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- PDB-3m7o: Crystal structure of mouse MD-1 in complex with phosphatidylcholine -

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Basic information

Entry
Database: PDB / ID: 3m7o
TitleCrystal structure of mouse MD-1 in complex with phosphatidylcholine
ComponentsLymphocyte antigen 86
KeywordsIMMUNE SYSTEM / BETA SHEET / Glycoprotein / Immunity / Inflammatory response / Innate immunity / Secreted
Function / homology
Function and homology information


Toll Like Receptor 4 (TLR4) Cascade / positive regulation of lipopolysaccharide-mediated signaling pathway / lipopolysaccharide-mediated signaling pathway / inflammatory response / innate immune response / extracellular region
Similarity search - Function
Lymphocyte antigen 86 / 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
BENZAMIDINE / Chem-L9R / Lymphocyte antigen 86
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.65 Å
AuthorsHarada, H. / Ohto, U. / Satow, Y.
CitationJournal: J.Mol.Biol. / Year: 2010
Title: Crystal structure of mouse MD-1 with endogenous phospholipid bound in its cavity
Authors: Harada, H. / Ohto, U. / Satow, Y.
History
DepositionMar 17, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 9, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Jan 22, 2014Group: Database references
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_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / 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_atom_id / _atom_site.auth_comp_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 / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _struct_asym.entity_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.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_comp_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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: Lymphocyte antigen 86
B: Lymphocyte antigen 86
C: Lymphocyte antigen 86
D: Lymphocyte antigen 86
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,56930
Polymers71,3004
Non-polymers5,26826
Water7,999444
1
A: Lymphocyte antigen 86
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6569
Polymers17,8251
Non-polymers1,8318
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Lymphocyte antigen 86
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6286
Polymers17,8251
Non-polymers8035
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Lymphocyte antigen 86
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,6286
Polymers17,8251
Non-polymers8035
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Lymphocyte antigen 86
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,6569
Polymers17,8251
Non-polymers1,8318
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.299, 90.299, 86.714
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
Lymphocyte antigen 86 / Ly-86 / Protein MD-1


Mass: 17825.047 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Ly86, Md1 / Production host: Pichia pastoris (fungus) / References: UniProt: O88188
#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


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 8
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-L9R / (2S)-3-(octadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate / 1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine


Mass: 788.129 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C44H86NO8P / Comment: SOPC, phospholipid*YM
#4: Chemical
ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C7H8N2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 3

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.4850.39
2
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 22% (w/v) PEG-8000, 0.2 M Ammonium sulfate and MES pH 6.5,supplemented with 1/10 volume of 20% (w/v) benzamidine hydrochloride as a crystallization additive, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
1951
21001
Diffraction source
SourceSiteBeamlineID
SYNCHROTRONPhoton Factory AR-NE3A1
SYNCHROTRONPhoton Factory AR-NW12A2
Detector
TypeIDDetectorDate
ADSC QUANTUM 2701CCDDec 23, 2009
ADSC QUANTUM 210r2CCD
Radiation
IDProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDRelative weight
11
21
ReflectionResolution: 1.65→30 Å / Num. obs: 82260 / % possible obs: 98.4 % / Rmerge(I) obs: 0.065
Reflection shellResolution: 1.65→1.68 Å / Rmerge(I) obs: 0.566 / Mean I/σ(I) obs: 2.1 / % possible all: 86.9

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Processing

Software
NameVersionClassification
HKL-2000data collection
autoSHARPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SIRAS / Resolution: 1.65→29.96 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.944 / SU B: 1.85 / SU ML: 0.064 / Cross valid method: THROUGHOUT / σ(F): 3 / ESU R: 0.106 / ESU R Free: 0.104 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22659 3551 5 %RANDOM
Rwork0.1946 ---
obs0.19624 67139 98.13 %-
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: 38.359 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 1.65→29.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4135 0 364 444 4943
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0224611
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4052.0466223
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5465531
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.48424.8200
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.63915711
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2551524
X-RAY DIFFRACTIONr_chiral_restr0.0950.2666
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0213524
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.0151.52696
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.37224280
X-RAY DIFFRACTIONr_scbond_it4.48131915
X-RAY DIFFRACTIONr_scangle_it7.0894.51939
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.693 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 135 -
Rwork0.216 2547 -
obs--79.12 %

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