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- PDB-3u8b: Functionally selective inhibition of Group IIA phospholipase A2 r... -

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Basic information

Entry
Database: PDB / ID: 3u8b
TitleFunctionally selective inhibition of Group IIA phospholipase A2 reveals a role for vimentin in regulating arachidonic acid metabolism
ComponentsPhospholipase A2, membrane associated
KeywordsHYDROLASE / secreted phospholipase A2 / Phospholipase A2 activity
Function / homology
Function and homology information


regulation of neutrophil activation / phosphatidylethanolamine metabolic process / phosphatidic acid metabolic process / Acyl chain remodelling of PG / intestinal stem cell homeostasis / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Synthesis of PA ...regulation of neutrophil activation / phosphatidylethanolamine metabolic process / phosphatidic acid metabolic process / Acyl chain remodelling of PG / intestinal stem cell homeostasis / Acyl chain remodelling of PC / Acyl chain remodelling of PI / Acyl chain remodelling of PS / Acyl chain remodelling of PE / Synthesis of PA / positive regulation of macrophage derived foam cell differentiation / phosphatidylcholine metabolic process / phospholipase A2 activity / calcium-dependent phospholipase A2 activity / low-density lipoprotein particle remodeling / phospholipase A2 / Antimicrobial peptides / arachidonic acid secretion / phospholipid metabolic process / lipid catabolic process / negative regulation of T cell proliferation / secretory granule / phospholipid binding / positive regulation of inflammatory response / killing of cells of another organism / mitochondrial outer membrane / positive regulation of ERK1 and ERK2 cascade / defense response to Gram-positive bacterium / inflammatory response / calcium ion binding / endoplasmic reticulum membrane / perinuclear region of cytoplasm / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain ...Phospholipase A2, aspartic acid active site / Phospholipase A2 aspartic acid active site. / Phospholipase A2 / Phospholipase A2, histidine active site / Phospholipase A2 histidine active site. / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 / Phospholipase A2 / Phospholipase A2 domain / Phospholipase A2 domain superfamily / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Phospholipase A2, membrane associated
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.299 Å
AuthorsLee, L.K. / Bryant, K.J. / Bouveret, R. / Lei, P.-W. / Duff, A.P. / Harrop, S.J. / Huang, E.P. / Harvey, R.P. / Gelb, M.H. / Gray, P.P. ...Lee, L.K. / Bryant, K.J. / Bouveret, R. / Lei, P.-W. / Duff, A.P. / Harrop, S.J. / Huang, E.P. / Harvey, R.P. / Gelb, M.H. / Gray, P.P. / Curmi, P.M. / Cunningham, A.M. / Church, W.B. / Scott, K.F.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Selective Inhibition of Human Group IIA-secreted Phospholipase A2 (hGIIA) Signaling Reveals Arachidonic Acid Metabolism Is Associated with Colocalization of hGIIA to Vimentin in Rheumatoid Synoviocytes.
Authors: Lee, L.K. / Bryant, K.J. / Bouveret, R. / Lei, P.W. / Duff, A.P. / Harrop, S.J. / Huang, E.P. / Harvey, R.P. / Gelb, M.H. / Gray, P.P. / Curmi, P.M. / Cunningham, A.M. / Church, W.B. / Scott, K.F.
History
DepositionOct 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 17, 2012Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phospholipase A2, membrane associated
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0965
Polymers13,9451
Non-polymers1514
Water95553
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Phospholipase A2, membrane associated
hetero molecules

A: Phospholipase A2, membrane associated
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,19210
Polymers27,8902
Non-polymers3028
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+1/61
Buried area2770 Å2
ΔGint-109 kcal/mol
Surface area12790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.683, 74.683, 89.159
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Space group name H-MP6122

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Components

#1: Protein Phospholipase A2, membrane associated / / GIIC sPLA2 / Group IIA phospholipase A2 / Non-pancreatic secretory phospholipase A2 / NPS-PLA2 / ...GIIC sPLA2 / Group IIA phospholipase A2 / Non-pancreatic secretory phospholipase A2 / NPS-PLA2 / Phosphatidylcholine 2-acylhydrolase 2A


Mass: 13945.012 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PLA2G2A, PLA2B, PLA2L, RASF-A / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P14555, phospholipase A2
#2: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 2.57 Å3/Da / Density % sol: 52.21 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 0.1 M Tris HCl pH 7.4, 10 mM CaCl2, 0.5 mM Beta-octyl glucoside and 4 M NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 19, 2006
RadiationMonochromator: Bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9002 Å / Relative weight: 1
ReflectionResolution: 2.299→24.446 Å / Num. all: 6955 / Num. obs: 6906 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3.5

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
PHASERphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.299→24.446 Å / SU ML: 0.6 / σ(F): 1.36 / Phase error: 27.02 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflectionSelection details
Rfree0.2573 319 4.62 %FREE R VALUE TEST SET SIZE (%): 4.62 FREE R VALUE TEST SET COUNT : 319
Rwork0.2074 ---
obs0.2096 6906 99.1 %-
Solvent computationShrinkage radii: 0.65 Å / VDW probe radii: 0.8 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 56.024 Å2 / ksol: 0.433 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.6425 Å2-0 Å2-0 Å2
2--1.6425 Å20 Å2
3----3.285 Å2
Refinement stepCycle: LAST / Resolution: 2.299→24.446 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms966 0 4 53 1023
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0181002
X-RAY DIFFRACTIONf_angle_d1.7651339
X-RAY DIFFRACTIONf_dihedral_angle_d11.553370
X-RAY DIFFRACTIONf_chiral_restr0.096134
X-RAY DIFFRACTIONf_plane_restr0.011170
LS refinement shellResolution: 2.299→2.8958 Å
RfactorNum. reflection% reflection
Rfree0.3082 157 -
Rwork0.2639 3233 -
obs--100 %
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)
13.44370.8114-0.80191.48120.08363.05990.3005-0.0910.41040.1059-0.19170.19480.18350.1824-0.08460.47210.02230.03040.4924-0.03560.4605-14.929435.46180.1399
24.99721.2205-0.80852.86680.98884.4858-0.23150.53470.0146-0.1360.2666-0.25460.2811-0.0729-0.01520.429-0.03710.03110.5372-0.07870.4173-13.93328.8354-7.4524
32.08590.1495-0.06162.130.44691.71890.26110.32660.1088-0.3293-0.70160.7157-0.1159-0.91770.35530.47340.07990.02820.8196-0.09590.6189-29.534833.79411.0355
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:31)
2X-RAY DIFFRACTION2chain 'A' and (resseq 32:104)
3X-RAY DIFFRACTION3chain 'A' and (resseq 105:124)

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