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- PDB-3wpf: Crystal structure of mouse TLR9 (unliganded form) -

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Basic information

Entry
Database: PDB / ID: 3wpf
TitleCrystal structure of mouse TLR9 (unliganded form)
ComponentsToll-like receptor 9
KeywordsDNA BINDING PROTEIN / Leucine rich repeat / Receptor / Innate immunity / DNA binding / Glycosylation
Function / homology
Function and homology information


Toll Like Receptor 9 (TLR9) Cascade / regulation of toll-like receptor 9 signaling pathway / positive regulation of intestinal epithelial cell development / regulation of B cell activation / cellular response to chloroquine / Trafficking and processing of endosomal TLR / PI3K Cascade / detection of molecule of bacterial origin / regulation of B cell differentiation / endolysosome ...Toll Like Receptor 9 (TLR9) Cascade / regulation of toll-like receptor 9 signaling pathway / positive regulation of intestinal epithelial cell development / regulation of B cell activation / cellular response to chloroquine / Trafficking and processing of endosomal TLR / PI3K Cascade / detection of molecule of bacterial origin / regulation of B cell differentiation / endolysosome / cellular response to metal ion / regulation of dendritic cell cytokine production / positive regulation of toll-like receptor 9 signaling pathway / maintenance of gastrointestinal epithelium / positive regulation of interleukin-18 production / positive regulation of B cell activation / 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 / pattern recognition receptor activity / positive regulation of immunoglobulin production / toll-like receptor signaling pathway / positive regulation of interleukin-10 production / positive regulation of interferon-alpha production / canonical NF-kappaB signal transduction / positive regulation of autophagy / positive regulation of B cell proliferation / positive regulation of chemokine production / phagocytic vesicle / activation of innate immune response / positive regulation of interleukin-12 production / positive regulation of interferon-beta production / positive regulation of cytokine production / positive regulation of interleukin-8 production / positive regulation of JNK cascade / regulation of protein phosphorylation / microglial cell activation / response to virus / response to molecule of bacterial origin / negative regulation of ERK1 and ERK2 cascade / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of interleukin-6 production / male gonad development / positive regulation of tumor necrosis factor production / positive regulation of type II interferon production / positive regulation of NF-kappaB transcription factor activity / regulation of inflammatory response / basolateral plasma membrane / positive regulation of canonical NF-kappaB signal transduction / defense response to virus / cellular response to lipopolysaccharide / defense response to Gram-negative bacterium / positive regulation of MAPK cascade / lysosome / endosome / immune response / apical plasma membrane / innate immune response / endoplasmic reticulum membrane / positive regulation of gene expression / endoplasmic reticulum / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / plasma membrane / cytoplasm
Similarity search - Function
Leucine-rich repeat unit / Leucine-rich repeat / TIR domain / Toll - interleukin 1 - resistance / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeat, SDS22-like subfamily / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily ...Leucine-rich repeat unit / Leucine-rich repeat / TIR domain / Toll - interleukin 1 - resistance / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeat, SDS22-like subfamily / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Alpha-Beta Horseshoe / 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
Toll-like receptor 9
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.959 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: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / 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 / _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 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,98916
Polymers90,1731
Non-polymers1,81615
Water4,252236
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)71.260, 119.280, 130.410
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 3
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
#3: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 236 / 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: 3.07 Å3/Da / Density % sol: 59.98 %
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: BL-17A / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 21, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.959→48.11 Å / Num. obs: 79163 / Biso Wilson estimate: 25.35 Å2 / Rsym value: 0.113

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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
Starting model: 3W3J

3w3j


Resolution: 1.959→44.614 Å / FOM work R set: 0.7943 / SU ML: 0.31 / σ(F): 1.39 / Phase error: 27.78 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.265 3971 5.02 %
Rwork0.2255 --
obs0.2275 79109 98.21 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.06 Å2 / Biso mean: 37.74 Å2 / Biso min: 12.51 Å2
Refinement stepCycle: LAST / Resolution: 1.959→44.614 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5858 0 102 236 6196
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0066088
X-RAY DIFFRACTIONf_angle_d1.178253
X-RAY DIFFRACTIONf_chiral_restr0.085956
X-RAY DIFFRACTIONf_plane_restr0.0041037
X-RAY DIFFRACTIONf_dihedral_angle_d16.2012208
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.959-1.98290.41011460.37422577272396
1.9829-2.0080.39811630.36282618278198
2.008-2.03440.36971520.334426842836100
2.0344-2.06230.36721280.313326782806100
2.0623-2.09170.35381440.310427142858100
2.0917-2.1230.3371470.293226732820100
2.123-2.15610.32751340.286827032837100
2.1561-2.19150.32341410.277427012842100
2.1915-2.22930.2731340.265427082842100
2.2293-2.26980.30591420.249327202862100
2.2698-2.31350.28361380.247626932831100
2.3135-2.36070.28151200.249127492869100
2.3607-2.4120.31571530.246526762829100
2.412-2.46810.31171510.2332693284499
2.4681-2.52980.26761280.23312715284399
2.5298-2.59820.24721500.22922687283799
2.5982-2.67470.27921360.21772723285999
2.6747-2.7610.26811560.21992691284799
2.761-2.85970.24591540.2172690284499
2.8597-2.97410.25341340.2182702283699
2.9741-3.10950.24951340.21832718285299
3.1095-3.27330.34381400.22342686282698
3.2733-3.47840.271450.20392685283098
3.4784-3.74680.22781260.18452722284898
3.7468-4.12360.2461420.16942677281997
4.1236-4.71970.17191390.17232672281196
4.7197-5.94410.22121490.19912663281294
5.9441-44.62530.23761450.23592520266586
Refinement TLS params.Method: refined / Origin x: 2.6459 Å / Origin y: 4.948 Å / Origin z: 22.5513 Å
111213212223313233
T0.1429 Å20.0693 Å20.0459 Å2-0.0834 Å2-0.0439 Å2--0.1738 Å2
L0.7802 °20.089 °20.5054 °2-0.3695 °2-0.2561 °2--1.7978 °2
S-0.041 Å °-0.0875 Å °-0.0249 Å °-0.0001 Å °0.0301 Å °-0.0411 Å °-0.0712 Å °-0.0058 Å °0.0101 Å °
Refinement TLS groupSelection details: all

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