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- PDB-3u8h: Functionally selective inhibition of Group IIA phospholipase A2 r... -

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Basic information

Entry
Database: PDB / ID: 3u8h
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 / 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
Chem-BHP / Phospholipase A2, membrane associated
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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)29,16712
Polymers27,8902
Non-polymers1,27710
Water1,802100
1
A: Phospholipase A2, membrane associated
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5846
Polymers13,9451
Non-polymers6395
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phospholipase A2, membrane associated
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5846
Polymers13,9451
Non-polymers6395
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4200 Å2
ΔGint-93 kcal/mol
Surface area12660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.792, 74.792, 49.926
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1114A1 - 124
2114B1 - 124

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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.: 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-BHP / (S)-5-(4-BENZYLOXY-PHENYL)-4-(7-PHENYL-HEPTANOYLAMINO)-PENTANOIC ACID


Mass: 487.630 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H37NO4
#3: Chemical
ChemComp-CA / CALCIUM ION


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


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.89 Å3/Da / Density % sol: 57.45 %
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: 1-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: 2.3→29.932 Å / Num. all: 13899 / Num. obs: 13593 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 3.5

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→24.48 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.935 / Occupancy max: 1 / Occupancy min: 0 / SU B: 13.082 / SU ML: 0.158 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.214 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.225 684 5 %RANDOM
Rwork0.192 ---
obs0.1937 13591 97.76 %-
all-13591 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 70.23 Å2 / Biso mean: 39.83 Å2 / Biso min: 2 Å2
Baniso -1Baniso -2Baniso -3
1--3.12 Å2-1.56 Å2-0 Å2
2---3.12 Å2-0 Å2
3---4.68 Å2
Refinement stepCycle: LAST / Resolution: 2.3→24.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1926 0 80 100 2106
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212047
X-RAY DIFFRACTIONr_bond_other_d0.0010.021469
X-RAY DIFFRACTIONr_angle_refined_deg1.1031.9742749
X-RAY DIFFRACTIONr_angle_other_deg0.77333517
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6465252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.81222.13589
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.6715336
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.761518
X-RAY DIFFRACTIONr_chiral_restr0.0660.2273
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022301
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02475
X-RAY DIFFRACTIONr_mcbond_it0.7441.51231
X-RAY DIFFRACTIONr_mcbond_other0.2171.5515
X-RAY DIFFRACTIONr_mcangle_it1.35421956
X-RAY DIFFRACTIONr_scbond_it2.5743816
X-RAY DIFFRACTIONr_scangle_it3.8594.5790
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Number: 1640 / Refine-ID: X-RAY DIFFRACTION

TypeRms dev position (Å)Weight position
MEDIUM POSITIONAL0.240.5
MEDIUM THERMAL0.32
LS refinement shellResolution: 2.3→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.428 43 -
Rwork0.291 989 -
all-1032 -
obs--97.54 %
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)
13.4332-0.11170.55371.50040.6011.50630.2575-0.2015-0.2793-0.0581-0.1233-0.01670.11680.025-0.13430.08360.04290.00190.10220.02910.142118.8698-13.5943-12.3072
25.7537-0.56710.19981.8928-0.2532.29110.16650.45990.3267-0.3304-0.1323-0.0444-0.02460.1023-0.03420.10680.06510.00680.09220.04490.080817.9439-7.5464-20.5648
35.4847-0.36480.61431.3744-0.20031.95220.07240.18930.1392-0.15080.0098-0.1327-0.02170.4063-0.08230.09870.03680.02810.17760.03280.110134.2206-11.0168-10.8398
43.0361-3.9271-0.23356.3939-0.52920.76340.2321-0.12130.0068-0.4749-0.0490.24170.0258-0.0378-0.18310.07760.0522-0.04630.1851-0.00370.096116.0513-11.99652.4529
53.2909-2.89040.29874.9455-0.2042.2789-0.0973-0.52870.15370.26080.1498-0.2185-0.1076-0.0161-0.05260.03730.0158-0.03010.1717-0.0320.070521.8273-9.865510.7062
62.718-1.4330.94846.0697-0.72084.1096-0.04340.01580.13250.01490.2403-0.1764-0.3204-0.1264-0.19690.08770.0827-0.01080.1325-0.05640.132410.79012.46620.9841
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 31
2X-RAY DIFFRACTION2A32 - 104
3X-RAY DIFFRACTION3A105 - 124
4X-RAY DIFFRACTION4B1 - 31
5X-RAY DIFFRACTION5B32 - 104
6X-RAY DIFFRACTION6B105 - 124

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