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- PDB-7nux: Crystal structure of the TIR domain of human TLR1 (crystallised w... -

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Basic information

Entry
Database: PDB / ID: 7nux
TitleCrystal structure of the TIR domain of human TLR1 (crystallised without ZN2+ ions)
ComponentsToll-like receptor 1
KeywordsSIGNALING PROTEIN / TOLL-LIKE RECEPTOR / TIR DOMAIN
Function / homology
Function and homology information


Toll-like receptor 1-Toll-like receptor 2 protein complex / detection of triacyl bacterial lipopeptide / cellular response to triacyl bacterial lipopeptide / Toll Like Receptor TLR1:TLR2 Cascade / Beta defensins / positive regulation of toll-like receptor 2 signaling pathway / lipopeptide binding / Toll-like receptor 2 binding / macrophage activation / Regulation of TLR by endogenous ligand ...Toll-like receptor 1-Toll-like receptor 2 protein complex / detection of triacyl bacterial lipopeptide / cellular response to triacyl bacterial lipopeptide / Toll Like Receptor TLR1:TLR2 Cascade / Beta defensins / positive regulation of toll-like receptor 2 signaling pathway / lipopeptide binding / Toll-like receptor 2 binding / macrophage activation / Regulation of TLR by endogenous ligand / NAD+ nucleosidase activity, cyclic ADP-ribose generating / MyD88 deficiency (TLR2/4) / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor signaling pathway / positive regulation of interleukin-8 production / microglial cell activation / positive regulation of interleukin-6 production / phagocytic vesicle membrane / positive regulation of tumor necrosis factor production / transmembrane signaling receptor activity / signaling receptor activity / ER-Phagosome pathway / receptor complex / immune response / membrane raft / inflammatory response / innate immune response / SARS-CoV-2 activates/modulates innate and adaptive immune responses / Golgi apparatus / signal transduction / identical protein binding / membrane / plasma membrane
Similarity search - Function
Leucine rich repeat C-terminal domain / Toll/interleukin-1 receptor homology (TIR) domain / Toll-like receptor / TIR domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / Leucine-rich repeats, bacterial type / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain ...Leucine rich repeat C-terminal domain / Toll/interleukin-1 receptor homology (TIR) domain / Toll-like receptor / TIR domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / Leucine-rich repeats, bacterial type / 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 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.47 Å
AuthorsVakhrameev, D.D. / Luginina, A.P. / Shevtsov, M.B. / Lushpa, V.A. / Mineev, K.S. / Borshchevskiy, V.I.
Funding support Russian Federation, 1items
OrganizationGrant numberCountry
Ministry of Science and Higher Education of the Russian Federationagreement #075-00337-20-03, project FSMG-2020-0003 Russian Federation
CitationJournal: Commun Biol / Year: 2021
Title: Modulation of Toll-like receptor 1 intracellular domain structure and activity by Zn 2+ ions.
Authors: Lushpa, V.A. / Goncharuk, M.V. / Lin, C. / Zalevsky, A.O. / Talyzina, I.A. / Luginina, A.P. / Vakhrameev, D.D. / Shevtsov, M.B. / Goncharuk, S.A. / Arseniev, A.S. / Borshchevskiy, V.I. / Wang, X. / Mineev, K.S.
History
DepositionMar 15, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 25, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 13, 2021Group: Data collection / Database references
Category: citation / citation_author ...citation / citation_author / pdbx_database_proc / pdbx_seq_map_depositor_info
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Toll-like receptor 1


Theoretical massNumber of molelcules
Total (without water)19,0751
Polymers19,0751
Non-polymers00
Water19811
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.260, 101.260, 68.850
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Space group name HallP622(x,y,z+1/3)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/3
#3: y,-x+y,z+2/3
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+1/3
#8: -x,-y,z
#9: y,x,-z+2/3
#10: -y,-x,-z+2/3
#11: -x+y,y,-z
#12: x,x-y,-z+1/3

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Components

#1: Protein Toll-like receptor 1 / Toll/interleukin-1 receptor-like protein / TIL


Mass: 19074.959 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TLR1, KIAA0012 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): pLysS
References: UniProt: Q15399, ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 5.6
Details: 170 mM Ammonium acetate, 85 mM Sodium citrate tribasic dihydrate pH 5.6, 25.5% w/v Polyethylene glycol 4,000, 15% v/v glycerol (#9 from HR2-122 Hampton) Growth at +4 for 3-4 months.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 17, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.47→50.63 Å / Num. obs: 7879 / % possible obs: 99.92 % / Redundancy: 37.5 % / Biso Wilson estimate: 53.06 Å2 / CC1/2: 0.999 / CC star: 1 / Rpim(I) all: 0.02972 / Net I/σ(I): 21.19
Reflection shellResolution: 2.47→2.558 Å / Num. unique obs: 752 / CC1/2: 0.836 / CC star: 0.954 / Rpim(I) all: 0.2996

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
autoPROCdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1FYV

1fyv


Resolution: 2.47→50.63 Å / SU ML: 0.4535 / Cross valid method: FREE R-VALUE / Phase error: 32.3443
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2788 398 5.05 %
Rwork0.2292 7478 -
obs0.2317 7876 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.61 Å2
Refinement stepCycle: LAST / Resolution: 2.47→50.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1296 0 0 11 1307
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00131342
X-RAY DIFFRACTIONf_angle_d0.39071825
X-RAY DIFFRACTIONf_chiral_restr0.0396198
X-RAY DIFFRACTIONf_plane_restr0.0034230
X-RAY DIFFRACTIONf_dihedral_angle_d10.7587482
LS refinement shellResolution: 2.47→2.558 Å
RfactorNum. reflection% reflection
Rfree0.3795 46 -
Rwork0.3164 753 -
obs--100 %

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