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- PDB-5ijd: The crystal structure of mouse TLR4/MD-2/lipid A complex -

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Basic information

Entry
Database: PDB / ID: 5ijd
TitleThe crystal structure of mouse TLR4/MD-2/lipid A complex
Components
  • Lymphocyte antigen 96
  • Toll-like receptor 4, Variable lymphocyte receptor B chimera
KeywordsIMMUNE SYSTEM / immune response / protein complex / natural agonist
Function / homology
Function and homology information


MyD88-independent TLR4 cascade / Caspase activation via Death Receptors in the presence of ligand / TRIF-mediated programmed cell death / Toll Like Receptor 4 (TLR4) Cascade / nitric oxide production involved in inflammatory response / MHC class II biosynthetic process / Heme signaling / Regulation of TLR by endogenous ligand / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / TRAF6-mediated induction of TAK1 complex within TLR4 complex ...MyD88-independent TLR4 cascade / Caspase activation via Death Receptors in the presence of ligand / TRIF-mediated programmed cell death / Toll Like Receptor 4 (TLR4) Cascade / nitric oxide production involved in inflammatory response / MHC class II biosynthetic process / Heme signaling / Regulation of TLR by endogenous ligand / positive regulation of cellular response to macrophage colony-stimulating factor stimulus / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / lipopolysaccharide immune receptor activity / Toll-like receptor 4 binding / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / IKK complex recruitment mediated by RIP1 / lipopolysaccharide receptor complex / positive regulation of matrix metallopeptidase secretion / innate immune response-activating signaling pathway / regulation of dendritic cell cytokine production / positive regulation of lymphocyte proliferation / detection of lipopolysaccharide / mast cell activation / intestinal epithelial structure maintenance / negative regulation of interleukin-23 production / lymphocyte proliferation / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / cellular response to oxidised low-density lipoprotein particle stimulus / wound healing involved in inflammatory response / B cell proliferation involved in immune response / leukotriene metabolic process / nucleotide-binding oligomerization domain containing 1 signaling pathway / positive regulation of interleukin-1 production / positive regulation of stress-activated MAPK cascade / positive regulation of lipopolysaccharide-mediated signaling pathway / macrophage activation / positive regulation of interleukin-13 production / TRIF-dependent toll-like receptor signaling pathway / astrocyte development / microglia differentiation / response to fatty acid / activation of NF-kappaB-inducing kinase activity / regulation of tumor necrosis factor production / nucleotide-binding oligomerization domain containing 2 signaling pathway / NAD+ nucleotidase, cyclic ADP-ribose generating / positive regulation of MHC class II biosynthetic process / negative regulation of interleukin-17 production / positive regulation of platelet activation / positive regulation of cytokine production involved in inflammatory response / positive regulation of extrinsic apoptotic signaling pathway / positive regulation of macrophage activation / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of macrophage cytokine production / negative regulation of cold-induced thermogenesis / MyD88-dependent toll-like receptor signaling pathway / positive regulation of reactive oxygen species biosynthetic process / toll-like receptor 4 signaling pathway / positive regulation of NLRP3 inflammasome complex assembly / toll-like receptor signaling pathway / cellular response to platelet-derived growth factor stimulus / positive regulation of smooth muscle cell migration / B cell proliferation / positive regulation of nitric-oxide synthase biosynthetic process / cellular response to lipoteichoic acid / detection of temperature stimulus involved in sensory perception of pain / negative regulation of interleukin-6 production / phagocytic cup / positive regulation of interleukin-10 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / positive regulation of interferon-alpha production / phosphatidylinositol 3-kinase binding / detection of mechanical stimulus involved in sensory perception of pain / phagocytosis / stress-activated MAPK cascade / positive regulation of chemokine production / positive regulation of B cell proliferation / JNK cascade / lipopolysaccharide-mediated signaling pathway / ruffle / nitric oxide biosynthetic process / ERK1 and ERK2 cascade / positive regulation of interleukin-12 production / activation of innate immune response / positive regulation of interferon-beta production / neurogenesis / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / lipopolysaccharide binding / positive regulation of JNK cascade / positive regulation of smooth muscle cell proliferation / response to bacterium / microglial cell activation / positive regulation of MAP kinase activity / negative regulation of ERK1 and ERK2 cascade / cellular response to type II interferon / positive regulation of inflammatory response / positive regulation of non-canonical NF-kappaB signal transduction / cellular response to mechanical stimulus / cellular response to amyloid-beta
Similarity search - Function
Lymphocyte antigen 96 / Immunoglobulin-like - #770 / Variable lymphocyte receptor, C-terminal / ML domain / Domain of unknown function (DUF3439) / MD-2-related lipid-recognition domain / Domain involved in innate immunity and lipid metabolism. / Toll-like receptor / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain ...Lymphocyte antigen 96 / Immunoglobulin-like - #770 / Variable lymphocyte receptor, C-terminal / ML domain / Domain of unknown function (DUF3439) / MD-2-related lipid-recognition domain / Domain involved in innate immunity and lipid metabolism. / 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 / 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 / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
LAURIC ACID / Chem-LP4 / Chem-LP5 / MYRISTIC ACID / Variable lymphocyte receptor B / Lymphocyte antigen 96 / Toll-like receptor 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
Eptatretus burgeri (inshore hagfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsWang, Y. / Su, L. / Morin, M.D. / Jones, B.T. / Whitby, L.R. / Surakattula, M. / Huang, H. / Shi, H. / Choi, J.H. / Wang, K. ...Wang, Y. / Su, L. / Morin, M.D. / Jones, B.T. / Whitby, L.R. / Surakattula, M. / Huang, H. / Shi, H. / Choi, J.H. / Wang, K. / Moresco, E.M. / Berger, M. / Zhan, X. / Zhang, H. / Boger, D.L. / Beutler, B.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2016
Title: TLR4/MD-2 activation by a synthetic agonist with no similarity to LPS.
Authors: Wang, Y. / Su, L. / Morin, M.D. / Jones, B.T. / Whitby, L.R. / Surakattula, M.M. / Huang, H. / Shi, H. / Choi, J.H. / Wang, K.W. / Moresco, E.M. / Berger, M. / Zhan, X. / Zhang, H. / Boger, D.L. / Beutler, B.
History
DepositionMar 1, 2016Deposition site: RCSB / Processing site: RCSB
SupersessionApr 27, 2016ID: 5HG6
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1May 4, 2016Group: Database references
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 / citation / 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_struct_mod_residue / pdbx_struct_oper_list / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral / struct_asym / struct_conn / 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 / _citation.journal_id_CSD / _database_PDB_caveat.text / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_mod_residue.auth_asym_id / _pdbx_struct_mod_residue.auth_seq_id / _pdbx_struct_mod_residue.label_asym_id / _pdbx_struct_oper_list.symmetry_operation / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _pdbx_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Apr 3, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: Toll-like receptor 4, Variable lymphocyte receptor B chimera
C: Lymphocyte antigen 96
D: Lymphocyte antigen 96
B: Toll-like receptor 4, Variable lymphocyte receptor B chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,12924
Polymers169,3474
Non-polymers7,78220
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20200 Å2
ΔGint48 kcal/mol
Surface area60170 Å2
MethodPISA
2
A: Toll-like receptor 4, Variable lymphocyte receptor B chimera
C: Lymphocyte antigen 96
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,46312
Polymers84,6732
Non-polymers3,78910
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8300 Å2
ΔGint33 kcal/mol
Surface area31790 Å2
MethodPISA
3
D: Lymphocyte antigen 96
B: Toll-like receptor 4, Variable lymphocyte receptor B chimera
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,66612
Polymers84,6732
Non-polymers3,99210
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8480 Å2
ΔGint33 kcal/mol
Surface area31800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.843, 145.737, 136.195
Angle α, β, γ (deg.)90.00, 100.67, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Toll-like receptor 4, Variable lymphocyte receptor B chimera


Mass: 67280.703 Da / Num. of mol.: 2
Fragment: TLR4 ectodomain (UNP residues 26-544) + VLRB (UNP residues 126-200)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Eptatretus burgeri (inshore hagfish)
Gene: Tlr4, Lps, VLRB / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9QUK6, UniProt: Q4G1L2
#2: Protein Lymphocyte antigen 96 / Ly-96 / ESOP-1 / Protein MD-2


Mass: 17392.793 Da / Num. of mol.: 2 / Fragment: UNP residues 19-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ly96, Esop1, Md2 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: Q9JHF9

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Sugars , 2 types, 12 molecules

#3: 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.: 7
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)][a-D-GlcpNAc]{}}}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.: 5
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 , 5 types, 240 molecules

#5: Chemical ChemComp-LP4 / 2-deoxy-3-O-[(3R)-3-hydroxytetradecanoyl]-2-{[(3R)-3-hydroxytetradecanoyl]amino}-4-O-phosphono-beta-D-glucopyranose


Mass: 711.861 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H66NO12P
#6: Chemical ChemComp-LP5 / (R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE


Mass: 711.861 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H66NO12P
#7: Chemical ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H24O2
#8: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 3.93 Å3/Da / Density % sol: 68.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1 M Tris, pH 8.0, 0.2 M lithium chloride, 14% PEG8000, 2.5% PEG400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 54848 / % possible obs: 96.2 % / Redundancy: 4 % / Rmerge(I) obs: 0.058 / Net I/av σ(I): 22.386 / Net I/σ(I): 8.3
Reflection shellResolution: 2.7→2.75 Å

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Processing

Software
NameVersionClassification
REFMAC5.8.0049refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5IJD

5ijd


Resolution: 2.7→39.34 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.842 / SU B: 14.782 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R: 1.232 / ESU R Free: 0.41 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28534 1978 3.6 %RANDOM
Rwork0.21476 ---
obs0.21727 52860 77.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 43.652 Å2
Baniso -1Baniso -2Baniso -3
1--0.81 Å20 Å20.82 Å2
2--0.21 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.7→39.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11903 0 242 232 12377
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.01912451
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211856
X-RAY DIFFRACTIONr_angle_refined_deg1.82.00116846
X-RAY DIFFRACTIONr_angle_other_deg2.739327316
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.78251454
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.60624.716545
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.137152110
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.011545
X-RAY DIFFRACTIONr_chiral_restr0.0920.21944
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0213565
X-RAY DIFFRACTIONr_gen_planes_other0.0060.022822
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8144.1975822
X-RAY DIFFRACTIONr_mcbond_other2.8134.1975821
X-RAY DIFFRACTIONr_mcangle_it4.7036.2867271
X-RAY DIFFRACTIONr_mcangle_other4.7036.2877272
X-RAY DIFFRACTIONr_scbond_it2.7954.6396629
X-RAY DIFFRACTIONr_scbond_other2.7944.6396630
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.8086.8619575
X-RAY DIFFRACTIONr_long_range_B_refined8.01634.58514190
X-RAY DIFFRACTIONr_long_range_B_other8.00934.61114161
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.691→2.761 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 53 -
Rwork0.328 1411 -
obs--27.92 %

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