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- PDB-4glp: The crystal structure of soluble human CD14 reveals a bent soleno... -

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Basic information

Entry
Database: PDB / ID: 4glp
TitleThe crystal structure of soluble human CD14 reveals a bent solenoid with a hydrophobic amino-terminal pocket.
ComponentsMonocyte differentiation antigen CD14
KeywordsIMMUNE SYSTEM / ALPHA BETA BENT SOLENOID / LRR / LIPOPOLYSACCHARIDE / SERUM / CD14 / LEUCINE-RICH REPEAT / PATTERN RECOGNITION / ENDOTOXIN / SEPSIS
Function / homology
Function and homology information


opsonin receptor activity / Transfer of LPS from LBP carrier to CD14 / Toll Like Receptor TLR6:TLR2 Cascade / cellular response to diacyl bacterial lipopeptide / cellular response to triacyl bacterial lipopeptide / cellular response to molecule of bacterial origin / lipoteichoic acid binding / Toll Like Receptor TLR1:TLR2 Cascade / lipopolysaccharide immune receptor activity / peptidoglycan immune receptor activity ...opsonin receptor activity / Transfer of LPS from LBP carrier to CD14 / Toll Like Receptor TLR6:TLR2 Cascade / cellular response to diacyl bacterial lipopeptide / cellular response to triacyl bacterial lipopeptide / cellular response to molecule of bacterial origin / lipoteichoic acid binding / Toll Like Receptor TLR1:TLR2 Cascade / lipopolysaccharide immune receptor activity / peptidoglycan immune receptor activity / lipopolysaccharide receptor complex / cell surface pattern recognition receptor signaling pathway / MyD88-independent TLR4 cascade / TRIF-mediated programmed cell death / positive regulation of toll-like receptor 4 signaling pathway / Caspase activation via Death Receptors in the presence of ligand / Toll Like Receptor 4 (TLR4) Cascade / 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 / RSV-host interactions / response to magnesium ion / cellular response to lipoteichoic acid / positive regulation of endocytosis / positive regulation of type I interferon production / Respiratory syncytial virus (RSV) attachment and entry / response to tumor necrosis factor / response to electrical stimulus / phagocytosis / 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 / receptor-mediated endocytosis / Activation of IRF3, IRF7 mediated by TBK1, IKKε (IKBKE) / IKK complex recruitment mediated by RIP1 / secretory granule membrane / positive regulation of cytokine production / positive regulation of interleukin-8 production / lipopolysaccharide binding / positive regulation of type II interferon production / positive regulation of tumor necrosis factor production / ER-Phagosome pathway / cellular response to lipopolysaccharide / response to ethanol / cell surface receptor signaling pathway / endosome membrane / inflammatory response / membrane raft / external side of plasma membrane / innate immune response / Neutrophil degranulation / apoptotic process / Golgi apparatus / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Monocyte differentiation antigen CD14 / Leucine Rich repeat / 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 speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 4.002 Å
AuthorsKelley, S.L. / Lukk, T. / Nair, S.K. / Tapping, R.I.
CitationJournal: J.Immunol. / Year: 2013
Title: The Crystal Structure of Human Soluble CD14 Reveals a Bent Solenoid with a Hydrophobic Amino-Terminal Pocket.
Authors: Kelley, S.L. / Lukk, T. / Nair, S.K. / Tapping, R.I.
History
DepositionAug 14, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 26, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 16, 2013Group: Database references
Revision 1.2Feb 6, 2013Group: Database references
Revision 1.3Nov 15, 2017Group: Refinement description / Category: software
Revision 1.4May 26, 2021Group: Database references / Source and taxonomy / Category: entity_src_gen / struct_ref_seq_dif
Item: _entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line ..._entity_src_gen.host_org_common_name / _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_strain / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Monocyte differentiation antigen CD14


Theoretical massNumber of molelcules
Total (without water)33,5091
Polymers33,5091
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)147.520, 147.520, 44.070
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Monocyte differentiation antigen CD14 / Myeloid cell-specific leucine-rich glycoprotein / Monocyte differentiation antigen CD14 / urinary ...Myeloid cell-specific leucine-rich glycoprotein / Monocyte differentiation antigen CD14 / urinary form / Monocyte differentiation antigen CD14 / membrane-bound form


Mass: 33509.277 Da / Num. of mol.: 1 / Fragment: UNP residues 26-335 / Mutation: C306S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CD14 / Plasmid: pDisplay / Cell line (production host): HEK 293F / Production host: Homo sapiens (human) / References: UniProt: P08571

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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: 4.13 Å3/Da / Density % sol: 70.23 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 30% PEG 6000, 0.1 M 2-(N-morpholino)ethanesulfonic acid, 0.2 M calcium acetate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97857 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 23, 2012
RadiationMonochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 4→29.31 Å / Num. all: 4780 / Num. obs: 4780 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 151.72 Å2 / Rmerge(I) obs: 0.086 / Net I/σ(I): 17.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obs% possible all
4-4.10.8423.193887341100
4.1-4.220.6314.153858336100
4.22-4.340.4016.323803334100
4.34-4.470.2888.213527315100
4.47-4.620.22710.353585313100
4.62-4.780.19411.813376299100
4.78-4.960.15313.973521316100
4.96-5.160.13815.732951260100
5.16-5.390.15214.883173283100
5.39-5.660.12316.432917262100
5.66-5.960.11318.842722242100
5.96-6.330.10619.662649239100
6.33-6.760.08224.672478223100
6.76-7.30.06928.472314209100
7.3-80.05533.442037188100
8-8.950.0536.571944180100
8.95-10.330.04541.781620151100
10.33-12.650.04841.451317130100
12.65-17.890.05141.251012110100
17.890.05629.353114974.2

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Processing

Software
NameVersionClassificationNB
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
XDSdata reduction
PHASERphasing
Cootmodel building
RefinementResolution: 4.002→27.879 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7728 / SU ML: 0.43 / σ(F): 41.09 / Phase error: 29.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3211 216 4.53 %
Rwork0.2834 4552 -
obs0.285 4768 99.85 %
Solvent computationShrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 30.342 Å2 / ksol: 0.289 e/Å3
Displacement parametersBiso max: 153.79 Å2 / Biso mean: 54.5678 Å2 / Biso min: 7.05 Å2
Baniso -1Baniso -2Baniso -3
1--0.0595 Å2-0 Å2-0 Å2
2---0.0595 Å20 Å2
3----7.6459 Å2
Refinement stepCycle: LAST / Resolution: 4.002→27.879 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2346 0 0 0 2346
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012399
X-RAY DIFFRACTIONf_angle_d1.643271
X-RAY DIFFRACTIONf_chiral_restr0.101380
X-RAY DIFFRACTIONf_plane_restr0.008433
X-RAY DIFFRACTIONf_dihedral_angle_d15.929888
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 2 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
4.002-5.03780.281040.258722402344
5.0378-27.87930.36061120.308823122424
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)
10.0455-0.0222-0.01670.05360.02850.0244-0.0309-0.0283-0.03040.01410.06010.0627-0.0443-0.0401-0.10290.41130.1906-0.24140.18280.19390.263641.259751.9279-12.4634
20.0561-0.03190.02140.0829-0.0147-0.00950.0247-0.19540.12150.10030.04720.1889-0.1323-0.05140.04260.22210.8298-0.47780.14990.35230.245145.88257.6113-2.721
30.1214-0.15180.15750.1661-0.18910.2007-0.0204-0.08940.05740.05360.07880.1619-0.073-0.1271-0.10350.11160.1178-0.3662-0.10530.49720.293142.530352.1971.9557
40.00690.00290.02820.01360.01990.00730.1515-0.19190.1122-0.02960.0370.1651-0.17270.10910.1693-1.17350.208-0.33-0.3090.76-0.598753.565546.60715.8502
50.02860.06750.04490.15230.04390.05940.0532-0.13170.06060.1548-0.02920.10520.00480.02670.14160.03280.2568-0.0258-0.43460.6436-0.18758.735330.46197.8983
60.02130.00730.01550.07490.03620.0276-0.0254-0.03220.0437-0.00690.0012-0.02230.0065-0.02510.01750.22060.00410.22820.14570.2832-0.008156.81620.3710.7008
70.0267-0.0083-0.01370.00070.00660.0119-0.0993-0.09330.00650.0220.0393-0.0250.09650.1102-0.00430.63150.02680.1321-0.0271-0.05240.61161.327813.18764.8513
80.0584-0.08750.0150.1129-0.00960.0105-0.0035-0.1124-0.08110.0514-0.0105-0.0250.06580.04680.0650.42090.138-0.09150.19250.11260.255953.387312.9131.161
90.0238-0.0057-0.01960.01730.00750.0392-0.02010.0124-0.03630.01430.0245-0.0250.05650.0028-0.00160.4120.15110.14620.28330.21550.288748.87238.3918-0.2178
100.11910.0187-0.02510.03690.03160.0456-0.0066-0.157-0.0378-0.0333-0.0609-0.0174-0.00530.0109-0.01890.4091-0.19860.15830.3096-0.20050.501946.02356.8544-4.1469
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 26:45)A26 - 45
2X-RAY DIFFRACTION2chain 'A' and (resseq 46:81)A46 - 81
3X-RAY DIFFRACTION3chain 'A' and (resseq 82:102)A82 - 102
4X-RAY DIFFRACTION4chain 'A' and (resseq 103:181)A103 - 181
5X-RAY DIFFRACTION5chain 'A' and (resseq 182:236)A182 - 236
6X-RAY DIFFRACTION6chain 'A' and (resseq 237:255)A237 - 255
7X-RAY DIFFRACTION7chain 'A' and (resseq 256:275)A256 - 275
8X-RAY DIFFRACTION8chain 'A' and (resseq 276:295)A276 - 295
9X-RAY DIFFRACTION9chain 'A' and (resseq 296:315)A296 - 315
10X-RAY DIFFRACTION10chain 'A' and (resseq 316:335)A316 - 335

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