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- PDB-3vq1: Crystal structure of mouse TLR4/MD-2/lipid IVa complex -

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Basic information

Entry
Database: PDB / ID: 3vq1
TitleCrystal structure of mouse TLR4/MD-2/lipid IVa complex
Components
  • Lymphocyte antigen 96
  • Toll-like receptor 4
KeywordsIMMUNE SYSTEM / Leucine rich repeat MD-2 related lipid recognition / receptor innate immunity / lipid binding / glycosylation / secreted
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 / Heme signaling / Regulation of TLR by endogenous ligand / MHC class II biosynthetic process / 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 / Heme signaling / Regulation of TLR by endogenous ligand / MHC class II biosynthetic process / 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 / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / lipopolysaccharide immune receptor activity / positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway / positive regulation of matrix metallopeptidase secretion / Toll-like receptor 4 binding / mast cell activation / positive regulation of lymphocyte proliferation / lipopolysaccharide receptor complex / detection of lipopolysaccharide / intestinal epithelial structure maintenance / regulation of dendritic cell cytokine production / negative regulation of interleukin-23 production / lymphocyte proliferation / cellular response to oxidised low-density lipoprotein particle stimulus / wound healing involved in inflammatory response / B cell proliferation involved in immune response / positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway / nucleotide-binding oligomerization domain containing 1 signaling pathway / activation of NF-kappaB-inducing kinase activity / positive regulation of stress-activated MAPK cascade / positive regulation of interleukin-1 production / positive regulation of interleukin-13 production / macrophage activation / TRIF-dependent toll-like receptor signaling pathway / astrocyte development / microglia differentiation / nucleotide-binding oligomerization domain containing 2 signaling pathway / positive regulation of MHC class II biosynthetic process / positive regulation of macrophage activation / NAD+ nucleosidase activity, cyclic ADP-ribose generating / positive regulation of platelet activation / positive regulation of lipopolysaccharide-mediated signaling pathway / negative regulation of interleukin-17 production / positive regulation of cytokine production involved in inflammatory response / positive regulation of chemokine (C-X-C motif) ligand 2 production / positive regulation of extrinsic apoptotic signaling pathway / negative regulation of cold-induced thermogenesis / MyD88-dependent toll-like receptor signaling pathway / positive regulation of macrophage cytokine production / toll-like receptor 4 signaling pathway / toll-like receptor signaling pathway / positive regulation of smooth muscle cell migration / positive regulation of reactive oxygen species biosynthetic process / positive regulation of NLRP3 inflammasome complex assembly / : / cellular response to lipoteichoic acid / negative regulation of interleukin-6 production / positive regulation of interferon-alpha production / negative regulation of type II interferon production / B cell proliferation / positive regulation of interleukin-10 production / phagocytic cup / negative regulation of tumor necrosis factor production / phagocytosis / stress-activated MAPK cascade / positive regulation of chemokine production / JNK cascade / ruffle / cellular response to platelet-derived growth factor stimulus / positive regulation of B cell proliferation / nitric oxide biosynthetic process / positive regulation of interleukin-12 production / ERK1 and ERK2 cascade / activation of innate immune response / positive regulation of MAP kinase activity / positive regulation of interferon-beta production / lipopolysaccharide-mediated signaling pathway / positive regulation of interleukin-1 beta production / neurogenesis / positive regulation of interleukin-8 production / positive regulation of smooth muscle cell proliferation / response to bacterium / positive regulation of JNK cascade / lipopolysaccharide binding / positive regulation of non-canonical NF-kappaB signal transduction / negative regulation of ERK1 and ERK2 cascade / cellular response to type II interferon / positive regulation of interleukin-6 production / cellular response to mechanical stimulus / positive regulation of inflammatory response / positive regulation of type II interferon production / cellular response to amyloid-beta / positive regulation of tumor necrosis factor production / transmembrane signaling receptor activity / positive regulation of nitric oxide biosynthetic process / positive regulation of NF-kappaB transcription factor activity / cellular response to lipopolysaccharide
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. / Alpha-Beta Horseshoe / 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 / Leucine-rich repeat domain superfamily / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-LP4 / Chem-LP5 / Lymphocyte antigen 96 / Toll-like receptor 4
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsOhto, U. / Shimizu, T.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural basis of species-specific endotoxin sensing by innate immune receptor TLR4/MD-2
Authors: Ohto, U. / Fukase, K. / Miyake, K. / Shimizu, T.
History
DepositionMar 17, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 9, 2012Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / 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 / pdbx_validate_close_contact / 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 / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_2 / _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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_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_atom_id / _struct_conn.ptnr2_label_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 8, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
B: Toll-like receptor 4
D: Lymphocyte antigen 96
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,24613
Polymers170,6824
Non-polymers4,5639
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15610 Å2
ΔGint-9 kcal/mol
Surface area60800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.160, 150.519, 181.847
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 , 2 types, 4 molecules ABCD

#1: Protein Toll-like receptor 4 / TLR4


Mass: 68713.336 Da / Num. of mol.: 2 / Fragment: UNP residues 22-627
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Tlr4 / Cell (production host): S2 / Production host: Drosophila (fruit flies) / References: UniProt: Q9QUK6
#2: Protein Lymphocyte antigen 96 / Ly-96 / ESOP-1 / Protein MD-2


Mass: 16627.900 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Md2 / Cell (production host): S2 / Production host: Drosophila (fruit flies) / References: UniProt: Q9JHF9

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Sugars , 2 types, 5 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.: 3
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: 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.: 2
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, 41 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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

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Sample preparation

CrystalDensity Matthews: 3.09 Å3/Da / Density % sol: 60.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 15% PEG4000, 0.2M Na acetate, 0.1M Tris-HCl, pH 8.5, 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: RAYONIX MX225HE / Detector: CCD / Date: Jul 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→116 Å / Num. obs: 54275 / Rsym value: 0.147

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Z64

2z64


Resolution: 2.7→50 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.88 / SU B: 27.394 / SU ML: 0.268 / Cross valid method: THROUGHOUT / ESU R: 0.947 / ESU R Free: 0.364 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27743 2877 5 %RANDOM
Rwork0.23427 ---
obs0.23645 54275 96.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 55.119 Å2
Baniso -1Baniso -2Baniso -3
1--1.76 Å2-0 Å20 Å2
2---1.25 Å20 Å2
3---3.01 Å2
Refinement stepCycle: LAST / Resolution: 2.7→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11682 0 298 37 12017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0212396
X-RAY DIFFRACTIONr_bond_other_d0.0070.0242
X-RAY DIFFRACTIONr_angle_refined_deg1.4241.98216788
X-RAY DIFFRACTIONr_angle_other_deg0.742372
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.30651468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.67724.982554
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.569152096
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.4761536
X-RAY DIFFRACTIONr_chiral_restr0.0890.21949
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0219099
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.697→2.767 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.373 200 -
Rwork0.32 3678 -
obs--95.12 %
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)
10.1650.12010.03660.2250.01090.01540.0273-0.044-0.01710.0132-0.0222-0.0006-0.0145-0.0095-0.00510.0857-0.00690.00310.12550.02680.109714.745318.194229.5376
20.55770.19730.24940.40340.11270.28730.0631-0.03630.05660.008-0.16230.0792-0.0268-0.01040.09920.0690.01310.01380.1045-0.05840.1431-1.245135.09520.3753
30.0811-0.0341-0.06510.1196-0.01250.09040.0222-0.0187-0.0048-0.0898-0.02920.02830.0038-0.00810.0070.11070.0275-0.01330.10290.02010.1211-7.2332-4.428-13.5706
40.4041-0.19560.09840.20830.07140.740.06140.0314-0.0033-0.0141-0.0775-0.03260.1727-0.02750.0160.18170.00590.02030.03190.0140.11019.2528-20.9925-4.8714
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 625
2X-RAY DIFFRACTION2C21 - 155
3X-RAY DIFFRACTION3B27 - 625
4X-RAY DIFFRACTION4D21 - 155

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