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- PDB-2e59: Crystal structure of human MD-2 in complex with lipid IVa -

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Basic information

Entry
Database: PDB / ID: 2.0E+59
TitleCrystal structure of human MD-2 in complex with lipid IVa
ComponentsLymphocyte antigen 96
KeywordsLIPID BINDING PROTEIN / INNATE IMMUNITY / LIPID-BINDING
Function / homology
Function and homology information


lipopolysaccharide immune receptor activity / Toll-like receptor 4 binding / lipopolysaccharide receptor complex / detection of lipopolysaccharide / MyD88-independent TLR4 cascade / TRIF-mediated programmed cell death / Toll Like Receptor 4 (TLR4) Cascade / Caspase activation via Death Receptors in the presence of ligand / positive regulation of lipopolysaccharide-mediated signaling pathway / Regulation of TLR by endogenous ligand ...lipopolysaccharide immune receptor activity / Toll-like receptor 4 binding / lipopolysaccharide receptor complex / detection of lipopolysaccharide / MyD88-independent TLR4 cascade / TRIF-mediated programmed cell death / Toll Like Receptor 4 (TLR4) Cascade / Caspase activation via Death Receptors in the presence of ligand / positive regulation of lipopolysaccharide-mediated signaling pathway / Regulation of TLR by endogenous ligand / MyD88 deficiency (TLR2/4) / IRAK4 deficiency (TLR2/4) / toll-like receptor 4 signaling pathway / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor signaling pathway / cellular defense response / coreceptor activity / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / TRAF6-mediated induction of TAK1 complex within TLR4 complex / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / lipopolysaccharide binding / Heme signaling / positive regulation of tumor necrosis factor production / ER-Phagosome pathway / cellular response to lipopolysaccharide / response to lipopolysaccharide / cell surface receptor signaling pathway / receptor complex / endosome membrane / inflammatory response / innate immune response / extracellular region / plasma membrane
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. / Immunoglobulin E-set / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-LP4 / Chem-LP5 / Lymphocyte antigen 96
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å
AuthorsOhto, U. / Satow, Y.
CitationJournal: Science / Year: 2007
Title: Crystal structures of human MD-2 and its complex with antiendotoxic lipid IVa
Authors: Ohto, U. / Fukase, K. / Miyake, K. / Satow, Y.
History
DepositionDec 19, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2007Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Oct 25, 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

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Assembly

Deposited unit
A: Lymphocyte antigen 96
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,4525
Polymers16,5861
Non-polymers1,8664
Water1,60389
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)52.795, 52.795, 110.889
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Lymphocyte antigen 96 / / MD-2 protein / ESOP-1


Mass: 16586.135 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LY96, ESOP1, MD2 / Plasmid: pPIC9, pPICZa, pPIC6a / Production host: Pichia pastoris (fungus) / References: UniProt: Q9Y6Y9
#2: 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.: 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
#3: 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.: 1 / Source method: obtained synthetically / Formula: C34H66NO12P
#4: 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.: 1 / Source method: obtained synthetically / Formula: C34H66NO12P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 89 / 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: 2.33 Å3/Da / Density % sol: 47.18 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 15% PEG3350, 40mM Na-citrate, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Oct 10, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→27.72 Å / Num. obs: 7629 / % possible obs: 90.7 % / Redundancy: 11.2 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2E56

2e56


Resolution: 2.21→27.72 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.909 / Cross valid method: THROUGHOUT / σ(F): 2.5 / ESU R: 0.674 / ESU R Free: 0.3 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26326 297 4.5 %RANDOM
Rwork0.20583 ---
obs0.20842 6291 78.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.455 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å20 Å2
2--1.08 Å20 Å2
3----2.16 Å2
Refinement stepCycle: LAST / Resolution: 2.21→27.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1162 0 123 89 1374
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0221326
X-RAY DIFFRACTIONr_angle_refined_deg1.4952.0591782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5975145
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.86224.3453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.27815220
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.002155
X-RAY DIFFRACTIONr_chiral_restr0.0840.2197
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02921
X-RAY DIFFRACTIONr_nbd_refined0.2590.3554
X-RAY DIFFRACTIONr_nbtor_refined0.3440.5899
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2330.5134
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2550.346
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2180.512
X-RAY DIFFRACTIONr_mcbond_it4.0142725
X-RAY DIFFRACTIONr_mcangle_it6.07231181
X-RAY DIFFRACTIONr_scbond_it4.3892601
X-RAY DIFFRACTIONr_scangle_it6.1813601
LS refinement shellResolution: 2.213→2.27 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.299 8 -
Rwork0.192 184 -
obs--31.95 %

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