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- PDB-3a7c: Crystal structure of TLR2-PE-DTPA complex -

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Basic information

Entry
Database: PDB / ID: 3a7c
TitleCrystal structure of TLR2-PE-DTPA complex
ComponentsToll-like receptor 2, Variable lymphocyte receptor B
KeywordsIMMUNE SYSTEM / Toll-like receptor / PE-DTPA / Leucine Rich Repeat / Cell membrane / Cytoplasmic vesicle / Disulfide bond / Glycoprotein / Immune response / Inflammatory response / Membrane / Receptor / Transmembrane / Phosphoprotein
Function / homology
Function and homology information


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 ...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 / negative regulation of synapse assembly / Regulation of TLR by endogenous ligand / response to molecule of fungal origin / response to peptidoglycan / regulation of dendritic cell cytokine production / positive regulation of interleukin-18 production / positive regulation of xenophagy / xenophagy / neutrophil migration / negative regulation of actin filament polymerization / cell surface pattern recognition receptor signaling pathway / cellular response to peptidoglycan / negative regulation of interleukin-12 production / NAD+ nucleosidase activity, cyclic ADP-ribose generating / negative regulation of interleukin-17 production / microglia development / positive regulation of leukocyte migration / MyD88-dependent toll-like receptor signaling pathway / positive regulation of macrophage cytokine production / negative regulation of phagocytosis / leukocyte migration / pattern recognition receptor activity / cellular response to lipoteichoic acid / positive regulation of intracellular signal transduction / positive regulation of chemokine production / nitric oxide biosynthetic process / positive regulation of interleukin-12 production / Neutrophil degranulation / ERK1 and ERK2 cascade / positive regulation of interferon-beta production / positive regulation of interleukin-1 beta production / learning / positive regulation of cytokine production / response to bacterium / defense response / positive regulation of interleukin-6 production / phagocytic vesicle membrane / positive regulation of inflammatory response / positive regulation of tumor necrosis factor production / positive regulation of nitric oxide biosynthetic process / transmembrane signaling receptor activity / amyloid-beta binding / positive regulation of ERK1 and ERK2 cascade / defense response to Gram-positive bacterium / inflammatory response / membrane raft / external side of plasma membrane / innate immune response / protein-containing complex binding / Golgi apparatus / positive regulation of transcription by RNA polymerase II / plasma membrane
Similarity search - Function
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 ...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 / 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
Similarity search - Domain/homology
: / Chem-PDK / Variable lymphocyte receptor B / Toll-like receptor 2
Similarity search - Component
Biological speciesMus musculus (house mouse)
Eptatretus burgeri (inshore hagfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 1.2Aug 9, 2017Group: Advisory / Source and taxonomy / Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / Item: _pdbx_unobs_or_zero_occ_atoms.label_asym_id
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 / 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_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._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_struct_assembly_gen.asym_id_list / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_conn.pdbx_leaving_atom_flag / _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 / _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
Revision 2.2Oct 23, 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 2, Variable lymphocyte receptor B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9546
Polymers65,5351
Non-polymers2,4185
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.625, 81.322, 89.968
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#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

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Sugars , 3 types, 3 molecules

#2: 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
#3: 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
#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 , 3 types, 225 molecules

#5: Chemical ChemComp-PDK / (10S,13R)-3-{2-[{2-[bis(carboxymethyl)amino]ethyl}(carboxymethyl)amino]ethyl}-10-hydroxy-5,16-dioxo-13-(tetradecanoyloxy)-9,11,15-trioxa-3,6-diaza-10-phosphanonacosan-1-oic acid 10-oxide / PE-DTPA


Mass: 1011.184 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C47H87N4O17P
#6: Chemical ChemComp-LU / LUTETIUM (III) ION / LU


Mass: 174.967 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Lu
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.36 Å3/Da / Density % sol: 47.85 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2M ammonium sulfate, 0.1M Na-HEPES pH 7.5, 25% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1.34027 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 10, 2007 / Details: Silicon 111
RadiationMonochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34027 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. all: 24792 / Num. obs: 24346 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.82 % / Biso Wilson estimate: 27.3 Å2 / Rsym value: 0.089 / Net I/σ(I): 29.3
Reflection shellResolution: 2.4→2.49 Å / Rsym value: 0.26 / % possible all: 86.2

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Processing

Software
NameVersionClassificationNB
CNS1.2refinement
PDB_EXTRACT3.005data extraction
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z81

2z81


Resolution: 2.4→49.12 Å / Rfactor Rfree error: 0.008 / Occupancy max: 1 / Occupancy min: 1 / Data cutoff high absF: 248308 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.29 1188 4.9 %RANDOM
Rwork0.215 ---
obs0.215 24308 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 40.753 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso max: 141.32 Å2 / Biso mean: 38.682 Å2 / Biso min: 2.44 Å2
Baniso -1Baniso -2Baniso -3
1--3.45 Å20 Å20 Å2
2---5.29 Å20 Å2
3---8.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.47 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.4→49.12 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4346 0 142 223 4711
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d0.8
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.341 161 4.5 %
Rwork0.27 3384 -
all-6188 -
obs--86.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramdna-rna.top
X-RAY DIFFRACTION3water.paramwater.top
X-RAY DIFFRACTION4carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION5ligand.paramligand.top

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