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- PDB-5d3i: Crystal structure of the SSL3-TLR2 complex -

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Basic information

Entry
Database: PDB / ID: 5d3i
TitleCrystal structure of the SSL3-TLR2 complex
Components
  • Staphylococcal Superantigen-Like protein 3
  • Toll-like receptor 2
KeywordsIMMUNE SYSTEM / Superantigens / Superantigen-like proteins / SSL / SSL3 / Toll-like Receptor 2 / TLR2 / TLR6 / Immunology / Inflammation / Inhibition / Lipopeptide / phosphatidylcholine / PC / immune evasion / innate immunity
Function / homology
Function and homology information


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 / cellular response to diacyl bacterial lipopeptide / positive regulation of neutrophil migration / Toll-like receptor 1-Toll-like receptor 2 protein complex / detection of triacyl bacterial lipopeptide ...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 / cellular response to diacyl bacterial lipopeptide / positive regulation of neutrophil migration / 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 / lipoteichoic acid binding / Regulation of TLR by endogenous ligand / negative regulation of synapse assembly / response to molecule of fungal origin / cell surface pattern recognition receptor signaling pathway / regulation of dendritic cell cytokine production / response to peptidoglycan / positive regulation of interleukin-18 production / central nervous system myelin formation / positive regulation of xenophagy / xenophagy / leukotriene metabolic process / neutrophil migration / negative regulation of actin filament polymerization / lipopeptide binding / cellular response to peptidoglycan / response to fatty acid / negative regulation of interleukin-12 production / NAD+ nucleotidase, cyclic ADP-ribose generating / negative regulation of interleukin-17 production / microglia development / negative regulation of phagocytosis / positive regulation of leukocyte migration / MyD88-dependent toll-like receptor signaling pathway / positive regulation of intracellular signal transduction / positive regulation of macrophage cytokine production / pattern recognition receptor activity / toll-like receptor signaling pathway / nitric oxide metabolic process / leukocyte migration / positive regulation of oligodendrocyte differentiation / positive regulation of nitric-oxide synthase biosynthetic process / cellular response to lipoteichoic acid / positive regulation of interleukin-10 production / positive regulation of chemokine production / nitric oxide biosynthetic process / positive regulation of interleukin-12 production / positive regulation of interferon-beta production / ERK1 and ERK2 cascade / Neutrophil degranulation / learning / positive regulation of interleukin-1 beta production / cell projection / positive regulation of cytokine production / response to bacterium / microglial cell activation / defense response / positive regulation of inflammatory response / positive regulation of interleukin-6 production / phagocytic vesicle membrane / positive regulation of nitric oxide biosynthetic process / positive regulation of tumor necrosis factor production / transmembrane signaling receptor activity / signaling receptor activity / amyloid-beta binding / cell body / positive regulation of ERK1 and ERK2 cascade / defense response to Gram-positive bacterium / inflammatory response / membrane raft / negative regulation of cell population proliferation / external side of plasma membrane / innate immune response / protein-containing complex binding / Golgi apparatus / cell surface / positive regulation of transcription by RNA polymerase II / extracellular region / plasma membrane
Similarity search - Function
Staphylococcus aureus exotoxin / Staphylococcal superantigen-like OB-fold domain / Staphylococcal superantigen-like OB-fold domain / Toll-like receptor / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Ubiquitin-like (UB roll) - #120 ...Staphylococcus aureus exotoxin / Staphylococcal superantigen-like OB-fold domain / Staphylococcal superantigen-like OB-fold domain / Toll-like receptor / Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin, conserved site / Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2. / Superantigen, staphylococcal/streptococcal toxin, bacterial / Staphylococcal/Streptococcal toxin, beta-grasp domain / Staphylococcal/Streptococcal toxin, beta-grasp domain / Ubiquitin-like (UB roll) - #120 / Superantigen toxin, C-terminal / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #110 / Leucine Rich repeat / TIR domain / Enterotoxin / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeats, bacterial type / Toll - interleukin 1 - resistance / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / TIR domain profile. / Alpha-Beta Horseshoe / 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 / Ubiquitin-like (UB roll) / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Roll / Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / Staphylococcal superantigen-like 3 / Toll-like receptor 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Staphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsFeitsma, L.J. / Huizinga, E.G.
Funding support Netherlands, 3items
OrganizationGrant numberCountry
Netherlands Organization for Scientific ResearchECHO Grant 700.58.006 Netherlands
Netherlands Organization for Health Research and DevelopmentZonMw Grant 205200004 Netherlands
Dutch Top Institute Pharma ProjectD1-101 Netherlands
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2015
Title: Structural basis for inhibition of TLR2 by staphylococcal superantigen-like protein 3 (SSL3).
Authors: Koymans, K.J. / Feitsma, L.J. / Brondijk, T.H. / Aerts, P.C. / Lukkien, E. / Lossl, P. / van Kessel, K.P. / de Haas, C.J. / van Strijp, J.A. / Huizinga, E.G.
History
DepositionAug 6, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 19, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Sep 9, 2015Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_unobs_or_zero_occ_atoms / 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 / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.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 2.1May 1, 2024Group: 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
Revision 2.2Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Toll-like receptor 2
B: Staphylococcal Superantigen-Like protein 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,1566
Polymers86,6882
Non-polymers1,4684
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4180 Å2
ΔGint-24 kcal/mol
Surface area34210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.198, 104.198, 153.625
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein Toll-like receptor 2


Mass: 63839.773 Da / Num. of mol.: 1 / Fragment: UNP residues 25-589
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tlr2 / Cell line (production host): HEK293-EBNA1-S / Production host: Homo sapiens (human) / References: UniProt: Q9QUN7
#2: Protein Staphylococcal Superantigen-Like protein 3


Mass: 22848.506 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (strain NCTC 8325) (bacteria)
Gene: SAOUHSC_00386 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): Rosetta-gami / References: UniProt: Q2G0X7

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Sugars , 2 types, 2 molecules

#3: 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.: 1
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
#4: 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.: 1
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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Non-polymers , 2 types, 2 molecules

#5: Chemical ChemComp-PCW / 1,2-DIOLEOYL-SN-GLYCERO-3-PHOSPHOCHOLINE / (Z,Z)-4-HYDROXY-N,N,N-TRIMETHYL-10-OXO-7-[(1-OXO-9-OCTADECENYL)OXY]-3,5,9-TRIOXA-4-PHOSPHAHEPTACOS-18-EN-1-AMINIUM-4-OXIDE


Mass: 787.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C44H85NO8P / Comment: DOPC, phospholipid*YM
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.86 Å3/Da / Density % sol: 57.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: PCB, PEG1500 / PH range: 5

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Sep 26, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.2→52.1 Å / Num. obs: 14687 / % possible obs: 94.1 % / Redundancy: 2.5 % / Biso Wilson estimate: 44.6 Å2 / Rmerge(I) obs: 0.225 / Net I/σ(I): 5.6
Reflection shellResolution: 3.2→3.31 Å / Redundancy: 2.4 % / Rmerge(I) obs: 1.08 / Mean I/σ(I) obs: 2 / % possible all: 96.7

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Processing

Software
NameVersionClassification
XDSMarch 2013data reduction
Aimless1.7.6data scaling
PHASER2.5.2phasing
PHENIX1.9_1692refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TLR2, SSL3

Resolution: 3.2→52.099 Å / SU ML: 0.53 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.271 697 4.78 %Random
Rwork0.2308 ---
obs0.2327 14583 93.36 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 57.4 Å2
Refinement stepCycle: LAST / Resolution: 3.2→52.099 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5885 0 86 0 5971
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076092
X-RAY DIFFRACTIONf_angle_d1.1998225
X-RAY DIFFRACTIONf_dihedral_angle_d13.1482286
X-RAY DIFFRACTIONf_chiral_restr0.054954
X-RAY DIFFRACTIONf_plane_restr0.0051034
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.2001-3.44710.3571460.35012812X-RAY DIFFRACTION95
3.4471-3.79390.3641430.29122862X-RAY DIFFRACTION97
3.7939-4.34270.27661450.22942797X-RAY DIFFRACTION94
4.3427-5.47040.21671440.19262780X-RAY DIFFRACTION93
5.4704-52.10590.23211190.18362635X-RAY DIFFRACTION87
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)
13.3166-0.29921.50231.8609-0.45433.8451.04630.1676-1.43750.0904-0.1604-1.03051.56161.22781.96361.09560.5172-0.34411.0655-0.0651.331527.37495.08142.0196
27.5393-2.88462.54194.8226-2.91065.82140.276-0.7359-0.73560.17930.3317-0.13450.83470.02160.99590.55690.0262-0.02240.51150.19790.49394.756714.702-1.3176
33.39460.7791-2.48567.8467-0.1866.4492-0.1268-0.16840.5126-0.43710.10820.50560.1323-0.688-0.26640.5038-0.01680.04580.39550.04330.3492-3.491729.4781-14.4205
47.08551.96531.6862.00060.15233.8754-0.22980.63760.34950.07070.0416-0.2379-0.11820.8733-0.06540.38730.0350.07030.51710.20150.513721.999247.6699-25.9604
51.125-0.85780.87680.8819-0.09651.7342-0.1104-1.3626-0.748-0.03390.2291-0.91260.14881.280.01590.5819-0.0479-0.02181.54030.43071.485350.187842.478-15.4302
65.2608-2.9381-0.09663.69480.77710.8109-0.4305-0.97320.6459-0.0228-0.11891.48830.4042-1.8179-0.12520.6124-0.26690.01151.12610.14120.6029-29.692637.878-41.8451
75.139-2.0963-2.46965.27686.10798.26840.82171.0036-0.89740.4064-1.90120.98810.7738-0.485-1.71780.7911-0.0002-0.31710.59910.07890.755-5.96835.4062-40.5031
84.92550.11293.37291.52730.33721.9162-0.08770.5902-0.2735-0.26770.22840.22280.10070.328-0.00160.5456-0.0083-0.03750.58910.11690.5952-10.261237.6539-40.8185
95.2204-2.36521.59037.83144.87195.87050.20450.84780.18650.30840.721-1.44640.02180.79262.2550.5209-0.0267-0.00070.53760.04270.4794-6.726442.9528-43.5175
104.1394-0.82372.50911.48460.52127.1228-0.0775-0.3717-0.1686-0.69210.05320.20250.5222-0.5782-0.010.3723-0.0984-0.04920.70010.09140.6045-15.862540.2186-41.2233
117.9191.32981.44350.8937-0.50671.9016-0.05540.4710.880.7981.1551.9467-0.7912-1.36841.9480.44090.1975-0.05391.23860.19421.2917-39.399851.1233-53.0525
121.0519-0.63011.50282.5755-0.43651.59210.28391.28340.62320.0968-0.70660.4203-0.5361-1.19530.12831.00860.2407-0.02111.4397-0.13910.7923-30.990355.3566-49.5372
134.66512.6183-0.18525.8729-0.80136.3674-0.0758-0.29020.14780.05750.02090.34180.3322-0.93040.00040.4938-0.01320.0280.6950.00650.5128-27.734345.3789-52.4823
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-IDSelection details
1X-RAY DIFFRACTION1B257 - 326
2X-RAY DIFFRACTION2chain 'A' and (resid 146 through 240 )
3X-RAY DIFFRACTION3chain 'A' and (resid 241 through 344 )
4X-RAY DIFFRACTION4chain 'A' and (resid 345 through 538 )
5X-RAY DIFFRACTION5chain 'A' and (resid 539 through 575 )
6X-RAY DIFFRACTION6chain 'B' and (resid 137 through 152 )
7X-RAY DIFFRACTION7chain 'B' and (resid 153 through 167 )
8X-RAY DIFFRACTION8chain 'B' and (resid 168 through 189 )
9X-RAY DIFFRACTION9chain 'B' and (resid 190 through 202 )
10X-RAY DIFFRACTION10chain 'B' and (resid 203 through 228 )
11X-RAY DIFFRACTION11chain 'B' and (resid 229 through 243 )
12X-RAY DIFFRACTION12chain 'B' and (resid 244 through 256 )
13X-RAY DIFFRACTION13chain 'B' and (resid 257 through 326 )

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