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- PDB-2z64: Crystal structure of mouse TLR4 and mouse MD-2 complex -

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Basic information

Entry
Database: PDB / ID: 2z64
TitleCrystal structure of mouse TLR4 and mouse MD-2 complex
Components
  • Lymphocyte antigen 96
  • Toll-like receptor 4
KeywordsIMMUNE SYSTEM / TLR4 / toll-like receptor / MD-2 / LPS / Disease mutation / Glycoprotein / Immune response / Inflammatory response / Innate immunity / Leucine-rich repeat / Membrane / Transmembrane / Secreted
Function / homology
Function and homology information


MyD88-independent TLR4 cascade / Caspase activation via Death Receptors in the presence of ligand / Heme signaling / Toll Like Receptor 4 (TLR4) Cascade / TRIF-mediated programmed cell death / nitric oxide production involved in inflammatory response / MHC class II biosynthetic process / 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 / Heme signaling / Toll Like Receptor 4 (TLR4) Cascade / TRIF-mediated programmed cell death / nitric oxide production involved in inflammatory response / MHC class II biosynthetic process / 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 / innate immune response-activating signaling pathway / mast cell activation / positive regulation of matrix metallopeptidase secretion / detection of lipopolysaccharide / regulation of dendritic cell cytokine production / intestinal epithelial structure maintenance / positive regulation of lymphocyte proliferation / negative regulation of interleukin-23 production / positive regulation of stress-activated MAPK cascade / 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 lipopolysaccharide-mediated signaling pathway / macrophage activation / microglia differentiation / TRIF-dependent toll-like receptor signaling pathway / astrocyte development / response to fatty acid / activation of NF-kappaB-inducing kinase activity / positive regulation of macrophage activation / regulation of tumor necrosis factor production / NAD+ nucleotidase, cyclic ADP-ribose generating / negative regulation of interleukin-17 production / NADP+ nucleosidase activity / positive regulation of platelet activation / positive regulation of cytokine production involved in inflammatory response / nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of MHC class II biosynthetic process / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of extrinsic apoptotic signaling pathway / negative regulation of cold-induced thermogenesis / positive regulation of macrophage cytokine production / MyD88-dependent toll-like receptor signaling pathway / positive regulation of reactive oxygen species biosynthetic process / toll-like receptor 4 signaling pathway / phagocytic cup / positive regulation of NLRP3 inflammasome complex assembly / toll-like receptor signaling pathway / positive regulation of interleukin-13 production / 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 / detection of temperature stimulus involved in sensory perception of pain / positive regulation of interferon-alpha production / cellular response to lipoteichoic acid / negative regulation of interleukin-6 production / positive regulation of interleukin-10 production / negative regulation of type II interferon production / negative regulation of tumor necrosis factor production / stress-activated MAPK cascade / phosphatidylinositol 3-kinase binding / detection of mechanical stimulus involved in sensory perception of pain / phagocytosis / positive regulation of B cell proliferation / positive regulation of chemokine production / JNK cascade / lipopolysaccharide-mediated signaling pathway / ruffle / ERK1 and ERK2 cascade / nitric oxide biosynthetic process / positive regulation of interferon-beta production / activation of innate immune response / positive regulation of interleukin-12 production / neurogenesis / positive regulation of interleukin-1 beta production / positive regulation of interleukin-8 production / lipopolysaccharide binding / response to bacterium / positive regulation of JNK cascade / microglial cell activation / positive regulation of smooth muscle cell proliferation / positive regulation of MAP kinase activity / negative regulation of ERK1 and ERK2 cascade / positive regulation of inflammatory response / cellular response to type II interferon / positive regulation of interleukin-6 production / positive regulation of non-canonical NF-kappaB signal transduction
Similarity search - Function
Lymphocyte antigen 96 / Immunoglobulin-like - #770 / ML domain / MD-2-related lipid-recognition domain / Domain involved in innate immunity and lipid metabolism. / Toll-like receptor / TIR domain / Cysteine-rich flanking region, C-terminal / Leucine rich repeat C-terminal domain / Toll - interleukin 1 - resistance ...Lymphocyte antigen 96 / Immunoglobulin-like - #770 / ML domain / MD-2-related lipid-recognition domain / Domain involved in innate immunity and lipid metabolism. / Toll-like receptor / 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 / Leucine-rich repeat domain superfamily / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Lymphocyte antigen 96 / Toll-like receptor 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.84 Å
AuthorsLee, J.-O. / Kim, H.M. / Park, B.S.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2007
Title: Crystal Structure of the TLR4-MD-2 Complex with Bound Endotoxin Antagonist Eritoran
Authors: Kim, H.M. / Park, B.S. / Kim, J.-I. / Kim, S.E. / Lee, J. / Oh, S.C. / Enkhbayar, P. / Matsushima, N. / Lee, H. / Yoo, O.J. / Lee, J.-O.
History
DepositionJul 22, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 18, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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_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.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 / _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_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
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

Downloads & links

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Assembly

Deposited unit
A: Toll-like receptor 4
C: Lymphocyte antigen 96
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,78215
Polymers83,4612
Non-polymers4,32113
Water2,774154
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2210 Å2
ΔGint-2 kcal/mol
Surface area33330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.158, 101.882, 126.364
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsAUTHOR DETERMINED BIOLOGICAL UNIT: UNKNOWN

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Components

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Protein , 2 types, 2 molecules AC

#1: Protein Toll-like receptor 4 / / CD284 antigen


Mass: 67950.461 Da / Num. of mol.: 1 / Fragment: TLR4, UNP residues 27-625
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tlr4 / Plasmid: pVL1393 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi-5 / References: UniProt: Q9QUK6
#2: Protein Lymphocyte antigen 96 / / MD-2 protein / ESOP-1


Mass: 15510.707 Da / Num. of mol.: 1 / Fragment: MD-2, UNP residues 21-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Md2 / Plasmid: pVL1393 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): Hi-5 / References: UniProt: Q9JHF9

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Sugars , 4 types, 13 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.: 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
#4: 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.: 2
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
#5: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6) ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 732.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4[LFucpb1-6]DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1221m-1b_1-5]/1-1-2-3/a4-b1_a6-d1_b4-c1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}[(6+1)][b-L-Fucp]{}}LINUCSPDB-CARE
#6: 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 / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 9
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 , 1 types, 154 molecules

#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsALL POLYSACCHARIDES WERE ORIGINALLY ASSIGNED TO CHAIN N.

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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: 3.21 Å3/Da / Density % sol: 61.64 %
Crystal growTemperature: 296 K / Method: vapor diffusion / pH: 6.5
Details: 0.1M Na-Cacodylate, 23% PEG 8000, pH 6.5, VAPOR DIFFUSION, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 28, 2007 / Details: mirrors
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: 2.8→50 Å / Num. obs: 23932 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Rsym value: 0.095

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Z63

2z63


Resolution: 2.84→20 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.877 / SU B: 36.744 / SU ML: 0.355 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.464 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: CYS388 AND CYS389 FORMS AN UNUSUAL DISULFIDE BRIDGE AND A DISTORTED CIS PEPTIDE BOND
RfactorNum. reflection% reflectionSelection details
Rfree0.29043 1183 5.1 %RANDOM
Rwork0.24206 ---
obs0.24449 22180 90.1 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.87 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20 Å2
2---5.87 Å20 Å2
3---5.01 Å2
Refinement stepCycle: LAST / Resolution: 2.84→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5867 0 281 154 6302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226307
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4212.0078573
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8145732
X-RAY DIFFRACTIONr_dihedral_angle_2_deg44.94625278
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.404151054
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5561518
X-RAY DIFFRACTIONr_chiral_restr0.0870.21024
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024547
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2470.23025
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3250.24206
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1590.2255
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2360.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2860.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.6021.53755
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.79325952
X-RAY DIFFRACTIONr_scbond_it4.42632807
X-RAY DIFFRACTIONr_scangle_it6.9524.52621
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.835→2.907 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.317 40 -
Rwork0.325 743 -
obs--41.72 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0374-0.0046-0.08170.65460.08520.4853-0.02210.0219-0.1763-0.03860.0217-0.01730.0695-0.05270.0004-0.0332-0.00460.0096-0.10540.0588-0.2676-16.61350.3578-1.2051
21.91420.03240.25213.2907-2.42793.2950.0158-0.3642-0.17370.3350.0289-0.20460.27840.2491-0.04470.05050.0237-0.05380.1247-0.0354-0.1756-27.618-11.8520.0202
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA27 - 6251 - 599
2X-RAY DIFFRACTION2CB21 - 1551 - 135

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