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- PDB-5y3k: Crystal structure of horse TLR9 in complex with two DNAs (CpG DNA... -

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Basic information

Entry
Database: PDB / ID: 5y3k
TitleCrystal structure of horse TLR9 in complex with two DNAs (CpG DNA and GCGCAC DNA)
Components
  • DNA (5'-D(*AP*GP*GP*CP*GP*TP*TP*TP*TP*T)-3')
  • DNA (5'-D(*GP*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


regulation of B cell differentiation / endolysosome / positive regulation of toll-like receptor 9 signaling pathway / positive regulation of B cell activation / unmethylated CpG binding / siRNA binding / pattern recognition receptor activity / positive regulation of immunoglobulin production / toll-like receptor signaling pathway / canonical NF-kappaB signal transduction ...regulation of B cell differentiation / endolysosome / positive regulation of toll-like receptor 9 signaling pathway / positive regulation of B cell activation / unmethylated CpG binding / siRNA binding / pattern recognition receptor activity / positive regulation of immunoglobulin production / toll-like receptor signaling pathway / canonical NF-kappaB signal transduction / positive regulation of interferon-alpha production / positive regulation of B cell proliferation / activation of innate immune response / positive regulation of interferon-beta production / phagocytic vesicle / positive regulation of interleukin-6 production / positive regulation of type II interferon production / positive regulation of NF-kappaB transcription factor activity / defense response to virus / positive regulation of MAPK cascade / lysosome / inflammatory response / innate immune response / endoplasmic reticulum membrane / protein homodimerization activity / identical protein binding / nucleus / plasma membrane / cytoplasm
Similarity search - Function
Leucine-rich repeat unit / Leucine-rich repeat / Leucine Rich repeat / TIR domain / Leucine Rich Repeat / Leucine-rich repeats, bacterial type / Toll - interleukin 1 - resistance / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeat, SDS22-like subfamily ...Leucine-rich repeat unit / Leucine-rich repeat / Leucine Rich repeat / TIR domain / Leucine Rich Repeat / Leucine-rich repeats, bacterial type / 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 speciesEquus caballus (horse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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 / 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 / _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(*GP*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(*GP*CP*GP*CP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,74223
Polymers188,5766
Non-polymers4,16717
Water1,26170
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(*GP*CP*GP*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)96,26111
Polymers94,2883
Non-polymers1,9738
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4850 Å2
ΔGint21 kcal/mol
Surface area34660 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(*GP*CP*GP*CP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)96,48212
Polymers94,2883
Non-polymers2,1949
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area5090 Å2
ΔGint26 kcal/mol
Surface area34860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.849, 126.502, 140.716
Angle α, β, γ (deg.)90.00, 98.49, 90.00
Int Tables number5
Space group name H-MC121
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: ARG / End label comp-ID: ARG / Refine code: _ / 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(*GP*CP*GP*CP*AP*C)-3')


Mass: 1794.207 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Protein / Non-polymers , 2 types, 72 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


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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Sugars , 2 types, 17 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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 15
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: 50.68 %
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: 2.7→47.14 Å / Num. obs: 50239 / % possible obs: 98.9 % / Redundancy: 3.5 % / Net I/σ(I): 12

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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: 2.7→47.14 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.939 / SU B: 35.444 / SU ML: 0.308 / Cross valid method: THROUGHOUT / ESU R Free: 0.35 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24552 2533 5 %RANDOM
Rwork0.20533 ---
obs0.20739 47705 98.81 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 62.364 Å2
Baniso -1Baniso -2Baniso -3
1-2.38 Å2-0 Å21.01 Å2
2---2.96 Å2-0 Å2
3---0.27 Å2
Refinement stepCycle: 1 / Resolution: 2.7→47.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11786 644 266 70 12766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.01913081
X-RAY DIFFRACTIONr_bond_other_d0.0020.0211775
X-RAY DIFFRACTIONr_angle_refined_deg1.4461.94817954
X-RAY DIFFRACTIONr_angle_other_deg1.003327365
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4551496
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.70823.545536
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.546152004
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.711584
X-RAY DIFFRACTIONr_chiral_restr0.0710.22060
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02113878
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022625
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_it1.8675.265996
X-RAY DIFFRACTIONr_mcbond_other1.8645.265995
X-RAY DIFFRACTIONr_mcangle_it3.1667.8867488
X-RAY DIFFRACTIONr_mcangle_other3.1677.8877489
X-RAY DIFFRACTIONr_scbond_it1.8845.4727085
X-RAY DIFFRACTIONr_scbond_other1.8845.4717084
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.2248.14510466
X-RAY DIFFRACTIONr_long_range_B_refined5.09359.25513564
X-RAY DIFFRACTIONr_long_range_B_other5.09259.2513563
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 48188 / 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: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 178 -
Rwork0.361 3524 -
obs--99.22 %
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)
10.1872-0.029-0.12050.1745-0.02370.4102-0.03660.04580.0432-0.07220.01750.00680.08480.01540.01910.0796-0.0131-0.00580.03020.00370.05320.3843-0.69852.2402
20.0373-0.51960.02337.7305-0.33440.0148-0.0645-0.02910.0528-0.11280.0712-1.0958-0.0041-0.0126-0.00660.27760.22810.24240.19320.17190.341114.5147-14.838961.223
30.27281.2617-0.10396.2567-0.57940.06440.0598-0.0834-0.07260.0232-0.1398-0.36480.011-0.01790.080.1409-0.1117-0.01420.15560.00510.151416.291726.51467.9934
40.2210.0478-0.02810.1131-0.03410.6037-0.0794-0.086-0.03620.07760.0082-0.0313-0.0522-0.05580.07120.12490.0602-0.00210.04640.00380.0336-10.84834.700917.3775
50.26560.39010.66.73740.58031.3936-0.1928-0.01870.0223-0.20950.19610.7191-0.2037-0.0878-0.00330.2253-0.13410.17890.1626-0.13380.2949-24.7971-9.51188.379
60.7315-1.5966-0.0535.42570.93110.3479-0.16390.2148-0.12050.2678-0.07050.7554-0.05590.13460.23440.21350.0252-0.01820.20480.05110.1463-26.802131.9061.5259
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 1009
2X-RAY DIFFRACTION2C1 - 10
3X-RAY DIFFRACTION3E1 - 6
4X-RAY DIFFRACTION4B28 - 1010
5X-RAY DIFFRACTION5D1 - 10
6X-RAY DIFFRACTION6F1 - 6

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