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- PDB-2z80: Crystal structure of the TLR1-TLR2 heterodimer induced by binding... -

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Basic information

Entry
Database: PDB / ID: 2z80
TitleCrystal structure of the TLR1-TLR2 heterodimer induced by binding of a tri-acylated lipopeptide
ComponentsToll-like receptor 2, Variable lymphocyte receptor B
KeywordsIMMUNE SYSTEM / TLR2 / lipopeptide / innate immunity / Glycoprotein / Immune response / Inflammatory response / Leucine-rich repeat / Membrane / Receptor / Transmembrane
Function / homology
Function and homology information


Toll Like Receptor TLR6:TLR2 Cascade / triacyl lipopeptide binding / Toll-like receptor 2-Toll-like receptor 6 protein complex / detection of diacyl bacterial lipopeptide / 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 / negative regulation of synapse assembly ...Toll Like Receptor TLR6:TLR2 Cascade / triacyl lipopeptide binding / Toll-like receptor 2-Toll-like receptor 6 protein complex / detection of diacyl bacterial lipopeptide / 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 / negative regulation of synapse assembly / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / Toll Like Receptor TLR1:TLR2 Cascade / Beta defensins / toll-like receptor 2 signaling pathway / lipopolysaccharide immune receptor activity / positive regulation of matrix metallopeptidase secretion / I-kappaB phosphorylation / central nervous system myelin formation / leukotriene metabolic process / positive regulation of interleukin-18 production / Toll-like receptor binding / toll-like receptor TLR6:TLR2 signaling pathway / response to fatty acid / Regulation of TLR by endogenous ligand / peptidoglycan binding / NAD+ nucleosidase activity, cyclic ADP-ribose generating / microglia development / MyD88 deficiency (TLR2/4) / IRAK4 deficiency (TLR2/4) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / negative regulation of phagocytosis / toll-like receptor signaling pathway / pattern recognition receptor activity / RSV-host interactions / cellular response to lipoteichoic acid / positive regulation of interleukin-10 production / positive regulation of oligodendrocyte differentiation / positive regulation of Wnt signaling pathway / positive regulation of chemokine production / nitric oxide metabolic process / positive regulation of interleukin-12 production / positive regulation of interferon-beta production / secretory granule membrane / response to progesterone / learning / positive regulation of interleukin-8 production / cell projection / response to insulin / lipopolysaccharide binding / microglial cell activation / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to type II interferon / positive regulation of interleukin-6 production / response to toxic substance / phagocytic vesicle membrane / positive regulation of inflammatory response / positive regulation of NF-kappaB transcription factor activity / positive regulation of tumor necrosis factor production / Modulation by Mtb of host immune system / transmembrane signaling receptor activity / signaling receptor activity / amyloid-beta binding / ER-Phagosome pathway / cell body / defense response to virus / response to ethanol / response to hypoxia / receptor complex / defense response to Gram-positive bacterium / immune response / inflammatory response / membrane raft / negative regulation of cell population proliferation / innate immune response / intracellular membrane-bounded organelle / apoptotic process / Neutrophil degranulation / positive regulation of gene expression / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / cell surface / Golgi apparatus / signal transduction / positive regulation of transcription by RNA polymerase II / nucleoplasm / identical protein binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Leucine rich repeat C-terminal domain / Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / Toll-like receptor / : / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / TIR domain / Leucine Rich Repeat ...Leucine rich repeat C-terminal domain / Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / Toll-like receptor / : / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / TIR domain / Leucine Rich Repeat / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Toll - interleukin 1 - resistance / Leucine-rich repeats, bacterial type / 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 / Alpha Beta
Similarity search - Domain/homology
Toll-like receptor 2 / Variable lymphocyte receptor B
Similarity search - Component
Biological speciesHomo sapiens (human)
Eptatretus burgeri (inshore hagfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsLee, J.O. / Jin, M.S. / Kim, S.E. / Heo, J.Y.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: Crystal Structure of the TLR1-TLR2 Heterodimer Induced by Binding of a Tri-Acylated Lipopeptide
Authors: Jin, M.S. / Kim, S.E. / Heo, J.Y. / Lee, M.E. / Kim, H.M. / Paik, S.G. / Lee, H. / Lee, J.O.
History
DepositionAug 30, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.3Jul 29, 2020Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_ref_seq_dif
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 300BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION ...BIOMOLECULE: 1 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND PROGRAM GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON BURIED SURFACE AREA. DETAILS: AUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN

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Structure visualization

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)79,6423
Polymers79,4202
Non-polymers2211
Water4,738263
1
A: Toll-like receptor 2, Variable lymphocyte receptor B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,9312
Polymers39,7101
Non-polymers2211
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Toll-like receptor 2, Variable lymphocyte receptor B


Theoretical massNumber of molelcules
Total (without water)39,7101
Polymers39,7101
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.269, 101.383, 59.586
Angle α, β, γ (deg.)90.00, 99.82, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Toll-like receptor 2, Variable lymphocyte receptor B / Toll/interleukin-1 receptor-like protein 4 / CD282 antigen


Mass: 39710.156 Da / Num. of mol.: 2
Fragment: TLR2, UNP residues 1-284(human), VLRB.61, UNP residues 136-199(Inshore hagfish)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Eptatretus burgeri (inshore hagfish)
Genus: Homo, Eptatretus / Species: , / Strain: , / Gene: TLR2, TIL4, VLRB / Plasmid: pVL1393 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi-5 / References: UniProt: O60603, UniProt: Q4G1L2
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 263 / 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: 2.03 Å3/Da / Density % sol: 39.52 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris-HCl pH8.5, 28% PEG2000, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 10, 2006
RadiationMonochromator: SAGITALLY FOCUSED Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. all: 58798 / Num. obs: 57446 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 10.1 Å2 / Rsym value: 0.056
Reflection shellResolution: 1.8→1.91 Å / Rsym value: 0.212 / % possible all: 89.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.2refinement
MOSFLMdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→39.89 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 526063.37 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2907 5.1 %random
Rwork0.22 ---
obs0.22 57446 97.7 %-
all-58798 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.2744 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 15.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å20 Å2-0.15 Å2
2---0.34 Å20 Å2
3----0.33 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.06 Å-0.06 Å
Refinement stepCycle: LAST / Resolution: 1.8→39.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5069 0 14 263 5346
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.8
X-RAY DIFFRACTIONc_improper_angle_d0.76
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.26 472 5.4 %
Rwork0.212 8259 -
obs--89.6 %

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