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- PDB-3a7b: Crystal structure of TLR2-Streptococcus Pneumoniae lipoteichoic a... -

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Entry
Database: PDB / ID: 3a7b
TitleCrystal structure of TLR2-Streptococcus Pneumoniae lipoteichoic acid complex
ComponentsToll-like receptor 2, Variable lymphocyte receptor B
KeywordsIMMUNE SYSTEM / Toll-like receptor / lipoteichoic acid / Leucine Rich Repeat / Cell membrane / Cytoplasmic vesicle / Disulfide bond / Glycoprotein / Immune response / Inflammatory response / Membrane / Receptor / Transmembrane / Phosphoprotein
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 / membrane / 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 / Leucine Rich repeat / TIR domain / 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 / Leucine Rich repeat / TIR domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Leucine-rich repeats, bacterial type / Toll - interleukin 1 - resistance / 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-LTC / 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: 2.53 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: Source and taxonomy / Category: entity_src_gen
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 / 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_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.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_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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_comp_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

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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)66,9564
Polymers65,5351
Non-polymers1,4213
Water4,846269
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)68.578, 83.190, 214.658
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#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: 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: 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
#4: Chemical ChemComp-LTC / (2S)-1-({3-O-[2-(acetylamino)-4-amino-2,4,6-trideoxy-beta-D-galactopyranosyl]-alpha-D-glucopyranosyl}oxy)-3-(heptanoyloxy)propan-2-yl (7Z)-pentadec-7-enoate / Lipoteichoic acid


Mass: 774.979 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C39H70N2O13
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 269 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailslipoteichoic acid labeled as LTC was purified from streptococcus pneumonia

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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: 4.67 Å3/Da / Density % sol: 73.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 50mM ammonium citrate pH 7.0, 20% PEG 4000, 30% ethylene glycol, 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 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Feb 19, 2009 / Details: Silicon 111
RadiationMonochromator: Silicon 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 41199 / Num. obs: 40005 / % possible obs: 97.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.84 % / Biso Wilson estimate: 41.5 Å2 / Rsym value: 0.077 / Net I/σ(I): 42.5
Reflection shellResolution: 2.5→2.59 Å / Mean I/σ(I) obs: 5.3 / Num. unique all: 3719 / Rsym value: 0.262 / % possible all: 92.2

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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: 2.53→45.1 Å / Rfactor Rfree error: 0.004 / Occupancy max: 1 / Occupancy min: 0 / Data cutoff high absF: 151024 / 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
Rfree0.27 4014 10 %RANDOM
Rwork0.234 ---
obs0.242 39965 95.4 %-
all-41199 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.328 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso max: 127.32 Å2 / Biso mean: 59.073 Å2 / Biso min: 27.98 Å2
Baniso -1Baniso -2Baniso -3
1--1.66 Å20 Å20 Å2
2--6.14 Å20 Å2
3----4.47 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.35 Å
Luzzati d res low-5 Å
Luzzati sigma a0.48 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.53→45.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4355 0 96 269 4720
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.7
X-RAY DIFFRACTIONc_dihedral_angle_d26.3
X-RAY DIFFRACTIONc_improper_angle_d1
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.372 453 10.2 %
Rwork0.314 3995 -
all-4448 -
obs--62.7 %
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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