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- PDB-3a79: Crystal structure of TLR2-TLR6-Pam2CSK4 complex -

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Basic information

Entry
Database: PDB / ID: 3a79
TitleCrystal structure of TLR2-TLR6-Pam2CSK4 complex
Components
  • (Toll-like receptor ...) x 2
  • Pam2CSK4
KeywordsIMMUNE SYSTEM / Toll-like Receptor / diacyl lipopeptide / innate immunity / Leucine Rich Repeat / Cell membrane / Cytoplasmic vesicle / Disulfide bond / Glycoprotein / Immune response / Inflammatory response / LEUCINE-RICH REPEAT / Membrane / Receptor / Transmembrane / Phosphoprotein
Function / homology
Function and homology information


toll-like receptor 6 signaling pathway / negative regulation of tumor necrosis factor production => GO:0032720 / interleukin-1 beta production / : / response to bacterial lipoprotein / diacyl lipopeptide binding / Beta defensins / triacyl lipopeptide binding / Toll-like receptor 2-Toll-like receptor 6 protein complex / detection of diacyl bacterial lipopeptide ...toll-like receptor 6 signaling pathway / negative regulation of tumor necrosis factor production => GO:0032720 / interleukin-1 beta production / : / response to bacterial lipoprotein / diacyl lipopeptide binding / Beta defensins / triacyl lipopeptide binding / Toll-like receptor 2-Toll-like receptor 6 protein complex / detection of diacyl bacterial lipopeptide / toll-like receptor TLR6:TLR2 signaling pathway / positive regulation of neutrophil migration / cellular response to diacyl bacterial lipopeptide / Toll-like receptor 1-Toll-like receptor 2 protein complex / detection of triacyl bacterial lipopeptide / cellular response to triacyl bacterial lipopeptide / cellular response to bacterial lipopeptide / Regulation of TLR by endogenous ligand / lipoteichoic acid binding / negative regulation of synapse assembly / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / response to molecule of fungal origin / negative regulation of toll-like receptor 2 signaling pathway / toll-like receptor 2 signaling pathway / positive regulation of matrix metallopeptidase secretion / cell surface pattern recognition receptor signaling pathway / regulation of dendritic cell cytokine production / response to peptidoglycan / Toll-like receptor 2 binding / cellular response to oxidised low-density lipoprotein particle stimulus / positive regulation of xenophagy / central nervous system myelin formation / xenophagy / Toll-like receptor binding / positive regulation of interleukin-18 production / neutrophil migration / leukotriene metabolic process / negative regulation of actin filament polymerization / negative regulation of interleukin-8 production / cell activation / TRIF-dependent toll-like receptor signaling pathway / response to fatty acid / lipopeptide binding / peptidoglycan binding / cellular response to peptidoglycan / ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase / negative regulation of interleukin-12 production / positive regulation of macrophage activation / NAD+ nucleotidase, cyclic ADP-ribose generating / negative regulation of interleukin-17 production / positive regulation of cytokine production involved in inflammatory response / NADP+ nucleosidase activity / microglia development / negative regulation of phagocytosis / positive regulation of macrophage cytokine production / MyD88-dependent toll-like receptor signaling pathway / positive regulation of leukocyte migration / positive regulation of reactive oxygen species biosynthetic process / positive regulation of intracellular signal transduction / pattern recognition receptor activity / toll-like receptor signaling pathway / positive regulation of NLRP3 inflammasome complex assembly / positive regulation of oligodendrocyte differentiation / nitric oxide metabolic process / leukocyte migration / positive regulation of nitric-oxide synthase biosynthetic process / plasma membrane => GO:0005886 / cellular response to lipoteichoic acid / positive regulation of interleukin-10 production / regulation of presynapse assembly / positive regulation of Wnt signaling pathway / positive regulation of chemokine production / positive regulation of JUN kinase activity / ERK1 and ERK2 cascade / nitric oxide biosynthetic process / Neutrophil degranulation / positive regulation of interleukin-12 production / positive regulation of interferon-beta production / axonogenesis / learning / positive regulation of interleukin-1 beta production / cell projection / positive regulation of cytokine production / positive regulation of interleukin-8 production / lipopolysaccharide binding / response to bacterium / microglial cell activation / defense response / positive regulation of inflammatory response / cellular response to type II interferon / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction / phagocytic vesicle membrane / cellular response to amyloid-beta / positive regulation of nitric oxide biosynthetic process / transmembrane signaling receptor activity / positive regulation of tumor necrosis factor production / signaling receptor activity / cell body / positive regulation of NF-kappaB transcription factor activity
Similarity search - Function
Toll-like receptor 6 / Slitrk family / Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / Toll-like receptor / Leucine rich repeat N-terminal domain / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain ...Toll-like receptor 6 / Slitrk family / Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / Toll-like receptor / Leucine rich repeat N-terminal domain / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Leucine Rich repeat / TIR domain / Leucine-rich repeats, bacterial type / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / 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
(2S)-propane-1,2-diyl dihexadecanoate / Variable lymphocyte receptor B / Variable lymphocyte receptor B / Toll-like receptor 6 / Toll-like receptor 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Eptatretus burgeri (inshore hagfish)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsKang, J.Y. / Jin, M.S. / Lee, J.-O.
CitationJournal: Immunity / Year: 2009
Title: Recognition of lipopeptide patterns by Toll-like receptor 2-Toll-like receptor 6 heterodimer
Authors: Kang, J.Y. / Nan, X. / Jin, M.S. / Youn, S.-J. / Ryu, Y.H. / Mah, S. / Han, S.H. / Lee, H. / Paik, S.-G. / Lee, J.-O.
History
DepositionSep 20, 2009Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jun 27, 2012Group: Non-polymer description
Revision 1.3Aug 9, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Aug 16, 2017Group: Source and taxonomy / Category: pdbx_entity_src_syn
Item: _pdbx_entity_src_syn.ncbi_taxonomy_id / _pdbx_entity_src_syn.organism_scientific
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / database_PDB_caveat / 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_validate_chiral / struct_asym / struct_conn / struct_ref_seq / struct_ref_seq_dif / 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 / _atom_site_anisotrop.pdbx_label_asym_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 1, 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
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toll-like receptor 2, Variable lymphocyte receptor B
B: Toll-like receptor 6, Variable lymphocyte receptor B
C: Pam2CSK4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)134,73815
Polymers130,0463
Non-polymers4,69212
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7620 Å2
ΔGint53 kcal/mol
Surface area47840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)168.901, 168.901, 231.353
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

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Toll-like receptor ... , 2 types, 2 molecules AB

#1: Protein Toll-like receptor 2, Variable lymphocyte receptor B / / TLR2 / VLRB.61


Mass: 65535.309 Da / Num. of mol.: 1
Fragment: extracellular domain, UNP residues 1-506(mouse), UNP residues 133-200(Inshore hagfish)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Eptatretus burgeri (inshore hagfish)
Gene: Tlr2 / Plasmid: PVL1393 / Production host: TRICHOPLUSIA NI (cabbage looper) / Strain (production host): Hi-5 / References: UniProt: Q9QUN7, UniProt: Q4G1L2
#2: Protein Toll-like receptor 6, Variable lymphocyte receptor B / / TLR6 / VLRB.59


Mass: 63785.551 Da / Num. of mol.: 1
Fragment: extracellular domain, UNP residues 1-482(mouse), UNP residues 157-232(Inshore hagfish)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Eptatretus burgeri (inshore hagfish)
Gene: Tlr6 / Plasmid: PVL1393 / Production host: TRICHOPLUSIA NI (cabbage looper) / Strain (production host): Hi-5 / References: UniProt: Q9EPW9, UniProt: Q4G1L3

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Protein/peptide / Non-polymers , 2 types, 2 molecules C

#3: Protein/peptide Pam2CSK4


Mass: 724.955 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: synthetic peptide / Source: (synth.) synthetic construct (others)
#7: Chemical ChemComp-PXS / (2S)-propane-1,2-diyl dihexadecanoate


Mass: 552.912 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H68O4

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Sugars , 3 types, 11 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.: 3
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: 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.: 3
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
#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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 5
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: 3.66 Å3/Da / Density % sol: 66.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 2.0M ammonium sulfate, 0.1M MES pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Sep 24, 2008
RadiationMonochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 43746 / Num. obs: 43573 / % possible obs: 99.67 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 56.99 Å2 / Rsym value: 0.106 / Net I/σ(I): 8.27
Reflection shellResolution: 2.9→3 Å / Redundancy: 3.55 % / Mean I/σ(I) obs: 2.33 / Num. unique all: 3448 / Rsym value: 0.525 / % possible all: 98.4

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Processing

Software
NameVersionClassificationNB
PHENIXrefinement
PDB_EXTRACT3.005data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 2Z81, 2Z7X, 2O6R

2z81

2z7x

2o6r


Resolution: 2.9→34.11 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.799 / SU ML: 2.75 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.28 4429 10.16 %
Rwork0.208 --
obs0.215 43573 99.67 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.282 Å2 / ksol: 0.278 e/Å3
Displacement parametersBiso max: 445.89 Å2 / Biso mean: 88.661 Å2 / Biso min: 24.01 Å2
Baniso -1Baniso -2Baniso -3
1--1.214 Å20 Å2-0 Å2
2---1.214 Å20 Å2
3----28.384 Å2
Refinement stepCycle: LAST / Resolution: 2.9→34.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8596 0 310 0 8906
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089122
X-RAY DIFFRACTIONf_angle_d1.25112385
X-RAY DIFFRACTIONf_chiral_restr0.0761479
X-RAY DIFFRACTIONf_plane_restr0.0041526
X-RAY DIFFRACTIONf_dihedral_angle_d22.8583482
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection allNum. reflection obs% reflection obs (%)
2.9-2.9330.4121320.34128014121280100
2.933-2.9670.3981510.301128514361285100
2.967-3.0040.3541440.304128114251281100
3.004-3.0420.3771420.284127814201278100
3.042-3.0820.3331590.27128014391280100
3.082-3.1240.3161540.249127714311277100
3.124-3.1680.3371490.246125914081259100
3.168-3.2160.3311460.243129014361290100
3.216-3.2660.3171420.229129414361294100
3.266-3.3190.3191440.228128014241280100
3.319-3.3770.3191450.22130114461301100
3.377-3.4380.2851500.211128814381288100
3.438-3.5040.2981220.198130614281306100
3.504-3.5750.2841460.196130614521306100
3.575-3.6530.2521430.185129014331290100
3.653-3.7380.2541380.166130414421304100
3.738-3.8310.2381590.172128114401281100
3.831-3.9350.2341470.169130014471300100
3.935-4.050.2481620.17127914411279100
4.05-4.1810.2221450.16512961441129699
4.181-4.330.2481450.152131014551310100
4.33-4.5030.1981430.14512991442129999
4.503-4.7070.211470.143132014671320100
4.707-4.9550.2061550.135130414591304100
4.955-5.2640.2411430.161133814811338100
5.264-5.6690.2481490.171132714761327100
5.669-6.2360.2971590.198133614951336100
6.236-7.1320.2531440.204135615001356100
7.132-8.9580.3061670.214136515321365100
8.958-34.1110.2761570.24514341591143497
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)
12.2887-0.84010.98570.7151-0.12511.34470.20790.09340.0862-0.1321-0.0438-0.06040.27340.0322-0.14290.33030.0646-0.15180.1446-0.04880.372814.6701-35.826915.2995
21.8496-0.3520.10941.12340.02071.3299-0.0058-0.24480.1595-0.0351-0.05320.0233-0.27790.26880.05090.3214-0.0689-0.07210.3344-0.07610.279855.8446-34.550635.5039
30.6819-0.0475-0.64330.7414-0.0021-0.32020.0239-0.44670.1462-0.08660.09060.2312-0.01860.0657-0.01240.69760.0681-0.42550.6385-0.11030.619521.0865-41.919342.8576
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA26 - 575
2X-RAY DIFFRACTION2chain BB33 - 557
3X-RAY DIFFRACTION3chain CA - C10 - 16

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