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- PDB-5ijb: The ligand-free structure of the mouse TLR4/MD-2 complex -

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Basic information

Entry
Database: PDB / ID: 5ijb
TitleThe ligand-free structure of the mouse TLR4/MD-2 complex
Components
  • Lymphocyte antigen 96
  • Toll-like receptor 4, Variable lymphocyte receptor B chimera
KeywordsIMMUNE SYSTEM / leucine-rich repeats
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
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: 2.91 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: 5HG3
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 / atom_site_anisotrop ...atom_site / atom_site_anisotrop / 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_validate_chiral / 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_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_asym_id / _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_validate_chiral.auth_asym_id / _pdbx_validate_chiral.auth_seq_id / _pdbx_validate_chiral.details / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _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 2.1Sep 27, 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, Variable lymphocyte receptor B chimera
C: Lymphocyte antigen 96
B: Toll-like receptor 4, Variable lymphocyte receptor B chimera
D: Lymphocyte antigen 96
hetero molecules


Theoretical massNumber of molelcules
Total (without water)173,22116
Polymers169,3474
Non-polymers3,87412
Water00
1
A: Toll-like receptor 4, Variable lymphocyte receptor B chimera
C: Lymphocyte antigen 96
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,4078
Polymers84,6732
Non-polymers1,7346
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint29 kcal/mol
Surface area33300 Å2
MethodPISA
2
B: Toll-like receptor 4, Variable lymphocyte receptor B chimera
D: Lymphocyte antigen 96
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,8148
Polymers84,6732
Non-polymers2,1406
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint27 kcal/mol
Surface area33340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.320, 128.320, 277.507
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#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
#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.: 6
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.: 6
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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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.3 Å3/Da / Density % sol: 62.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1 M Bicine, pH 7.5, 12% PEG10000

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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: Nov 5, 2014
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: 2.9→50 Å / Num. obs: 51785 / % possible obs: 99.6 % / Redundancy: 7.9 % / Rmerge(I) obs: 0.083 / Net I/av σ(I): 27.052 / Net I/σ(I): 8.7
Reflection shellResolution: 2.9→2.95 Å

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2Z64

2z64


Resolution: 2.91→48.81 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.886 / SU B: 45.049 / SU ML: 0.379 / Cross valid method: THROUGHOUT / ESU R: 1.964 / ESU R Free: 0.448 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30775 2639 5.1 %RANDOM
Rwork0.24309 ---
obs0.24635 49091 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 100.275 Å2
Baniso -1Baniso -2Baniso -3
1--4.03 Å20 Å2-0 Å2
2---4.03 Å20 Å2
3---8.06 Å2
Refinement stepCycle: LAST / Resolution: 2.91→48.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11873 0 0 0 11873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01912173
X-RAY DIFFRACTIONr_bond_other_d0.0010.0211504
X-RAY DIFFRACTIONr_angle_refined_deg1.681.98416570
X-RAY DIFFRACTIONr_angle_other_deg0.8823.00226418
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.50351451
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.27224.723542
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.301152097
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1191544
X-RAY DIFFRACTIONr_chiral_restr0.0910.21912
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213549
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022815
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_it4.0266.5055816
X-RAY DIFFRACTIONr_mcbond_other4.0266.5045815
X-RAY DIFFRACTIONr_mcangle_it6.5749.757263
X-RAY DIFFRACTIONr_mcangle_other6.5749.7517264
X-RAY DIFFRACTIONr_scbond_it3.8736.8816357
X-RAY DIFFRACTIONr_scbond_other3.8726.8816357
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.44810.2289252
X-RAY DIFFRACTIONr_long_range_B_refined9.95952.18613428
X-RAY DIFFRACTIONr_long_range_B_other9.95952.1913429
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.905→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.408 191 -
Rwork0.355 3506 -
obs--97.8 %
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)
10.71370.0953-0.17430.2079-0.09930.08110.01810.0462-0.0619-0.06870.03620.12940.00910.0297-0.05440.4875-0.03800.5178-0.00380.144436.3131-5.6196-41.4559
20.70780.19440.38650.87540.25430.6102-0.0266-0.15780.13110.0330.150.16130.04290.013-0.12330.37120.00180.12210.56020.00320.270530.38155.4773-17.2534
30.51010.1447-0.04620.382-0.07610.0514-0.0965-0.04390.01930.17020.0344-0.1989-0.01-0.06430.06210.50580.0332-0.10890.53470.01330.149691.787912.0791-19.9894
42.1626-0.34630.74690.8784-0.94071.164-0.44220.26330.55060.09330.1997-0.1871-0.0412-0.07310.24250.4572-0.0545-0.12370.46980.06860.263391.021723.877-44.465
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A27 - 619
2X-RAY DIFFRACTION1A701 - 705
3X-RAY DIFFRACTION2C22 - 157
4X-RAY DIFFRACTION2C201 - 203
5X-RAY DIFFRACTION3B27 - 618
6X-RAY DIFFRACTION3B701 - 708
7X-RAY DIFFRACTION4D22 - 155
8X-RAY DIFFRACTION4D201 - 202

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