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- PDB-5y3l: Crystal structure of horse TLR9 in complex with two DNAs (CpG DNA... -

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Basic information

Entry
Database: PDB / ID: 5y3l
TitleCrystal structure of horse TLR9 in complex with two DNAs (CpG DNA and CCGCAC DNA)
Components
  • DNA (5'-D(*AP*GP*GP*CP*GP*TP*TP*TP*TP*T)-3')
  • DNA (5'-D(*CP*CP*GP*CP*AP*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 / cellular response to chloroquine / detection of molecule of bacterial origin / regulation of B cell differentiation / endolysosome / 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 ...positive regulation of intestinal epithelial cell development / cellular response to chloroquine / detection of molecule of bacterial origin / regulation of B cell differentiation / endolysosome / 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 / toll-like receptor signaling pathway / positive regulation of interferon-alpha production / positive regulation of interleukin-10 production / positive regulation of immunoglobulin production / canonical NF-kappaB signal transduction / phagocytic vesicle / positive regulation of B cell proliferation / positive regulation of chemokine production / positive regulation of interferon-beta production / activation of innate immune response / positive regulation of interleukin-12 production / positive regulation of interleukin-8 production / positive regulation of JNK cascade / regulation of protein phosphorylation / negative regulation of ERK1 and ERK2 cascade / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / positive regulation of NF-kappaB transcription factor activity / regulation of inflammatory response / basolateral plasma membrane / defense response to virus / positive regulation of canonical NF-kappaB signal transduction / defense response to Gram-negative bacterium / positive regulation of MAPK cascade / lysosome / inflammatory response / apical plasma membrane / innate immune response / endoplasmic reticulum membrane / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Leucine-rich repeat unit / Leucine-rich repeat / Leucine Rich repeat / TIR domain / Leucine-rich repeats, bacterial type / Leucine Rich Repeat / Toll - interleukin 1 - resistance / Leucine-rich repeat, SDS22-like subfamily / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor ...Leucine-rich repeat unit / Leucine-rich repeat / Leucine Rich repeat / TIR domain / Leucine-rich repeats, bacterial type / Leucine Rich Repeat / Toll - interleukin 1 - resistance / Leucine-rich repeat, SDS22-like subfamily / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / 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 speciesEquus caballus (horse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsOhto, U. / Shimizu, T.
CitationJournal: Immunity / Year: 2018
Title: Toll-like Receptor 9 Contains Two DNA Binding Sites that Function Cooperatively to Promote Receptor Dimerization and Activation
Authors: Ohto, U. / Ishida, H. / Shibata, T. / Sato, R. / Miyake, K. / Shimizu, T.
History
DepositionJul 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 18, 2018Provider: repository / Type: Initial release
Revision 1.1May 2, 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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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 / pdbx_struct_special_symmetry / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _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
C: DNA (5'-D(*AP*GP*GP*CP*GP*TP*TP*TP*TP*T)-3')
E: DNA (5'-D(*CP*CP*GP*CP*AP*C)-3')
B: Toll-like receptor 9
D: DNA (5'-D(*AP*GP*GP*CP*GP*TP*TP*TP*TP*T)-3')
F: DNA (5'-D(*CP*CP*GP*CP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,88424
Polymers188,4966
Non-polymers4,38818
Water1,56787
1
A: Toll-like receptor 9
C: DNA (5'-D(*AP*GP*GP*CP*GP*TP*TP*TP*TP*T)-3')
hetero molecules

E: DNA (5'-D(*CP*CP*GP*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)96,44212
Polymers94,2483
Non-polymers2,1949
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4980 Å2
ΔGint21 kcal/mol
Surface area34930 Å2
MethodPISA
2
B: Toll-like receptor 9
D: DNA (5'-D(*AP*GP*GP*CP*GP*TP*TP*TP*TP*T)-3')
hetero molecules

F: DNA (5'-D(*CP*CP*GP*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)96,44212
Polymers94,2483
Non-polymers2,1949
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5020 Å2
ΔGint22 kcal/mol
Surface area34900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)108.004, 125.617, 138.722
Angle α, β, γ (deg.)90.00, 94.67, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-1141-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: ARG / End label comp-ID: ARG / Refine code: 0 / Auth seq-ID: 28 - 807 / Label seq-ID: 7 - 786

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

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Components

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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(*CP*CP*GP*CP*AP*C)-3')


Mass: 1754.182 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein / Non-polymers , 2 types, 89 molecules AB

#1: Protein Toll-like receptor 9 /


Mass: 89427.562 Da / Num. of mol.: 2 / Fragment: UNP residues 26-819
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Equus caballus (horse) / Gene: TLR9 / Production host: Drosophila melanogaster (fruit fly) / References: UniProt: Q2EEY0
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 18 molecules

#4: 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.: 2
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
#5: 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.: 16
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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 4-6%(w/v) PEG 4000, 4-6%(v/v) 2-propanol, 0.2M NaCl, 0.1M citrate-NaOH pH 5.6

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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: Jun 28, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→48.83 Å / Num. obs: 55878 / % possible obs: 98.6 % / Redundancy: 3.5 % / Net I/σ(I): 13.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3WPC

3wpc


Resolution: 2.6→48.83 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.931 / SU B: 34.628 / SU ML: 0.304 / Cross valid method: THROUGHOUT / ESU R: 1.457 / ESU R Free: 0.339 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25936 2804 5 %RANDOM
Rwork0.21171 ---
obs0.21396 53074 98.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 60.527 Å2
Baniso -1Baniso -2Baniso -3
1-1.27 Å2-0 Å21.51 Å2
2---3.61 Å20 Å2
3---2.07 Å2
Refinement stepCycle: 1 / Resolution: 2.6→48.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11786 638 280 87 12791
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01913088
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211786
X-RAY DIFFRACTIONr_angle_refined_deg1.4971.95117962
X-RAY DIFFRACTIONr_angle_other_deg1.024327392
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.47951496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.76723.545536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.696152004
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2441584
X-RAY DIFFRACTIONr_chiral_restr0.0760.22064
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.02113882
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022626
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_it1.3993.8985996
X-RAY DIFFRACTIONr_mcbond_other1.3983.8975995
X-RAY DIFFRACTIONr_mcangle_it2.4285.8427488
X-RAY DIFFRACTIONr_mcangle_other2.4285.8437489
X-RAY DIFFRACTIONr_scbond_it1.5564.1857091
X-RAY DIFFRACTIONr_scbond_other1.5564.1857090
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.736.22810474
X-RAY DIFFRACTIONr_long_range_B_refined4.37544.57413499
X-RAY DIFFRACTIONr_long_range_B_other4.37444.57413499
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 47908 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.01 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.6→2.668 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.426 248 -
Rwork0.412 3881 -
obs--97.82 %
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)
10.2770.0152-0.11250.2364-0.00530.2582-0.10770.0815-0.0364-0.08970.033-0.0219-0.0054-0.01550.07470.2684-0.05360.0680.1416-0.02210.25024.95380.082851.5677
21.5225-2.36632.58627.42-3.31934.5504-0.3472-0.14490.430.5226-0.2206-1.5436-0.349-0.26860.56780.34230.19010.20160.18430.270.704318.9648-12.968462.4002
31.85972.91450.35068.1749-1.38131.1084-0.0983-0.1899-0.201-0.1974-0.1023-0.6532-0.0308-0.11670.20060.2502-0.0620.00360.2138-0.01640.335221.190527.220167.0271
40.30160.0402-0.23350.25750.01440.4318-0.0871-0.07570.03210.07010.05660.01660.0650.01140.03050.25950.04860.05220.1260.00980.2318-10.6151-1.308217.5637
51.30291.20272.46663.34881.62034.9246-0.39560.17220.3246-0.5252-0.02481.1234-0.42570.30980.42040.4122-0.19430.13780.1647-0.19390.7034-24.7291-14.19316.5724
61.8033-2.60930.51897.91091.14161.0321-0.07220.3373-0.09160.1887-0.20860.6334-0.0290.18660.28080.24940.07610.00460.22510.02260.357-26.761825.96622.0692
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 1010
2X-RAY DIFFRACTION2C1 - 10
3X-RAY DIFFRACTION3E1 - 6
4X-RAY DIFFRACTION4B28 - 1010
5X-RAY DIFFRACTION5D1 - 10
6X-RAY DIFFRACTION6F1 - 6

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