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- PDB-2z7x: Crystal structure of the TLR1-TLR2 heterodimer induced by binding... -

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Entry
Database: PDB / ID: 2z7x
TitleCrystal structure of the TLR1-TLR2 heterodimer induced by binding of a tri-acylated lipopeptide
Components
  • (Toll-like receptor ...) x 2
  • Pam3CSK4
KeywordsIMMUNE SYSTEM / TLR2 / TLR1 / Pam3CSK4 / lipopeptide / innate immunity / Glycoprotein / Immune response / Inflammatory response / Leucine-rich repeat / Membrane / Receptor / Transmembrane / Cytoplasmic vesicle
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 / positive regulation of toll-like receptor 2 signaling pathway / Toll Like Receptor TLR1:TLR2 Cascade / Beta defensins / lipopolysaccharide immune receptor activity / toll-like receptor 2 signaling pathway / positive regulation of matrix metallopeptidase secretion / lipopeptide binding / Toll-like receptor 2 binding / I-kappaB phosphorylation / central nervous system myelin formation / positive regulation of interleukin-18 production / leukotriene metabolic process / Toll-like receptor binding / toll-like receptor TLR6:TLR2 signaling pathway / response to fatty acid / macrophage activation / 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) / negative regulation of phagocytosis / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / nitric oxide metabolic process / 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 / positive regulation of interleukin-12 production / positive regulation of interferon-beta production / secretory granule membrane / response to progesterone / cell projection / learning / positive regulation of interleukin-8 production / 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 / positive regulation of inflammatory response / phagocytic vesicle membrane / positive regulation of tumor necrosis factor production / transmembrane signaling receptor activity / Modulation by Mtb of host immune system / signaling receptor activity / positive regulation of NF-kappaB transcription factor activity / amyloid-beta binding / cell body / ER-Phagosome pathway / defense response to virus / 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 / apoptotic process / positive regulation of gene expression / Neutrophil degranulation / protein-containing complex binding / SARS-CoV-2 activates/modulates innate and adaptive immune responses / Golgi apparatus / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / identical protein binding / membrane / plasma membrane / 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 / Cysteine-rich flanking region, C-terminal ...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 / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine Rich Repeat / Toll - interleukin 1 - resistance / Leucine-rich repeats, bacterial type / 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 / Alpha Beta
Similarity search - Domain/homology
PALMITIC ACID / (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate / Toll-like receptor 2 / Toll-like receptor 1 / Variable lymphocyte receptor B
Similarity search - Component
Biological speciesHomo sapiens (human)
Eptatretus burgeri (inshore hagfish)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 29, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 2, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Aug 16, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Item: _pdbx_unobs_or_zero_occ_atoms.label_asym_id
Revision 1.3Aug 23, 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 / Structure summary
Category: atom_site / chem_comp ...atom_site / 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_unobs_or_zero_occ_atoms / pdbx_validate_chiral / struct_asym / struct_conn / 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 / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.auth_asym_id / _pdbx_unobs_or_zero_occ_atoms.auth_seq_id / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _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_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 3.0Feb 7, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_entity_nonpoly / pdbx_entity_src_syn / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_asym / struct_conn / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_name_com.name / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.gene_src_common_name / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_seq_type / _pdbx_entity_src_syn.pdbx_beg_seq_num / _pdbx_entity_src_syn.pdbx_end_seq_num / _pdbx_struct_assembly_gen.asym_id_list / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end
Revision 3.1Nov 13, 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,Variable lymphocyte receptor B
B: Toll-like receptor 1,Variable lymphocyte receptor B
C: Pam3CSK4
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,18113
Polymers122,3283
Non-polymers3,85310
Water4,450247
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7950 Å2
ΔGint31 kcal/mol
Surface area48180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)200.303, 120.140, 74.120
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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 / Toll/interleukin-1 receptor-like protein 4


Mass: 62236.109 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: TLR2, UNP residues 27-508(human), VLRB.61, UNP residues 133-199(Inshore hagfish)
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Eptatretus burgeri (inshore hagfish)
Genus: Homo, Eptatretus / Species: , / Gene: TLR2, TIL4, VLRB / Plasmid: pVL1393 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi-5 / References: UniProt: O60603, UniProt: Q4G1L2
#2: Protein Toll-like receptor 1,Variable lymphocyte receptor B / Toll/interleukin-1 receptor-like protein / TIL


Mass: 59367.199 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: TLR1, UNP residues 25-476(human), VLRB.61, UNP residues 133-199(Inshore hagfish)
Source: (gene. exp.) Homo sapiens (human), (gene. exp.) Eptatretus burgeri (inshore hagfish)
Genus: Homo, Eptatretus / Species: , / Gene: TLR1, KIAA0012, VLRB / Plasmid: pVL1393 / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi-5 / References: UniProt: Q15399, UniProt: Q4G1L2

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Pam3CSK4


Mass: 724.955 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Peptide synthesis / Source: (synth.) synthetic construct (others)

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Sugars , 5 types, 8 molecules

#4: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAca1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,3,2/[a2122h-1b_1-5_2*NCC/3=O][a2122h-1a_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-2-3/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#5: Polysaccharide alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...alpha-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.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][a-D-Manp]{}}}}LINUCSPDB-CARE
#6: 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.: 1
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
#7: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 383.349 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-Manp]{}}LINUCSPDB-CARE
#8: 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.: 4
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 , 3 types, 249 molecules

#9: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#10: Chemical ChemComp-Z41 / (2S)-3-hydroxypropane-1,2-diyl dihexadecanoate


Mass: 568.911 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C35H68O5
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.65 Å3/Da / Density % sol: 66.29 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop
Details: 0.2M sodium citrate, 20% PEG3350, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 12, 2007
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: 2.1→50 Å / Num. all: 105091 / Num. obs: 99311 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rsym value: 0.095
Reflection shellResolution: 2.1→2.2 Å / Rsym value: 0.33 / % possible all: 83.5

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
CNS1.2refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→45.85 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.27 --RANDOM
Rwork0.244 ---
obs0.244 99311 94.5 %-
all-105091 --
Displacement parametersBiso mean: 54.5 Å2
Baniso -1Baniso -2Baniso -3
1--5.18 Å20 Å20 Å2
2--6.86 Å20 Å2
3----1.69 Å2
Refine analyzeLuzzati coordinate error obs: 0.31 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.41 Å
Refinement stepCycle: LAST / Resolution: 2.1→45.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8581 0 260 247 9088
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d25.4
X-RAY DIFFRACTIONc_improper_angle_d0.89
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.014
RfactorNum. reflection% reflection
Rfree0.385 756 -
Rwork0.376 --
obs-14430 87.8 %

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