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- PDB-3u8i: Functionally selective inhibition of Group IIA phospholipase A2 r... -

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Basic information

Entry
Database: PDB / ID: 3u8i
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
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 / phosphatidylcholine metabolic process / phospholipase A2 activity / positive regulation of macrophage derived foam cell differentiation / low-density lipoprotein particle remodeling / calcium-dependent phospholipase A2 activity / 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: 1.1 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 17, 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

Downloads & links

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Assembly

Deposited unit
A: Phospholipase A2, membrane associated
B: Phospholipase A2, membrane associated
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,67614
Polymers28,2822
Non-polymers39412
Water7,368409
1
A: Phospholipase A2, membrane associated
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3387
Polymers14,1411
Non-polymers1976
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phospholipase A2, membrane associated
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,3387
Polymers14,1411
Non-polymers1976
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)70.426, 70.426, 47.301
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number76
Space group name H-MP41
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111chain A and (resseq 1:46 ) and (not element H)A0
211chain B and (resseq 1:46 ) and (not element H)B0

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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: 14141.032 Da / Num. of mol.: 2
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-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.07 Å3/Da / Density % sol: 40.69 %
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: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9002 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 29, 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: 1.1→40 Å / Num. all: 93921 / Num. obs: 93827 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3.5 / Biso Wilson estimate: 10.68 Å2

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Processing

Software
NameVersionClassificationNB
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.1→34.3125 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.9264 / SU ML: 0.18 / σ(F): 0 / Phase error: 13.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1861 4594 5.02 %RANDOM
Rwork0.1639 ---
obs0.165 91537 97.38 %-
all-91537 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 50.991 Å2 / ksol: 0.399 e/Å3
Displacement parametersBiso max: 45.97 Å2 / Biso mean: 16.6278 Å2 / Biso min: 8.33 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å2-0 Å2
2---1.2 Å20 Å2
3---2.4 Å2
Refinement stepCycle: LAST / Resolution: 1.1→34.3125 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 12 409 2373
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012091
X-RAY DIFFRACTIONf_angle_d1.3332777
X-RAY DIFFRACTIONf_chiral_restr0.081286
X-RAY DIFFRACTIONf_plane_restr0.006358
X-RAY DIFFRACTIONf_dihedral_angle_d12.356807
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A342X-RAY DIFFRACTIONPOSITIONAL0.016
12B342X-RAY DIFFRACTIONPOSITIONAL0.016
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.1-1.11210.29631690.26782649281891
1.1121-1.12520.26641600.252771293193
1.1252-1.13890.25671550.23082756291194
1.1389-1.15330.24241490.20932848299796
1.1533-1.16850.22131610.20282811297296
1.1685-1.18450.22641460.18852864301095
1.1845-1.20140.23181410.18482826296796
1.2014-1.21930.2161460.16872851299796
1.2193-1.23840.18611520.15982897304996
1.2384-1.25870.17471300.14082873300397
1.2587-1.28040.15431490.13252876302597
1.2804-1.30370.1481520.12052888304097
1.3037-1.32880.16381400.11582902304297
1.3288-1.35590.15691480.1162906305498
1.3559-1.38540.15591640.10672892305698
1.3854-1.41760.12941560.10312906306298
1.4176-1.4530.11951650.09472895306099
1.453-1.49230.13391410.09232996313798
1.4923-1.53620.13471580.09932911306999
1.5362-1.58580.14521600.10332919307999
1.5858-1.64250.15031610.11362968312999
1.6425-1.70830.15921330.13472966309999
1.7083-1.7860.1921770.15312923310099
1.786-1.88020.18761550.16552948310399
1.8802-1.99790.18891520.16022959311199
1.9979-2.15220.17251420.16722954309698
2.1522-2.36870.19111440.18672998314299
2.3687-2.71140.21811690.198929683137100
2.7114-3.41550.19081650.17692992315799
3.4155-34.31250.19191540.18343030318498

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