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- PDB-2e56: Crystal structure of human MD-2 -

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Basic information

Entry
Database: PDB / ID: 2.0E+56
TitleCrystal structure of human MD-2
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) / MyD88:MAL(TIRAP) cascade initiated on plasma membrane / toll-like receptor 4 signaling pathway / toll-like receptor signaling pathway / RSV-host interactions / Respiratory syncytial virus (RSV) attachment and entry / cellular defense response / coreceptor activity / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Regulation of TBK1, IKKε (IKBKE)-mediated activation of IRF3, IRF7 / 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 / receptor complex / cell surface receptor signaling pathway / 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
MYRISTIC ACID / Lymphocyte antigen 96
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 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

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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)17,7146
Polymers16,5861
Non-polymers1,1285
Water2,576143
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.113, 53.113, 111.447
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-998-

HOH

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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


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-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C14H28O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.37 Å3/Da / Density % sol: 48.07 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 20% PEG8000, 120mM Na-acetate,70mM Na-cacodylate, pH 6.3, 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→48.4 Å / Num. obs: 11389 / % possible obs: 99.5 % / Redundancy: 12.3 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.105 / Net I/σ(I): 11.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 2→48.39 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.923 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.241 / ESU R Free: 0.201 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24922 477 4.7 %RANDOM
Rwork0.19407 ---
obs0.19648 9641 88.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.557 Å2
Baniso -1Baniso -2Baniso -3
1-0.81 Å20 Å20 Å2
2--0.81 Å20 Å2
3----1.61 Å2
Refinement stepCycle: LAST / Resolution: 2→48.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1162 0 76 143 1381
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0221284
X-RAY DIFFRACTIONr_angle_refined_deg1.5432.0191722
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1465147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.98824.3453
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.40215223
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.207155
X-RAY DIFFRACTIONr_chiral_restr0.1170.2185
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02923
X-RAY DIFFRACTIONr_nbd_refined0.2790.3556
X-RAY DIFFRACTIONr_nbtor_refined0.3380.5846
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2460.5184
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3150.354
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2480.523
X-RAY DIFFRACTIONr_mcbond_it4.0992731
X-RAY DIFFRACTIONr_mcangle_it5.94731192
X-RAY DIFFRACTIONr_scbond_it5.3452553
X-RAY DIFFRACTIONr_scangle_it7.7363530
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.383 28 -
Rwork0.226 510 -
obs--64.74 %

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