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- PDB-2z82: Crystal structure of the TLR1-TLR2 heterodimer induced by binding... -

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Entry
Database: PDB / ID: 2z82
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 / Pam2CSK4 / lipopeptide / innate immunity / Cytoplasmic vesicle / Glycoprotein / Immune response / Inflammatory response / Leucine-rich repeat / Membrane / Receptor / Transmembrane
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 / positive regulation of neutrophil migration / cellular response to diacyl bacterial lipopeptide / 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 / positive regulation of neutrophil migration / 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 / Regulation of TLR by endogenous ligand / lipoteichoic acid binding / 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 xenophagy / positive regulation of interleukin-18 production / central nervous system myelin formation / xenophagy / leukotriene metabolic process / neutrophil migration / negative regulation of actin filament polymerization / response to fatty acid / lipopeptide binding / cellular response to peptidoglycan / 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 macrophage cytokine production / positive regulation of leukocyte migration / positive regulation of intracellular signal transduction / MyD88-dependent toll-like receptor signaling pathway / pattern recognition receptor activity / toll-like receptor signaling pathway / positive regulation of oligodendrocyte differentiation / nitric oxide metabolic process / leukocyte migration / 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 / ERK1 and ERK2 cascade / positive regulation of interleukin-12 production / positive regulation of interferon-beta production / Neutrophil degranulation / learning / positive regulation of interleukin-1 beta production / positive regulation of cytokine production / cell projection / response to bacterium / microglial cell activation / defense response / positive regulation of inflammatory response / phagocytic vesicle membrane / transmembrane signaling receptor activity / positive regulation of interleukin-6 production / positive regulation of tumor necrosis factor production / positive regulation of nitric oxide biosynthetic process / 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 / Leucine-rich repeats, bacterial type / 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 / Leucine-rich repeats, bacterial type / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / TIR domain profile. / Toll/interleukin-1 receptor homology (TIR) domain / Toll/interleukin-1 receptor homology (TIR) domain superfamily / Alpha-Beta Horseshoe / 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
Chem-PDJ / 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: 2.6 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 1.0Oct 2, 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 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
Remark 600HETROGEN PDJ is linked with five amino acid residues (SKKKK), which are not visible

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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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,8635
Polymers61,9731
Non-polymers1,8904
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)84.650, 81.334, 90.904
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 / CD282 antigen


Mass: 61972.961 Da / Num. of mol.: 1
Fragment: TLR2, UNP residues 27-506(Mouse), VLRB.61, UNP residues 133-199(Inshore hagfish)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Eptatretus burgeri (inshore hagfish)
Genus: Mus, Eptatretus / Species: , / Strain: , / Gene: Tlr2, VLRB / 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


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, 87 molecules

#5: Chemical ChemComp-PDJ / (2R)-3-{[(2R)-2-AMINO-3-HYDROXYPROPYL]THIO}PROPANE-1,2-DIYL DIHEXADECANOATE


Mass: 658.071 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H75NO5S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O

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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: 2.52 Å3/Da / Density % sol: 51.28 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2M ammonium sulfate, 0.1M Tris-HCl pH8.5 and 34% PEG1000, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 10, 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: 2.6→50 Å / Num. all: 19913 / Num. obs: 18898 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Biso Wilson estimate: 19.8 Å2 / Rsym value: 0.096
Reflection shellResolution: 2.6→2.76 Å / Rsym value: 0.363 / % possible all: 80.3

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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: 2.6→39.68 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 195675.32 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.277 921 4.9 %random
Rwork0.215 ---
obs0.215 18898 94.9 %-
all-19913 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 13.538 Å2 / ksol: 0.3 e/Å3
Displacement parametersBiso mean: 36.5 Å2
Baniso -1Baniso -2Baniso -3
1--5.88 Å20 Å20 Å2
2---10.23 Å20 Å2
3---16.11 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.59 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.6→39.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4353 0 126 86 4565
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.9
X-RAY DIFFRACTIONc_improper_angle_d1.02
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.035 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.363 109 4.2 %
Rwork0.304 --
obs-2509 80.3 %

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