-2.70650.27421390.26072624276398
2.7065-2.78610.29951460.24672615276197
2.7861-2.8760.30151110.23552618272997
2.876-2.97870.2391270.23722641276898
2.9787-3.09790.22771260.23952642276898
3.0979-3.23880.26861660.23582639280598
3.2388-3.40950.28441460.2222616276298
3.4095-3.62290.211400.2032642278298
3.6229-3.90230.21151450.16682626277198
3.9023-4.29450.21961270.17162667279498
4.2945-4.91460.19121550.17232638279399
4.9146-6.18690.23321320.20112684281699
6.1869-36.34560.25741350.23312554268993
Refinement TLS params.Method: refined / Origin x: 29.1498 Å / Origin y: -1.0189 Å / Origin z: 20.5212 Å
111213212223313233
T-0.0266 Å2-0.0996 Å2-0.112 Å2-0.3391 Å2-0.0421 Å2--0.2012 Å2
L0.2937 °2-0.3906 °2-0.0307 °2-3.9592 °2-1.0402 °2--1.558 °2
S0.0261 Å °0.013 Å °-0.009 Å °-0.0237 Å °0.0444 Å °0.2054 Å °0.0977 Å °-0.0271 Å °-0.0579 Å °
Refinement TLS groupSelection details: all

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