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- PDB-1wwl: Crystal structure of CD14 -

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Basic information

Entry
Database: PDB / ID: 1wwl
TitleCrystal structure of CD14
ComponentsMonocyte differentiation antigen CD14
KeywordsIMMUNE SYSTEM / cd14 / lps
Function / homology
Function and homology information


Transfer of LPS from LBP carrier to CD14 / : / MyD88-independent TLR4 cascade / Caspase activation via Death Receptors in the presence of ligand / positive regulation of cytokine production => GO:0001819 / Toll Like Receptor 4 (TLR4) Cascade / TRIF-mediated programmed cell death / cellular response to diacyl bacterial lipopeptide / cellular response to triacyl bacterial lipopeptide / Regulation of TLR by endogenous ligand ...Transfer of LPS from LBP carrier to CD14 / : / MyD88-independent TLR4 cascade / Caspase activation via Death Receptors in the presence of ligand / positive regulation of cytokine production => GO:0001819 / Toll Like Receptor 4 (TLR4) Cascade / TRIF-mediated programmed cell death / cellular response to diacyl bacterial lipopeptide / cellular response to triacyl bacterial lipopeptide / Regulation of TLR by endogenous ligand / cellular response to molecule of bacterial origin / lipoteichoic acid binding / TRAF6-mediated induction of TAK1 complex within TLR4 complex / IRAK2 mediated activation of TAK1 complex upon TLR7/8 or 9 stimulation / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / lipopolysaccharide receptor complex / lipopeptide binding / toll-like receptor 4 signaling pathway / positive regulation of endocytosis / cellular response to lipoteichoic acid / response to magnesium ion / positive regulation of type I interferon production / response to tumor necrosis factor / response to electrical stimulus / lipopolysaccharide-mediated signaling pathway / Neutrophil degranulation / receptor-mediated endocytosis / positive regulation of interleukin-8 production / lipopolysaccharide binding / response to bacterium / response to molecule of bacterial origin / positive regulation of non-canonical NF-kappaB signal transduction / positive regulation of tumor necrosis factor production / positive regulation of type II interferon production / response to heat / cellular response to lipopolysaccharide / response to ethanol / inflammatory response / membrane raft / external side of plasma membrane / innate immune response / Golgi apparatus / cell surface / extracellular space / plasma membrane
Similarity search - Function
Monocyte differentiation antigen CD14 / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Alpha Beta
Similarity search - Domain/homology
Monocyte differentiation antigen CD14
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 Å
AuthorsKim, J.-I. / Lee, C.J. / Jin, M.S. / Lee, C.-H. / Paik, S.-G. / Lee, H. / Lee, J.-O.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Crystal Structure of CD14 and Its Implications for Lipopolysaccharide Signaling
Authors: Kim, J.-I. / Lee, C.J. / Jin, M.S. / Lee, C.-H. / Paik, S.-G. / Lee, H. / Lee, J.-O.
History
DepositionJan 6, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 22, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3May 9, 2012Group: Other
Revision 1.4Sep 10, 2014Group: Database references
Revision 1.5Dec 11, 2019Group: Advisory / Database references / Derived calculations
Category: pdbx_distant_solvent_atoms / pdbx_validate_close_contact ...pdbx_distant_solvent_atoms / pdbx_validate_close_contact / struct_conn / struct_ref_seq_dif
Item: _struct_ref_seq_dif.details
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...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 / 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 / _chem_comp.name / _chem_comp.type / _pdbx_entity_nonpoly.entity_id / _pdbx_entity_nonpoly.name / _pdbx_struct_assembly_gen.asym_id_list / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Monocyte differentiation antigen CD14
B: Monocyte differentiation antigen CD14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)69,5638
Polymers67,4232
Non-polymers2,1406
Water7,134396
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Monocyte differentiation antigen CD14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7814
Polymers33,7111
Non-polymers1,0703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Monocyte differentiation antigen CD14
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,7814
Polymers33,7111
Non-polymers1,0703
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.519, 117.705, 102.395
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Monocyte differentiation antigen CD14 / Myeloid cell-specific leucine-rich glycoprotein


Mass: 33711.258 Da / Num. of mol.: 2 / Fragment: residues 3-314
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P10810
#2: 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.: 4
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
#3: 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.4 Å3/Da / Density % sol: 45.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM NaHepes, 1.9M Li2SO4, 5mM NiCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F2 / Wavelength: 0.9686 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 24, 2004
RadiationMonochromator: monochromator crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9686 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. all: 30868 / Num. obs: 29282 / % possible obs: 94.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 26.4 Å2
Reflection shellResolution: 2.5→2.59 Å / % possible all: 78.2

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MIR / Resolution: 2.5→19.79 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 283374.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1420 4.9 %RANDOM
Rwork0.215 ---
obs0.215 28951 96.1 %-
all-30868 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 48.1528 Å2 / ksol: 0.309412 e/Å3
Displacement parametersBiso mean: 51.3 Å2
Baniso -1Baniso -2Baniso -3
1-8.39 Å20 Å20 Å2
2---13.1 Å20 Å2
3---4.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.41 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.79 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4699 0 140 396 5235
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.8
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_improper_angle_d1.26
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.33 228 5.1 %
Rwork0.277 4254 -
obs--91 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION5CARBOHYDRATE.PARAMCARBOHYDRATE.TOP

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