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- PDB-2j67: The TIR domain of human Toll-Like Receptor 10 (TLR10) -

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Basic information

Entry
Database: PDB / ID: 2j67
TitleThe TIR domain of human Toll-Like Receptor 10 (TLR10)
ComponentsTOLL LIKE RECEPTOR 10Toll-like receptor
KeywordsRECEPTOR / TIR / IL-1 / TOLL / TLR10 / MEMBRANE / INFLAMMATORY RESPONSE / TOLL-LIKE RECEPTOR 10 / INNATE IMMUNITY / IMMUNE RESPONSE / LEUCINE-RICH REPEAT / GLYCOPROTEIN / TRANSMEMBRANE
Function / homology
Function and homology information


toll-like receptor 10 signaling pathway / Toll Like Receptor 10 (TLR10) Cascade / regulation of cytokine production => GO:0001817 / IRAK4 deficiency (TLR5) / MyD88 cascade initiated on plasma membrane / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / MyD88-dependent toll-like receptor signaling pathway / toll-like receptor signaling pathway ...toll-like receptor 10 signaling pathway / Toll Like Receptor 10 (TLR10) Cascade / regulation of cytokine production => GO:0001817 / IRAK4 deficiency (TLR5) / MyD88 cascade initiated on plasma membrane / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / NAD+ nucleotidase, cyclic ADP-ribose generating / NADP+ nucleosidase activity / MyD88-dependent toll-like receptor signaling pathway / toll-like receptor signaling pathway / plasma membrane => GO:0005886 / positive regulation of inflammatory response / transmembrane signaling receptor activity / signaling receptor activity / immune response / inflammatory response / innate immune response / membrane / identical protein binding / plasma membrane
Similarity search - Function
Toll-like receptor 10 / Toll/interleukin-1 receptor homology (TIR) domain / Toll-like receptor / TIR domain / Leucine Rich Repeat / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain ...Toll-like receptor 10 / Toll/interleukin-1 receptor homology (TIR) domain / Toll-like receptor / TIR domain / Leucine Rich Repeat / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / TIR domain profile. / 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 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Toll-like receptor 10
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsStenmark, P. / Ogg, D. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ericsson, U.B. / Flodin, S. / Flores, A. ...Stenmark, P. / Ogg, D. / Arrowsmith, C. / Berglund, H. / Busam, R. / Collins, R. / Edwards, A. / Ericsson, U.B. / Flodin, S. / Flores, A. / Graslund, S. / Hammarstrom, M. / Hallberg, B.M. / Holmberg Schiavone, L. / Hogbom, M. / Johansson, I. / Karlberg, T. / Kotenyova, T. / Magnusdottir, A. / Nilsson, M.E. / Nilsson-Ehle, P. / Nyman, T. / Persson, C. / Sagemark, J. / Sundstrom, M. / Uppenberg, J. / Thorsell, A.G. / Van Den Berg, S. / Wallden, K. / Weigelt, J. / Welin, M. / Nordlund, P.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: The Crystal Structure of the Human Toll-Like Receptor 10 Cytoplasmic Domain Reveals a Putative Signaling Dimer.
Authors: Nyman, T. / Stenmark, P. / Flodin, S. / Johansson, I. / Hammarstrom, M. / Nordlund, P.
History
DepositionSep 26, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 27, 2006Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: TOLL LIKE RECEPTOR 10
B: TOLL LIKE RECEPTOR 10


Theoretical massNumber of molelcules
Total (without water)42,5792
Polymers42,5792
Non-polymers00
Water2,108117
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)66.200, 43.300, 71.300
Angle α, β, γ (deg.)90.00, 101.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein TOLL LIKE RECEPTOR 10 / Toll-like receptor


Mass: 21289.283 Da / Num. of mol.: 2 / Fragment: TIR DOMAIN, RESIDUES 622-776
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PNIC-BSA4 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9BXR5
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 117 / 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: 2.89 Å3/Da / Density % sol: 57.16 %
Crystal growDetails: 0.2 M NASCN, 11% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.95373
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 22, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.2→23 Å / Num. obs: 19993 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.8
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.5 / % possible all: 92

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FYV

1fyv


Resolution: 2.2→23.43 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.903 / SU B: 12.12 / SU ML: 0.16 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.252 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.266 1000 5 %RANDOM
Rwork0.214 ---
obs0.216 18992 97.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.04 Å2
Baniso -1Baniso -2Baniso -3
1--2.02 Å20 Å2-0.93 Å2
2--1.53 Å20 Å2
3---0.14 Å2
Refinement stepCycle: LAST / Resolution: 2.2→23.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2345 0 0 117 2462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222438
X-RAY DIFFRACTIONr_bond_other_d0.0010.021689
X-RAY DIFFRACTIONr_angle_refined_deg1.5241.9323303
X-RAY DIFFRACTIONr_angle_other_deg0.95434085
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9335274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.40623.516128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.87115414
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.2171511
X-RAY DIFFRACTIONr_chiral_restr0.0970.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022651
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02548
X-RAY DIFFRACTIONr_nbd_refined0.2260.2478
X-RAY DIFFRACTIONr_nbd_other0.1880.21593
X-RAY DIFFRACTIONr_nbtor_refined0.1980.21137
X-RAY DIFFRACTIONr_nbtor_other0.0860.21183
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1920.285
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1440.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.190.229
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1710.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.35621845
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.71432246
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.18741448
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.53251055
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.2→2.26 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 66 -
Rwork0.233 1250 -
obs--88.74 %
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)
110.08754.1882-5.65215.235512.738920.02820.3307-0.014-0.3291.6831-0.92210.96631.1585-1.04680.59140.2050.13190.17650.05140.05950.090642.56622.26461.469
22.3318-0.49041.02483.267-1.91133.9553-0.0663-0.1140.01140.2120.29060.0124-0.6427-0.1939-0.22420.23840.03620.0894-0.0741-0.02150.051453.86125.81754.703
32.8241-2.00211.27733.8455-1.74495.7534-0.0191-0.0958-0.3387-0.1440.27810.27670.2083-0.4681-0.25890.1513-0.05740.047-0.0885-0.01340.053852.11516.31248.854
43.9884-3.175-2.62099.31923.88027.3404-0.04810.1069-0.2943-0.4593-0.08990.06610.5376-0.10130.13790.1463-0.03250.04650.0005-0.0665-0.002657.47111.64838.86
56.0024-2.21082.17248.9923-4.73965.1366-0.01120.49480.032-0.35360.09310.23080.0963-0.7513-0.0820.159-0.04690.04080.06470.0212-0.034246.12424.79537.386
66.96481.65220.27646.258-1.7195.7049-0.0205-0.23020.2080.2610.06270.2081-0.32340.3985-0.04230.09750.04540.030.0392-0.01380.099673.61311.29769.596
7047.36412.2078018.571611.99691.1079-1.6603-0.29763.0432-2.8356-2.8426-0.76021.06311.72780.2704-0.2964-0.15740.4611-0.00710.158282.95912.24376.784
82.32-2.29451.53592.7973-0.24744.07870.0039-0.05340.2217-0.1654-0.0395-0.0843-0.33710.50520.03570.0567-0.06050.04630.0146-0.01770.031771.95615.99361.634
94.0353-1.99293.97885.1819-4.50857.60240.41610.3743-0.7084-0.8835-0.08170.36611.04360.6573-0.33430.24340.0897-0.0585-0.0805-0.14630.084370.2543.26857.115
109.0845-1.72152.63918.8952-5.898612.5830.3089-0.2004-0.93670.08350.12780.28550.59510.5015-0.43660.01590.17660.07090.11220.03680.084378.903-2.49570.637
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A628 - 636
2X-RAY DIFFRACTION2A637 - 689
3X-RAY DIFFRACTION3A690 - 729
4X-RAY DIFFRACTION4A730 - 744
5X-RAY DIFFRACTION5A745 - 776
6X-RAY DIFFRACTION6B630 - 655
7X-RAY DIFFRACTION7B656 - 663
8X-RAY DIFFRACTION8B664 - 698
9X-RAY DIFFRACTION9B699 - 736
10X-RAY DIFFRACTION10B750 - 776

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