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- PDB-5zln: Crystal structure of mouse TLR9 in complex with two DNAs (CpG DNA... -

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Basic information

Entry
Database: PDB / ID: 5zln
TitleCrystal structure of mouse TLR9 in complex with two DNAs (CpG DNA and TCGCCA DNA)
Components
  • DNA (5'-D(*AP*GP*GP*CP*GP*TP*TP*TP*TP*T)-3')
  • DNA (5'-D(*TP*CP*GP*C)-3')
  • Toll-like receptor 9
KeywordsIMMUNE SYSTEM / Innate immunity / Toll-like receptor / Leucine-rich repeat / DNA binding
Function / homology
Function and homology information


positive regulation of intestinal epithelial cell development / Toll Like Receptor 9 (TLR9) Cascade / regulation of toll-like receptor 9 signaling pathway / cellular response to chloroquine / regulation of B cell activation / Trafficking and processing of endosomal TLR / PI3K Cascade / detection of molecule of bacterial origin / regulation of B cell differentiation / endolysosome ...positive regulation of intestinal epithelial cell development / Toll Like Receptor 9 (TLR9) Cascade / regulation of toll-like receptor 9 signaling pathway / cellular response to chloroquine / regulation of B cell activation / 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 / canonical NF-kappaB signal transduction / positive regulation of interferon-alpha production / positive regulation of autophagy / positive regulation of chemokine production / positive regulation of B cell proliferation / positive regulation of interleukin-12 production / activation of innate immune response / positive regulation of interferon-beta production / phagocytic vesicle / 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 / male gonad development / positive regulation of interleukin-6 production / 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 / cellular response to lipopolysaccharide / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / defense response to virus / positive regulation of MAPK cascade / lysosome / 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 / 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
DNA / Toll-like receptor 9
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsIshida, H. / Ohto, U. / Shimizu, T.
CitationJournal: FEBS Lett. / Year: 2018
Title: Structural basis for species-specific activation of mouse Toll-like receptor 9
Authors: Ishida, H. / Ohto, U. / Shibata, T. / Miyake, K. / Shimizu, T.
History
DepositionMar 28, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 25, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 8, 2018Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Sep 12, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / 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 / struct_asym / struct_conn / 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.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 22, 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 / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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


Theoretical massNumber of molelcules
Total (without water)193,49725
Polymers187,3606
Non-polymers6,13719
Water10,827601
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area18930 Å2
ΔGint-30 kcal/mol
Surface area62750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.306, 128.141, 156.798
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: _ / Auth seq-ID: 28 - 810 / Label seq-ID: 3 - 785

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Toll-like receptor 9


Mass: 88844.961 Da / Num. of mol.: 2 / Fragment: UNP residues 26-818
Mutation: L310M, T325Q, L378S, N495Q, N514Q, T573A, Q573A,Q579H, N670Q
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tlr9 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q9EQU3

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DNA chain , 2 types, 4 molecules CDEF

#2: DNA chain DNA (5'-D(*AP*GP*GP*CP*GP*TP*TP*TP*TP*T)-3')


Mass: 3066.012 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*TP*CP*GP*C)-3')


Mass: 1769.193 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Sugars , 3 types, 14 molecules

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


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE
#5: 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.: 9
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
#6: 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.: 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

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Non-polymers , 2 types, 606 molecules

#7: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: SO4
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 601 / 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: 3.16 Å3/Da / Density % sol: 61.03 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20%(w/v) PEG4000, 0.15M Ammonium sulfate, 0.1M HEPES-NaOH pH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→49.61 Å / Num. obs: 102418 / % possible obs: 99.8 % / Redundancy: 11.3 % / Net I/σ(I): 11.4
Reflection shellResolution: 2.3→2.34 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0218refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WPF

3wpf


Resolution: 2.3→49.61 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.928 / SU B: 7.117 / SU ML: 0.161 / Cross valid method: THROUGHOUT / ESU R: 0.249 / ESU R Free: 0.208 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23847 4986 4.9 %RANDOM
Rwork0.19145 ---
obs0.19369 97358 99.66 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 40.994 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0.03 Å2-0 Å2
3----0.02 Å2
Refinement stepCycle: 1 / Resolution: 2.3→49.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11888 560 397 601 13446
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.01913217
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211920
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.95618103
X-RAY DIFFRACTIONr_angle_other_deg0.898327755
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.83851500
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.22823.978538
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.195152101
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4341566
X-RAY DIFFRACTIONr_chiral_restr0.0890.22117
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113925
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022616
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_it2.5953.7936012
X-RAY DIFFRACTIONr_mcbond_other2.5823.7926011
X-RAY DIFFRACTIONr_mcangle_it3.935.687508
X-RAY DIFFRACTIONr_mcangle_other3.9325.6827509
X-RAY DIFFRACTIONr_scbond_it3.8814.5597205
X-RAY DIFFRACTIONr_scbond_other3.8674.5487184
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.1776.68110565
X-RAY DIFFRACTIONr_long_range_B_refined7.53245.51114157
X-RAY DIFFRACTIONr_long_range_B_other7.53445.46814087
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 23786 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.327 335 -
Rwork0.293 6980 -
obs--97.85 %

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